import urllib
import urlparse
+if not 'DJANGO_SETTINGS_MODULE' in os.environ:
+ os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings'
+
from htsworkflow.submission import daf, ucsc
from htsworkflow.util import api
load_encodedcc_files(model, **track_info )
if opts.sparql is not None:
- sparql_query(model, opts.sparql)
+ sparql_query(model, opts.sparql, 'html')
if opts.find_submission_with_no_library:
report_submissions_with_no_library(model)
SELECT distinct ?liburn ?cell ?replicate ?subid ?name ?submission_date
WHERE {
- ?subid ucscSubmission:name ?name .
- OPTIONAL { ?subid ucscSubmission:library_urn ?liburn ;
- libraryOntology:date ?submission_date .
- ?liburn libraryOntology:cell_line ?cell ;
- libraryOntology:replicate ?replicate . }
+ ?subid ucscSubmission:name ?name ;
+ ucscSubmission:library_urn ?liburn ;
+ libraryOntology:date ?submission_date.
+ ?liburn libraryOntology:cell_line ?cell ;
+ libraryOntology:replicate ?replicate ;
+ libraryOntology:species ?species .
+ OPTIONAL { ?liburn libraryOntology:treatement ?treatment . }
+ FILTER(regex(?species, "Homo sapiens", "i"))
#filter(?submission_date > "2011-04-01T00:00:00Z"^^xsd:dateTime)
#filter(!bound(?liburn))
}
-ORDER BY ?submission_date ?cell ?replicate ?liburn
+ORDER BY ?liburn ?submission_date
\ No newline at end of file
logger = logging.getLogger('ucsc_gather')
+TAR = '/bin/tar'
+LFTP = '/usr/bin/lftp'
+
def main(cmdline=None):
parser = make_parser()
opts, args = parser.parse_args(cmdline)
submission_uri = None
+ global TAR
+ global LFTP
+ TAR = opts.tar
+ LFTP = opts.lftp
+
if opts.debug:
logging.basicConfig(level = logging.DEBUG )
elif opts.verbose:
model = get_model(opts.model, opts.db_path)
mapper = None
if opts.name:
- mapper = UCSCSubmssion(opts.name, opts.daf, model)
+ mapper = UCSCSubmission(opts.name, opts.daf, model)
if opts.library_url is not None:
mapper.library_url = opts.library_url
submission_uri = get_submission_uri(opts.name)
mapper.scan_submission_dirs(results)
if opts.make_ddf:
+ if not os.path.exists(TAR):
+ parser.error("%s does not exist, please specify --tar" % (TAR,))
+ if not os.path.exists(LFTP):
+ parser.error("%s does not exist, please specify --lftp" % (LFTP,))
make_all_ddfs(mapper, results, opts.daf, force=opts.force)
if opts.zip_ddf:
model.add_option('--sparql', default=None, help="execute sparql query")
model.add_option('--print-rdf', action="store_true", default=False,
help="print ending model state")
+ model.add_option('--tar', default=TAR,
+ help="override path to tar command")
+ model.add_option('--lftp', default=LFTP,
+ help="override path to lftp command")
parser.add_option_group(model)
# commands
commands = OptionGroup(parser, 'commands')
def make_all_ddfs(view_map, library_result_map, daf_name, make_condor=True, force=False):
dag_fragment = []
- for lib_id, result_dir in library_result_map:
+ for lib_id, result_dir in library_result_map.items():
submissionNode = view_map.get_submission_node(result_dir)
dag_fragment.extend(
make_ddf(view_map, submissionNode, daf_name, make_condor, result_dir)
def make_condor_archive_script(name, files, outdir=None):
script = """Universe = vanilla
-Executable = /bin/tar
+Executable = %(tar)s
arguments = czvhf ../%(archivename)s %(filelist)s
Error = compress.out.$(Process).log
context = {'archivename': make_submission_name(name),
'filelist': " ".join(files),
'initialdir': os.path.abspath(outdir),
- 'user': os.getlogin()}
+ 'user': os.getlogin(),
+ 'tar': TAR}
condor_script = os.path.join(outdir, make_condor_name(name, 'archive'))
condor_stream = open(condor_script,'w')
return condor_script
-def make_condor_upload_script(name, outdir=None):
+def make_condor_upload_script(name, lftp, outdir=None):
script = """Universe = vanilla
-Executable = /usr/bin/lftp
-arguments = -c put ../%(archivename)s -o ftp://%(ftpuser)s:%(ftppassword)s@%(ftphost)s/%(archivename)s
+Executable = %(lftp)s
+arguments = -c put %(archivename)s -o ftp://%(ftpuser)s:%(ftppassword)s@%(ftphost)s/%(archivename)s
Error = upload.out.$(Process).log
Output = upload.out.$(Process).log
'user': os.getlogin(),
'ftpuser': ftpuser,
'ftppassword': ftppassword,
- 'ftphost': encodeftp}
+ 'ftphost': encodeftp,
+ 'lftp': LFTP}
condor_script = os.path.join(outdir, make_condor_name(name, 'upload'))
condor_stream = open(condor_script,'w')
"model": "samples.Cellline",
"pk": 2,
"fields": {
- "cellline_name": "C2C12 Exponential",
+ "cellline_name": "C2C12",
"notes": ""
}
},
if xml is not None:
self.set_elements(xml)
+ def update_attributes_from_pathname(self):
+ """Update version, date, user from bustard directory names
+ Obviously this wont work for BaseCalls or later runfolders
+ """
+ if self.pathname is None:
+ raise ValueError(
+ "Set pathname before calling update_attributes_from_pathname")
+ path, name = os.path.split(self.pathname)
+
+ if not re.match('bustard', name, re.IGNORECASE):
+ return
+
+ groups = name.split("_")
+ version = re.search(VERSION_RE, groups[0])
+ self.version = version.group(1)
+ t = time.strptime(groups[1], EUROPEAN_STRPTIME)
+ self.date = date(*t[0:3])
+ self.user = groups[2]
+
def _get_time(self):
if self.date is None:
return None
:Return:
Fully initialized Bustard object.
"""
- b = Bustard()
pathname = os.path.abspath(pathname)
+ bustard_filename = os.path.join(pathname, 'config.xml')
+ demultiplexed_filename = os.path.join(pathname,
+ 'DemultiplexedBustardConfig.xml')
+
+ if os.path.exists(demultiplexed_filename):
+ b = bustard_from_hiseq(pathname, demultiplexed_filename)
+ elif os.path.exists(bustard_filename):
+ b = bustard_from_ga2(pathname, bustard_filename)
+ else:
+ b = bustard_from_ga1(pathname)
+
+ return b
+
+def bustard_from_ga1(pathname):
+ """Initialize bustard class from ga1 era runfolders.
+ """
path, name = os.path.split(pathname)
+
groups = name.split("_")
- if groups[0].lower().startswith('bustard'):
- version = re.search(VERSION_RE, groups[0])
- b.version = version.group(1)
- t = time.strptime(groups[1], EUROPEAN_STRPTIME)
- b.date = date(*t[0:3])
- b.user = groups[2]
- elif groups[0] == 'BaseCalls':
- # stub values
- b.version = None
- b.date = None
- b.user = None
+ if len(groups) < 3:
+ msg = "Not enough information to create attributes"\
+ " from directory name: %s"
+ LOGGER.error(msg % (self.pathname,))
+ return None
+ b = Bustard()
b.pathname = pathname
- bustard_config_filename = os.path.join(pathname, 'config.xml')
- paramfiles = glob(os.path.join(pathname, "params?.xml"))
- for paramfile in paramfiles:
- phasing = Phasing(paramfile)
- assert (phasing.lane >= 1 and phasing.lane <= 8)
- b.phasing[phasing.lane] = phasing
+ b.update_attributes_from_pathname()
+ version = re.search(VERSION_RE, groups[0])
+ b.version = version.group(1)
+ t = time.strptime(groups[1], EUROPEAN_STRPTIME)
+ b.date = date(*t[0:3])
+ b.user = groups[2]
+
# I only found these in Bustard1.9.5/1.9.6 directories
if b.version in ('1.9.5', '1.9.6'):
# at least for our runfolders for 1.9.5 and 1.9.6 matrix[1-8].txt are always the same
crosstalk_file = os.path.join(pathname, "matrix1.txt")
b.crosstalk = CrosstalkMatrix(crosstalk_file)
+
+ add_phasing(b)
+ return b
+
+
+def bustard_from_ga2(pathname, config_filename):
+ """Initialize bustard class from ga2-era runfolder
+ Actually I don't quite remember if it is exactly the GA2s, but
+ its after the original runfolder style and before the HiSeq.
+ """
# for version 1.3.2 of the pipeline the bustard version number went down
# to match the rest of the pipeline. However there's now a nifty
# new (useful) bustard config file.
- elif os.path.exists(bustard_config_filename):
- bustard_config_root = ElementTree.parse(bustard_config_filename)
- b.bustard_config = bustard_config_root.getroot()
- b.crosstalk = crosstalk_matrix_from_bustard_config(b.pathname, b.bustard_config)
- software = bustard_config_root.find('*/Software')
- b.version = software.attrib['Version']
- #b.version = software.attrib['Name'] + "-" + software.attrib['Version']
+
+ # stub values
+ b = Bustard()
+ b.pathname = pathname
+ b.update_attributes_from_pathname()
+ bustard_config_root = ElementTree.parse(config_filename)
+ b.bustard_config = bustard_config_root.getroot()
+ b.crosstalk = crosstalk_matrix_from_bustard_config(b.pathname,
+ b.bustard_config)
+ software = bustard_config_root.find('*/Software')
+ b.version = software.attrib['Version']
+ add_phasing(b)
return b
+def bustard_from_hiseq(pathname, config_filename):
+ b = Bustard()
+ b.pathname = pathname
+ bustard_config_root = ElementTree.parse(config_filename)
+ b.bustard_config = bustard_config_root.getroot()
+ software = bustard_config_root.find('*/Software')
+ b.version = software.attrib['Version']
+ add_phasing(b)
+ return b
+
+def add_phasing(bustard_obj):
+ paramfiles = glob(os.path.join(bustard_obj.pathname,
+ "params?.xml"))
+ for paramfile in paramfiles:
+ phasing = Phasing(paramfile)
+ assert (phasing.lane >= 1 and phasing.lane <= 8)
+ bustard_obj.phasing[phasing.lane] = phasing
+
def fromxml(tree):
"""
Reconstruct a htsworkflow.pipelines.Bustard object from an xml block
if os.stat(self.pathname)[stat.ST_SIZE] == 0:
raise RuntimeError("Eland isn't done, try again later.")
- LOGGER.info("summarizing results for %s" % (self.pathname))
+ LOGGER.debug("summarizing results for %s" % (self.pathname))
stream = autoopen(self.pathname, 'r')
if self.eland_type == ELAND_SINGLE:
full_lane_id = "%d_%d" % ( lane_id, end )
basename = pattern % (full_lane_id,)
- LOGGER.info("Eland pattern: %s" %(basename,))
+ LOGGER.debug("Eland pattern: %s" %(basename,))
pathname = os.path.join(basedir, basename)
if os.path.exists(pathname):
LOGGER.info('found eland file in %s' % (pathname,))
from datetime import datetime, date
import logging
import os
+import stat
import time
-from htsworkflow.pipelines.summary import Summary
+from htsworkflow.pipelines.summary import Summary, SummaryGA, SummaryHiSeq
from htsworkflow.pipelines.eland import eland, ELAND
from htsworkflow.pipelines.runfolder import \
self._lanes = {}
tree = self._gerald.tree
analysis = tree.find('LaneSpecificRunParameters/ANALYSIS')
+ if analysis is None:
+ return
# according to the pipeline specs I think their fields
# are sampleName_laneID, with sampleName defaulting to s
# since laneIDs are constant lets just try using
if self._lane is None:
self._initalize_lanes()
return self._lanes[key]
+ def get(self, key, default):
+ if self._lane is None:
+ self._initalize_lanes()
+ return self._lanes.get(key, None)
def keys(self):
if self._lane is None:
self._initalize_lanes()
if self.tree is None:
return datetime.today()
timestamp = self.tree.findtext('ChipWideRunParameters/TIME_STAMP')
- epochstamp = time.mktime(time.strptime(timestamp, '%c'))
- return datetime.fromtimestamp(epochstamp)
+ if timestamp is not None:
+ epochstamp = time.mktime(time.strptime(timestamp, '%c'))
+ return datetime.fromtimestamp(epochstamp)
+ if self.pathname is not None:
+ epochstamp = os.stat(self.pathname)[stat.ST_MTIME]
+ return datetime.fromtimestamp(epochstamp)
+ return datetime.today()
date = property(_get_date)
def _get_time(self):
if self.tree is None:
return None
- root = self._get_experiment_root()
- if root is None:
- root = ''
- else:
- root = os.path.join(root,'')
+ expt_root = os.path.normpath(self._get_experiment_root())
+ chip_expt_dir = self.tree.findtext('ChipWideRunParameters/EXPT_DIR')
+ # hiseqs renamed the experiment dir location
+ defaults_expt_dir = self.tree.findtext('Defaults/EXPT_DIR')
- experiment_dir = self.tree.findtext('ChipWideRunParameters/EXPT_DIR')
- if experiment_dir is None:
- return None
- experiment_dir = experiment_dir.replace(root, '')
- if len(experiment_dir) == 0:
+ experiment_dir = None
+ if defaults_expt_dir is not None:
+ _, experiment_dir = os.path.split(defaults_expt_dir)
+ elif expt_root is not None and chip_expt_dir is not None:
+ experiment_dir = chip_expt_dir.replace(expt_root+os.path.sep, '')
+ experiment_dir = experiment_dir.split(os.path.sep)[0]
+
+ if experiment_dir is None or len(experiment_dir) == 0:
return None
+ return experiment_dir
- dirnames = experiment_dir.split(os.path.sep)
- return dirnames[0]
runfolder_name = property(_get_runfolder_name)
def _get_version(self):
if self.tree is None:
return None
- return self.tree.findtext('ChipWideRunParameters/SOFTWARE_VERSION')
+ ga_version = self.tree.findtext(
+ 'ChipWideRunParameters/SOFTWARE_VERSION')
+ if ga_version is not None:
+ return ga_version
+ hiseq_software_node = self.tree.find('Software')
+ hiseq_version = hiseq_software_node.attrib['Version']
+ return hiseq_version
+
version = property(_get_version)
def _get_chip_attribute(self, value):
g.tree = ElementTree.parse(config_pathname).getroot()
# parse Summary.htm file
- summary_pathname = os.path.join(g.pathname, 'Summary.xml')
- if os.path.exists(summary_pathname):
+ summary_xml = os.path.join(g.pathname, 'Summary.xml')
+ summary_htm = os.path.join(g.pathname, 'Summary.htm')
+ report_summary = os.path.join(g.pathname, '..', 'Data',
+ 'reports', 'Summary', )
+ if os.path.exists(summary_xml):
LOGGER.info("Parsing Summary.xml")
- else:
- summary_pathname = os.path.join(g.pathname, 'Summary.htm')
+ g.summary = SummaryGA(summary_xml)
+ g.eland_results = eland(g.pathname, g)
+ elif os.path.exists(summary_htm):
LOGGER.info("Parsing Summary.htm")
- g.summary = Summary(summary_pathname)
+ g.summary = SummaryGA(summary_htm)
+ g.eland_results = eland(g.pathname, g)
+ elif os.path.isdir(report_summary):
+ LOGGER.info("Parsing %s" % (report_summary,))
+ g.summary = SummaryHiSeq(report_summary)
+
# parse eland files
- g.eland_results = eland(g.pathname, g)
return g
if __name__ == "__main__":
self.pathname = None
self._name = None
self._flowcell_id = flowcell_id
+ self.datadir = None
self.image_analysis = None
self.bustard = None
self.gerald = None
from htsworkflow.pipelines import bustard
from htsworkflow.pipelines import gerald
- def scan_post_image_analysis(runs, runfolder, image_analysis, pathname):
+ def scan_post_image_analysis(runs, runfolder, datadir, image_analysis, pathname):
LOGGER.info("Looking for bustard directories in %s" % (pathname,))
bustard_dirs = glob(os.path.join(pathname, "Bustard*"))
# RTA BaseCalls looks enough like Bustard.
for bustard_pathname in bustard_dirs:
LOGGER.info("Found bustard directory %s" % (bustard_pathname,))
b = bustard.bustard(bustard_pathname)
- gerald_glob = os.path.join(bustard_pathname, 'GERALD*')
- LOGGER.info("Looking for gerald directories in %s" % (pathname,))
- for gerald_pathname in glob(gerald_glob):
- LOGGER.info("Found gerald directory %s" % (gerald_pathname,))
- try:
- g = gerald.gerald(gerald_pathname)
- p = PipelineRun(runfolder, flowcell_id)
- p.image_analysis = image_analysis
- p.bustard = b
- p.gerald = g
- runs.append(p)
- except IOError, e:
- LOGGER.error("Ignoring " + str(e))
+ build_gerald_runs(runs, b, image_analysis, bustard_pathname, datadir, pathname, runfolder)
+
+ build_aligned_runs(image_analysis, runs, b, datadir, runfolder)
+
+ def build_gerald_runs(runs, b, image_analysis, bustard_pathname, datadir, pathname, runfolder):
+ gerald_glob = os.path.join(bustard_pathname, 'GERALD*')
+ LOGGER.info("Looking for gerald directories in %s" % (pathname,))
+ for gerald_pathname in glob(gerald_glob):
+ LOGGER.info("Found gerald directory %s" % (gerald_pathname,))
+ try:
+ g = gerald.gerald(gerald_pathname)
+ p = PipelineRun(runfolder, flowcell_id)
+ p.datadir = datadir
+ p.image_analysis = image_analysis
+ p.bustard = b
+ p.gerald = g
+ runs.append(p)
+ except IOError, e:
+ LOGGER.error("Ignoring " + str(e))
+
+
+ def build_aligned_runs(image_analysis, runs, b, datadir, runfolder):
+ aligned_glob = os.path.join(runfolder, 'Aligned*')
+ for aligned in glob(aligned_glob):
+ LOGGER.info("Found aligned directory %s" % (aligned,))
+ try:
+ g = gerald.gerald(aligned)
+ p = PipelineRun(runfolder, flowcell_id)
+ p.datadir = datadir
+ p.image_analysis = image_analysis
+ p.bustard = b
+ p.gerald = g
+ runs.append(p)
+ except IOError, e:
+ LOGGER.error("Ignoring " + str(e))
datadir = os.path.join(runfolder, 'Data')
)
else:
scan_post_image_analysis(
- runs, runfolder, image_analysis, firecrest_pathname
+ runs, runfolder, datadir, image_analysis, firecrest_pathname
)
# scan for IPAR directories
ipar_dirs = glob(os.path.join(datadir, "IPAR_*"))
)
else:
scan_post_image_analysis(
- runs, runfolder, image_analysis, ipar_pathname
+ runs, runfolder, datadir, image_analysis, ipar_pathname
)
return runs
os.chdir(cwd)
-def save_summary_file(gerald_object, cycle_dir):
+def save_summary_file(pipeline, cycle_dir):
# Copy Summary.htm
- summary_path = os.path.join(gerald_object.pathname, 'Summary.htm')
- if os.path.exists(summary_path):
- LOGGER.info('Copying %s to %s' % (summary_path, cycle_dir))
- shutil.copy(summary_path, cycle_dir)
+ gerald_object = pipeline.gerald
+ gerald_summary = os.path.join(gerald_object.pathname, 'Summary.htm')
+ status_files_summary = os.path.join(pipeline.datadir, 'Status_Files', 'Summary.htm')
+ if os.path.exists(gerald_summary):
+ LOGGER.info('Copying %s to %s' % (gerald_summary, cycle_dir))
+ shutil.copy(gerald_summary, cycle_dir)
+ elif os.path.exists(status_files_summary):
+ LOGGER.info('Copying %s to %s' % (status_files_summary, cycle_dir))
+ shutil.copy(status_files_summary, cycle_dir)
else:
LOGGER.info('Summary file %s was not found' % (summary_path,))
if site is not None:
lanes = []
for lane in range(1, 9):
- if r.gerald.lanes[lane].analysis != 'none':
+ lane_parameters = r.gerald.lanes.get(lane, None)
+ if lane_parameters is not None and lane_parameters.analysis != 'none':
lanes.append(lane)
run_name = srf.pathname_to_run_name(r.pathname)
seq_cmds = []
+ LOGGER.info("Raw Format is: %s" % (raw_format, ))
if raw_format == 'fastq':
- srf.copy_hiseq_project_fastqs(run_name, r.bustard.pathname, site, cycle_dir)
+ rawpath = os.path.join(r.pathname, r.gerald.runfolder_name)
+ LOGGER.info("raw data = %s" % (rawpath,))
+ srf.copy_hiseq_project_fastqs(run_name, rawpath, site, cycle_dir)
elif raw_format == 'qseq':
seq_cmds = srf.make_qseq_commands(run_name, r.bustard.pathname, lanes, site, cycle_dir)
elif raw_format == 'srf':
g = r.gerald
# save summary file
- save_summary_file(g, cycle_dir)
+ save_summary_file(r, cycle_dir)
# compress eland result files
compress_eland_results(g, cycle_dir, num_jobs)
"""
Analyze the Summary.htm file produced by GERALD
"""
+import os
import logging
import re
import types
XML_VERSION = 3
SUMMARY = 'Summary'
- class LaneResultSummary(object):
- """
- Parse the LaneResultSummary table out of Summary.htm
- Mostly for the cluster number
- """
- LANE_RESULT_SUMMARY = 'LaneResultSummary'
- TAGS = {
- 'LaneYield': 'lane_yield',
- 'Cluster': 'cluster', # Raw
- 'ClusterPF': 'cluster_pass_filter',
- 'AverageFirstCycleIntensity': 'average_first_cycle_intensity',
- 'PercentIntensityAfter20Cycles': 'percent_intensity_after_20_cycles',
- 'PercentPassFilterClusters': 'percent_pass_filter_clusters',
- 'PercentPassFilterAlign': 'percent_pass_filter_align',
- 'AverageAlignmentScore': 'average_alignment_score',
- 'PercentErrorRate': 'percent_error_rate'
- }
- # These are tags that have mean/stdev as found in the GERALD Summary.xml file
- GERALD_TAGS = {
- #'laneYield': 'lane_yield', #this is just a number
- 'clusterCountRaw': 'cluster', # Raw
- 'clusterCountPF': 'cluster_pass_filter',
- 'oneSig': 'average_first_cycle_intensity',
- 'signal20AsPctOf1': 'percent_intensity_after_20_cycles',
- 'percentClustersPF': 'percent_pass_filter_clusters',
- 'percentUniquelyAlignedPF': 'percent_pass_filter_align',
- 'averageAlignScorePF': 'average_alignment_score',
- 'errorPF': 'percent_error_rate'
- }
-
- def __init__(self, html=None, xml=None):
- self.lane = None
- self.end = 0
- self.lane_yield = None
- self.cluster = None
- self.cluster_pass_filter = None
- self.average_first_cycle_intensity = None
- self.percent_intensity_after_20_cycles = None
- self.percent_pass_filter_clusters = None
- self.percent_pass_filter_align = None
- self.average_alignment_score = None
- self.percent_error_rate = None
-
- if html is not None:
- self.set_elements_from_source(html)
- if xml is not None:
- self.set_elements(xml)
-
- def set_elements_from_source(self, data):
- """Read from an initial summary data file. Either xml or html
- """
- if not len(data) in (8,10):
- raise RuntimeError("Summary.htm file format changed, len(data)=%d" % (len(data),))
-
- # same in pre-0.3.0 Summary file and 0.3 summary file
- self.lane = int(data[0])
-
- if len(data) == 8:
- parsed_data = [ parse_mean_range(x) for x in data[1:] ]
- # this is the < 0.3 Pipeline version
- self.cluster = parsed_data[0]
- self.average_first_cycle_intensity = parsed_data[1]
- self.percent_intensity_after_20_cycles = parsed_data[2]
- self.percent_pass_filter_clusters = parsed_data[3]
- self.percent_pass_filter_align = parsed_data[4]
- self.average_alignment_score = parsed_data[5]
- self.percent_error_rate = parsed_data[6]
- elif len(data) == 10:
- parsed_data = [ parse_mean_range(x) for x in data[2:] ]
- # this is the >= 0.3 summary file
- self.lane_yield = data[1]
- self.cluster = parsed_data[0]
- self.cluster_pass_filter = parsed_data[1]
- self.average_first_cycle_intensity = parsed_data[2]
- self.percent_intensity_after_20_cycles = parsed_data[3]
- self.percent_pass_filter_clusters = parsed_data[4]
- self.percent_pass_filter_align = parsed_data[5]
- self.average_alignment_score = parsed_data[6]
- self.percent_error_rate = parsed_data[7]
-
- def set_elements_from_gerald_xml(self, read, element):
- self.lane = int(element.find('laneNumber').text)
- self.end = read
- lane_yield_node = element.find('laneYield')
- if lane_yield_node is not None:
- self.lane_yield = int(lane_yield_node.text)
- else:
- self.lane_yield = None
-
- for GeraldName, LRSName in Summary.LaneResultSummary.GERALD_TAGS.items():
- node = element.find(GeraldName)
- if node is None:
- LOGGER.info("Couldn't find %s" % (GeraldName))
- setattr(self, LRSName, parse_xml_mean_range(node))
-
- def get_elements(self):
- lane_result = etree.Element(
- Summary.LaneResultSummary.LANE_RESULT_SUMMARY,
- {'lane': unicode(self.lane), 'end': unicode(self.end)})
- for tag, variable_name in Summary.LaneResultSummary.TAGS.items():
- value = getattr(self, variable_name)
- if value is None:
- continue
- # it looks like a sequence
- elif type(value) in (types.TupleType, types.ListType):
- element = make_mean_range_element(
- lane_result,
- tag,
- *value
- )
- else:
- element = etree.SubElement(lane_result, tag)
- element.text = unicode(value)
- return lane_result
-
- def set_elements(self, tree):
- if tree.tag != Summary.LaneResultSummary.LANE_RESULT_SUMMARY:
- raise ValueError('Expected %s' % (
- Summary.LaneResultSummary.LANE_RESULT_SUMMARY))
- self.lane = int(tree.attrib['lane'])
- # default to the first end, for the older summary files
- # that are single ended
- self.end = int(tree.attrib.get('end', 0))
- tags = Summary.LaneResultSummary.TAGS
- for element in list(tree):
- try:
- variable_name = tags[element.tag]
- setattr(self, variable_name,
- parse_summary_element(element))
- except KeyError, e:
- LOGGER.warn('Unrecognized tag %s' % (element.tag,))
-
def __init__(self, filename=None, xml=None):
# lane results is a list of 1 or 2 ends containing
# a dictionary of all the lanes reported in this
def __len__(self):
return len(self.lane_results)
+ def get_elements(self):
+ summary = etree.Element(Summary.SUMMARY,
+ {'version': unicode(Summary.XML_VERSION)})
+ for end in self.lane_results:
+ for lane in end.values():
+ summary.append(lane.get_elements())
+ return summary
+
+ def set_elements(self, tree):
+ if tree.tag != Summary.SUMMARY:
+ return ValueError("Expected %s" % (Summary.SUMMARY,))
+ xml_version = int(tree.attrib.get('version', 0))
+ if xml_version > Summary.XML_VERSION:
+ LOGGER.warn('Summary XML tree is a higher version than this class')
+ for element in list(tree):
+ lrs = LaneResultSummaryGA()
+ lrs.set_elements(element)
+ if len(self.lane_results) < (lrs.end + 1):
+ self.lane_results.append({})
+ self.lane_results[lrs.end][lrs.lane] = lrs
+
+ def is_paired_end(self):
+ return len(self.lane_results) == 2
+
+ def dump(self):
+ """
+ Debugging function, report current object
+ """
+ tree = self.get_elements()
+ print etree.tostring(tree)
+
+class SummaryGA(Summary):
+ def __init__(self, filename=None, xml=None):
+ super(SummaryGA, self).__init__(filename, xml)
+
def _flattened_row(self, row):
"""
flatten the children of a <tr>...</tr>
read = int(read_tree.find('readNumber').text)-1
for element in read_tree.getchildren():
if element.tag.lower() == "lane":
- lrs = Summary.LaneResultSummary()
+ lrs = LaneResultSummaryGA()
lrs.set_elements_from_gerald_xml(read, element)
self.lane_results[lrs.end][lrs.lane] = lrs
# probably not useful
self.lane_results.append({})
for r in lane_summary:
- lrs = Summary.LaneResultSummary(html=r)
+ lrs = LaneResultSummaryGA(html=r)
lrs.end = end
self.lane_results[lrs.end][lrs.lane] = lrs
###### END HTML Table Extraction ########
+
+class SummaryHiSeq(Summary):
+ def __init__(self, filename=None, xml=None):
+ super(SummaryHiSeq, self).__init__(filename, xml)
+
+ def _extract_lane_results(self, filename):
+ read1 = os.path.join(filename, 'read1.xml')
+ read2 = os.path.join(filename, 'read2.xml')
+
+ if os.path.exists(read1):
+ self._extract_lane_results_for_end(read1, 0)
+ else:
+ LOGGER.warn("No read1.xml at %s." % (read1,))
+ if os.path.exists(read2):
+ self.lane_results.append({})
+ self._extract_lane_results_for_end(read2, 1)
+
+ def _extract_lane_results_for_end(self, filename, end):
+ self.tree = etree.parse(filename)
+ root = self.tree.getroot()
+ for lane in root.getchildren():
+ lrs = LaneResultSummaryHiSeq(data=lane)
+ lrs.end = end
+ self.lane_results[lrs.end][lrs.lane] = lrs
+
+
+class LaneResultSummary(object):
+ """
+ Parse the LaneResultSummary table out of Summary.htm
+ Mostly for the cluster number
+ """
+ LANE_RESULT_SUMMARY = 'LaneResultSummary'
+ TAGS = {
+ 'LaneYield': 'lane_yield',
+ 'Cluster': 'cluster', # Raw
+ 'ClusterPF': 'cluster_pass_filter',
+ 'AverageFirstCycleIntensity': 'average_first_cycle_intensity',
+ 'PercentIntensityAfter20Cycles': 'percent_intensity_after_20_cycles',
+ 'PercentPassFilterClusters': 'percent_pass_filter_clusters',
+ 'PercentPassFilterAlign': 'percent_pass_filter_align',
+ 'AverageAlignmentScore': 'average_alignment_score',
+ 'PercentErrorRate': 'percent_error_rate'
+ }
+ # These are tags that have mean/stdev as found in the GERALD Summary.xml file
+ GERALD_TAGS = {
+ #'laneYield': 'lane_yield', #this is just a number
+ 'clusterCountRaw': 'cluster', # Raw
+ 'clusterCountPF': 'cluster_pass_filter',
+ 'oneSig': 'average_first_cycle_intensity',
+ 'signal20AsPctOf1': 'percent_intensity_after_20_cycles',
+ 'percentClustersPF': 'percent_pass_filter_clusters',
+ 'percentUniquelyAlignedPF': 'percent_pass_filter_align',
+ 'averageAlignScorePF': 'average_alignment_score',
+ 'errorPF': 'percent_error_rate'
+ }
+
+ def __init__(self, html=None, xml=None):
+ self.lane = None
+ self.end = 0
+ self.lane_yield = None
+ self.cluster = None
+ self.cluster_pass_filter = None
+ self.average_first_cycle_intensity = None
+ self.percent_intensity_after_20_cycles = None
+ self.percent_pass_filter_clusters = None
+ self.percent_pass_filter_align = None
+ self.average_alignment_score = None
+ self.percent_error_rate = None
+
+
def get_elements(self):
- summary = etree.Element(Summary.SUMMARY,
- {'version': unicode(Summary.XML_VERSION)})
- for end in self.lane_results:
- for lane in end.values():
- summary.append(lane.get_elements())
- return summary
+ lane_result = etree.Element(
+ LaneResultSummary.LANE_RESULT_SUMMARY,
+ {'lane': unicode(self.lane), 'end': unicode(self.end)})
+ for tag, variable_name in LaneResultSummary.TAGS.items():
+ value = getattr(self, variable_name)
+ if value is None:
+ continue
+ # it looks like a sequence
+ elif type(value) in (types.TupleType, types.ListType):
+ element = make_mean_range_element(
+ lane_result,
+ tag,
+ *value
+ )
+ else:
+ element = etree.SubElement(lane_result, tag)
+ element.text = unicode(value)
+ return lane_result
def set_elements(self, tree):
- if tree.tag != Summary.SUMMARY:
- return ValueError("Expected %s" % (Summary.SUMMARY,))
- xml_version = int(tree.attrib.get('version', 0))
- if xml_version > Summary.XML_VERSION:
- LOGGER.warn('Summary XML tree is a higher version than this class')
+ if tree.tag != LaneResultSummary.LANE_RESULT_SUMMARY:
+ raise ValueError('Expected %s' % (
+ LaneResultSummary.LANE_RESULT_SUMMARY))
+ self.lane = int(tree.attrib['lane'])
+ # default to the first end, for the older summary files
+ # that are single ended
+ self.end = int(tree.attrib.get('end', 0))
+ tags = LaneResultSummary.TAGS
for element in list(tree):
- lrs = Summary.LaneResultSummary()
- lrs.set_elements(element)
- if len(self.lane_results) < (lrs.end + 1):
- self.lane_results.append({})
- self.lane_results[lrs.end][lrs.lane] = lrs
+ try:
+ variable_name = tags[element.tag]
+ setattr(self, variable_name,
+ parse_summary_element(element))
+ except KeyError, e:
+ LOGGER.warn('Unrecognized tag %s' % (element.tag,))
- def is_paired_end(self):
- return len(self.lane_results) == 2
- def dump(self):
+class LaneResultSummaryGA(LaneResultSummary):
+ def __init__(self, html=None, xml=None):
+ super(LaneResultSummaryGA, self).__init__(html, xml)
+
+ if html is not None:
+ self.set_elements_from_source(html)
+ if xml is not None:
+ self.set_elements(xml)
+
+ def set_elements_from_gerald_xml(self, read, element):
+ self.lane = int(element.find('laneNumber').text)
+ self.end = read
+ lane_yield_node = element.find('laneYield')
+ if lane_yield_node is not None:
+ self.lane_yield = int(lane_yield_node.text)
+ else:
+ self.lane_yield = None
+
+ for GeraldName, LRSName in LaneResultSummary.GERALD_TAGS.items():
+ node = element.find(GeraldName)
+ if node is None:
+ LOGGER.info("Couldn't find %s" % (GeraldName))
+ setattr(self, LRSName, parse_xml_mean_range(node))
+
+ def set_elements_from_source(self, data):
+ """Read from an initial summary data file. Either xml or html
"""
- Debugging function, report current object
+ if not len(data) in (8,10):
+ raise RuntimeError("Summary.htm file format changed, len(data)=%d" % (len(data),))
+
+ # same in pre-0.3.0 Summary file and 0.3 summary file
+ self.lane = int(data[0])
+
+ if len(data) == 8:
+ parsed_data = [ parse_mean_range(x) for x in data[1:] ]
+ # this is the < 0.3 Pipeline version
+ self.cluster = parsed_data[0]
+ self.average_first_cycle_intensity = parsed_data[1]
+ self.percent_intensity_after_20_cycles = parsed_data[2]
+ self.percent_pass_filter_clusters = parsed_data[3]
+ self.percent_pass_filter_align = parsed_data[4]
+ self.average_alignment_score = parsed_data[5]
+ self.percent_error_rate = parsed_data[6]
+ elif len(data) == 10:
+ parsed_data = [ parse_mean_range(x) for x in data[2:] ]
+ # this is the >= 0.3 summary file
+ self.lane_yield = data[1]
+ self.cluster = parsed_data[0]
+ self.cluster_pass_filter = parsed_data[1]
+ self.average_first_cycle_intensity = parsed_data[2]
+ self.percent_intensity_after_20_cycles = parsed_data[3]
+ self.percent_pass_filter_clusters = parsed_data[4]
+ self.percent_pass_filter_align = parsed_data[5]
+ self.average_alignment_score = parsed_data[6]
+ self.percent_error_rate = parsed_data[7]
+
+
+class LaneResultSummaryHiSeq(LaneResultSummary):
+ def __init__(self, data=None, xml=None):
+ super(LaneResultSummaryHiSeq, self).__init__(data, xml)
+
+ if data is not None:
+ self.set_elements_from_source(data)
+ if xml is not None:
+ self.set_elements(xml)
+
+ def set_elements_from_source(self, element):
+ """Read from an initial summary data file. Either xml or html
"""
- tree = self.get_elements()
- print etree.tostring(tree)
+ # same in pre-0.3.0 Summary file and 0.3 summary file
+ lane = element.attrib
+ self.lane = int(lane['key'])
+ #self.lane_yield = data[1]
+ self.cluster = (int(lane['ClustersRaw']),
+ float(lane['ClustersRawSD']))
+ self.cluster_pass_filter = (int(lane['ClustersPF']),
+ float(lane['ClustersPFSD']))
+ self.average_first_cycle_intensity = (int(lane['FirstCycleIntPF']),
+ float(lane['FirstCycleIntPFSD']))
+ self.percent_intensity_after_20_cycles = (
+ float(lane['PrcIntensityAfter20CyclesPF']),
+ float(lane['PrcIntensityAfter20CyclesPFSD']))
+ self.percent_pass_filter_clusters = (
+ float(lane['PrcPFClusters']),
+ float(lane['PrcPFClustersSD']))
+ self.percent_pass_filter_align = (
+ float(lane['PrcAlign']),
+ float(lane['PrcAlignSD']))
+ self.percent_error_rate = (
+ float(lane['ErrRatePhiX']),
+ float(lane['ErrRatePhiXSD']),)
+
def tonumber(v):
"""
def make_aligned_config_1_12(aligned_dir):
"""This is rouglhly equivalent to the old gerald file"""
- source = os.path.join(TESTDATA_DIR, 'aligned_config_1_12.xml')
+ source = os.path.join(TESTDATA_DIR, '1_12', 'aligned_config_1_12.xml')
destination = os.path.join(aligned_dir, 'config.xml')
shutil.copy(source, destination)
def make_unaligned_config_1_12(unaligned_dir):
demultiplex_pairs = [ # (src,
# dest),
- (os.path.join(TESTDATA_DIR, 'demultiplex_1.12.4.2.xml'),
- os.path.join(unaligned_dir, 'DemultiplexConfig.xml')),
- (os.path.join(TESTDATA_DIR, 'demultiplexed_bustard_1.12.4.2.xml'),
- os.path.join(unaligned_dir, 'DemultiplexConfig.xml')),
- (os.path.join(TESTDATA_DIR, 'demultiplexed_summary_1.12.4.2.xml'),
+ (os.path.join(TESTDATA_DIR, '1_12', 'demultiplex_1.12.4.2.xml'),
os.path.join(unaligned_dir, 'DemultiplexConfig.xml')),
+ (os.path.join(TESTDATA_DIR, '1_12',
+ 'demultiplexed_bustard_1.12.4.2.xml'),
+ os.path.join(unaligned_dir, 'DemultiplexedBustardConfig.xml')),
+ (os.path.join(TESTDATA_DIR, '1_12',
+ 'demultiplexed_summary_1.12.4.2.xml'),
+ os.path.join(unaligned_dir, 'DemultiplexedBustardSummary.xml')),
]
for src, dest in demultiplex_pairs:
shutil.copy(src, dest)
if not os.path.exists(intensities_dir):
os.mkdir(intensities_dir)
- param_file = os.path.join(TESTDATA_DIR, 'rta_intensities_config_1.12.4.2.xml')
+ param_file = os.path.join(TESTDATA_DIR, '1_12',
+ 'rta_intensities_config_1.12.4.2.xml')
shutil.copy(param_file, os.path.join(intensities_dir, 'RTAConfig.xml'))
return intensities_dir
os.mkdir(basecalls_dir)
make_qseqs(basecalls_dir, basecall_info=ABXX_BASE_CALL_INFO)
- param_file = os.path.join(TESTDATA_DIR, 'rta_basecalls_config_1.12.4.2.xml')
+ param_file = os.path.join(TESTDATA_DIR, '1_12',
+ 'rta_basecalls_config_1.12.4.2.xml')
shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
return basecalls_dir
destination = os.path.join(gerald_dir, 'Summary.xml')
shutil.copy(source, destination)
+def make_status_rta1_12(datadir):
+ sourcedir = os.path.join(TESTDATA_DIR, '1_12')
+ status_htm = os.path.join(sourcedir, 'Status.htm')
+ destination = os.path.join(datadir, 'Status.htm')
+ shutil.copy(status_htm, destination)
+
+ status_dir = os.path.join(datadir, 'Status_Files')
+ status_source_dir = os.path.join(sourcedir, 'Status_Files')
+ shutil.copytree(status_source_dir, status_dir)
+
+ report_source_dir = os.path.join(sourcedir, 'reports')
+ report_dir = os.path.join(datadir, 'reports')
+ shutil.copytree(report_source_dir, report_dir)
def make_eland_results(gerald_dir):
eland_result = """>HWI-EAS229_24_207BTAAXX:1:7:599:759 ACATAGNCACAGACATAAACATAGACATAGAC U0 1 1 3 chrUextra.fa 28189829 R D.
#!/usr/bin/env python
from datetime import datetime, date
+import logging
import os
import tempfile
import shutil
os.mkdir(data_dir)
intensities_dir = make_rta_intensities_1_12(data_dir)
+ make_status_rta1_12(data_dir)
basecalls_dir = make_rta_basecalls_1_12(intensities_dir)
make_matrix_dir_rta_1_12(basecalls_dir)
def test_bustard(self):
"""Construct a bustard object"""
b = bustard.bustard(self.bustard_dir)
- self.failUnlessEqual(b.version, '1.8.70.0')
+ self.failUnlessEqual(b.version, '1.12.4.2')
self.failUnlessEqual(b.date, None)
self.failUnlessEqual(b.user, None)
self.failUnlessEqual(len(b.phasing), 0)
# need to update gerald and make tests for it
g = gerald.gerald(self.gerald_dir)
- self.failUnlessEqual(g.version,
- '@(#) Id: GERALD.pl,v 1.171 2008/05/19 17:36:14 mzerara Exp')
- self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
+ self.failUnlessEqual(g.version, 'CASAVA-1.8.1')
self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
-
# list of genomes, matches what was defined up in
# make_gerald_config.
# the first None is to offset the genomes list to be 1..9
return unittest.makeSuite(RunfolderTests,'test')
if __name__ == "__main__":
- #unittest.main(defaultTest="suite")
- class Test(object): pass
- t = Test()
- make_runfolder(t)
- print ('path ' + t.runfolder_dir)
+ logging.basicConfig(level=logging.WARN)
+ unittest.main(defaultTest="suite")
def test_xml_summary_file(self):
pathname = os.path.join(TESTDATA_DIR, 'Summary-casava1.7.xml')
- s = summary.Summary(pathname)
+ s = summary.SummaryGA(pathname)
self.failUnlessEqual(len(s.lane_results[0]), 8)
self.failUnlessEqual(s.lane_results[0][1].cluster, (1073893, 146344))
def test_html_summary_file(self):
pathname = os.path.join(TESTDATA_DIR, 'Summary-ipar130.htm')
- s = summary.Summary(pathname)
+ s = summary.SummaryGA(pathname)
self.failUnlessEqual(len(s.lane_results[0]), 8)
self.failUnlessEqual(s.lane_results[0][1].cluster, (126910, 4300))
def test_hiseq_sample_summary_file(self):
pathname = os.path.join(TESTDATA_DIR, 'sample_summary_1_12.htm')
- s = summary.Summary(pathname)
+ s = summary.SummaryGA(pathname)
def suite():
return unittest.makeSuite(SummaryTests,'test')
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">\r
+<head>\r
+ <link rel="stylesheet" href="./Status_Files/Status.css" type="text/css" media="screen"/>\r
+ <script src="./Status_Files/Status.js" type="text/javascript"></script>\r
+ <title>Status</title>\r
+</head>\r
+<body>\r
+<table style="border:none"><tr>\r
+ <td><img alt="Refresh" title="Refresh" name="RefreshBtn" height="25" width="25" src="./Status_Files/RefreshBtn/r1.png" onmouseout="this.src='./Status_Files/RefreshBtn/r1.png'" onmouseover="this.src='./Status_Files/RefreshBtn/r2.png'" onmousedown="this.src='./Status_Files/RefreshBtn/r3.png'" onmouseup="this.src='./Status_Files/RefreshBtn/r2.png'" onclick="window.location.reload(true)" /> </td>\r
+ <td id="StatUpdateDiv" >\r
+ <table class="StatusTable"><tr>\r
+ <th>Total:</th><td>0</td><th>Extracted:</th><td>0</td><th>Called:</th><td>0</td>\r
+ <th>Scored:</th><td>0</td><th>Copied:</th><td>0</td><th>Err.Rated:</th><td>0</td>\r
+ </tr></table></td> \r
+ <td id="RunNameTD">Loading Run Data ...</td>\r
+ </tr></table>\r
+ <script type="text/javascript">\r
+ loadXSLTable('./reports/StatusUpdate.xml', './Status_Files/StatusUpdate.xsl', 'StatUpdateDiv');\r
+ runName = xslTransform(loadXMLDoc('./reports/Status.xml'), loadXMLDoc('./Status_Files/RunName.xsl'));\r
+ document.getElementById("RunNameTD").innerHTML = runName;\r
+ document.title = runName + " Status";\r
+</script>\r
+<ul id="tabmenu">\r
+ <li><a href="./Status_Files/RunInfo.htm">Run Info</a></li>\r
+ <li><a class="selected" href="Status.htm">Tile Status</a></li>\r
+ <li><a href="./Status_Files/Charts.htm">Charts</a></li>\r
+ <li><a href="./Status_Files/Summary.htm">Summary</a></li>\r
+ <li><a class="space">Plots:</a></li>\r
+ <li><a href="./Status_Files/ByLane.htm">Cluster Density</a></li>\r
+ <li><a href="./Status_Files/ByCycle.htm">Data By Cycle</a></li>\r
+</ul>\r
+<div id="container">\r
+ <img class="Chart" id="ProcessControlImg" src="./reports/Process Control.png" alt="Cannot display image"/>\r
+</div>\r
+ \r
+</body>\r
+</html>\r
+\r
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">\r
+<head>\r
+ <link rel="stylesheet" href="./Status.css" type="text/css" media="screen"/>\r
+ <script src="./Status.js" type="text/javascript"></script>\r
+ <script src="./ByCycle.js" type="text/javascript"></script>\r
+ <title>Status</title>\r
+</head>\r
+ \r
+<body>\r
+ <table style="border:none"><tr>\r
+ <td><img alt="Refresh" title="Refresh" name="RefreshBtn" height="25" width="25" src="./RefreshBtn/r1.png" onmouseout="this.src='./RefreshBtn/r1.png'" onmouseover="this.src='./RefreshBtn/r2.png'" onmousedown="this.src='./RefreshBtn/r3.png'" onmouseup="this.src='./RefreshBtn/r2.png'" onclick="window.location.reload(true)" /> </td>\r
+ <td id="StatUpdateDiv" >\r
+ <table class="StatusTable"><tr>\r
+ <th>Total:</th><td>0</td><th>Extracted:</th><td>0</td><th>Called:</th><td>0</td>\r
+ <th>Scored:</th><td>0</td><th>Copied:</th><td>0</td><th>Err.Rated:</th><td>0</td>\r
+ </tr></table></td> \r
+ <td id="RunNameTD">Loading Run Data ...</td>\r
+ </tr></table>\r
+ <script type="text/javascript">\r
+ loadXSLTable('../reports/StatusUpdate.xml', './StatusUpdate.xsl', 'StatUpdateDiv');\r
+ var runName = xslTransform(loadXMLDoc('../reports/Status.xml'), loadXMLDoc('./RunName.xsl'));\r
+ document.getElementById("RunNameTD").innerHTML = runName;\r
+ document.title = runName + " Status";\r
+ </script>\r
+\r
+<ul id="tabmenu">\r
+\r
+\r
+ <li><a href="./RunInfo.htm">Run Info</a></li>\r
+ <li><a href="../Status.htm">Tile Status</a></li>\r
+ <li><a href="./Charts.htm">Charts</a></li>\r
+ <li><a href="./Summary.htm">Summary</a></li>\r
+ <li><a class="space">Plots:</a></li>\r
+ <li><a href="./ByLane.htm">Cluster Density</a></li>\r
+ <li><a class="selected" href="./ByCycle.htm">Data By Cycle</a></li>\r
+</ul>\r
+ \r
+<div id="container">\r
+ <form action="" name="Plot1" id="Plot1" style="margin: 0px 0px 0px 0px;">\r
+ <table style="border:none"><tr>\r
+ <td><img style="margin: 0px 0px -5px 0px;" alt="Refresh" name="RefreshBtn" height="25" width="25" src="./RefreshBtn/r1.png" onmouseout="this.src='./RefreshBtn/r1.png'" onmouseover="this.src='./RefreshBtn/r2.png'" onmousedown="this.src='./RefreshBtn/r3.png'" onmouseup="this.src='./RefreshBtn/r2.png'" onclick="changeFrameSrc(Plot1)" /> </td>\r
+ <td><select size="1" name="QCOptDropDown" onchange="changeFrameSrc(this.form)">\r
+ <option value="Intensity" selected="selected">Intensity</option>\r
+ <option value="FWHM">Focus Quality</option>\r
+ <option value="QScore">Quality Score</option>\r
+ <option value="NumGT30">%Q>=30</option>\r
+ <option value="ErrRate">Error Rate</option>\r
+ </select>  </td> \r
+ <td><select size="1" name="lanesDropDown" style="display:inline" onchange="changeFrameSrc(this.form)">\r
+ <option value="L0" selected="selected">All Lanes</option>\r
+ <option value="L1">Lane 1</option>\r
+ <option value="L2">Lane 2</option>\r
+ <option value="L3">Lane 3</option>\r
+ <option value="L4">Lane 4</option>\r
+ <option value="L5">Lane 5</option>\r
+ <option value="L6">Lane 6</option>\r
+ <option value="L7">Lane 7</option>\r
+ <option value="L8">Lane 8</option>\r
+ </select>  </td>\r
+ <td><select size="1" name="baseDropDown" style="display:inline" onchange="changeFrameSrc(this.form)">\r
+ <option value="A">Base A</option>\r
+ <option value="C">Base C</option>\r
+ <option value="G">Base G</option>\r
+ <option value="T">Base T</option>\r
+ </select></td>\r
+ </tr></table> \r
+ <iframe name="Plot1Fr" src="./ByCycleFrame.htm?../reports/ByCycle/Intensity_L0a.png" height="387" width="95%" frameborder="0" >\r
+ <img name="imgPlot" alt="No Data" src="../reports/ByCycle/Intensity_L0a.png"/>\r
+ </iframe >\r
+ </form >\r
+ <form action="" name="Plot2" id="Plot2" style="margin: 0px 0px 0px 0px;">\r
+ <table style="border:none"><tr>\r
+ <td><img style="margin: 0px 0px -5px 0px;" alt="Refresh" name="RefreshBtn" height="25" width="25" src="./RefreshBtn/r1.png" onmouseout="this.src='./RefreshBtn/r1.png'" onmouseover="this.src='./RefreshBtn/r2.png'" onmousedown="this.src='./RefreshBtn/r3.png'" onmouseup="this.src='./RefreshBtn/r2.png'" onclick="changeFrameSrc(Plot2)" /> </td>\r
+ <td><select size="1" name="QCOptDropDown" onchange="changeFrameSrc(this.form)">\r
+ <option value="Intensity">Intensity</option>\r
+ <option value="FWHM" selected="selected">Focus Quality</option>\r
+ <option value="QScore">Quality Score</option>\r
+ <option value="NumGT30">%Q>=30</option>\r
+ <option value="ErrRate">Error Rate</option>\r
+ </select>  </td> \r
+ <td><select size="1" name="lanesDropDown" style="display:inline" onchange="changeFrameSrc(this.form)">\r
+ <option value="L0" selected="selected">All Lanes</option>\r
+ <option value="L1">Lane 1</option>\r
+ <option value="L2">Lane 2</option>\r
+ <option value="L3">Lane 3</option>\r
+ <option value="L4">Lane 4</option>\r
+ <option value="L5">Lane 5</option>\r
+ <option value="L6">Lane 6</option>\r
+ <option value="L7">Lane 7</option>\r
+ <option value="L8">Lane 8</option>\r
+ </select>  </td>\r
+ <td><select size="1" name="baseDropDown" style="display:inline" onchange="changeFrameSrc(this.form)">\r
+ <option value="A">Base A</option>\r
+ <option value="C">Base C</option>\r
+ <option value="G">Base G</option>\r
+ <option value="T">Base T</option>\r
+ </select></td>\r
+ </tr></table> \r
+ <iframe name="Plot2Fr" src="./ByCycleFrame.htm?../reports/ByCycle/FWHM_L0a.png" height="387" width="95%" frameborder="0">\r
+ <img name="imgPlot" alt="No Data" src="../reports/ByCycle/FWHM_L0a.png"/>\r
+ </iframe >\r
+ </form >\r
+</div>\r
+</body>\r
+</html>\r
+\r
--- /dev/null
+\r
+window.onerror = function() {\r
+ parent.location = './Error.htm';\r
+}\r
+\r
+function changeFrameSrc(form) {\r
+ var imgName = null;\r
+ var base = "";\r
+ var qc = form.QCOptDropDown.value;\r
+ if (qc == 'QScore' || qc == 'NumGT30' || qc == 'ErrRate') {\r
+ form.baseDropDown.style.display = 'none';\r
+ } else {\r
+ form.baseDropDown.style.display = 'inline';\r
+ base = form.baseDropDown.value.toLowerCase();\r
+ };\r
+ var intensityURL = "../reports/IntensityFrame.htm?";\r
+\r
+ imgName = "../reports/ByCycle/" + form.QCOptDropDown.value + "_" + form.lanesDropDown.value + base + ".png";\r
+ if (window.frames[form.name + "Fr"] != null) window.frames[form.name + "Fr"].location = "./ByCycleFrame.htm?" + imgName;\r
+ if (form.imgPlot != null) form.imgPlot.src = "../reports/" + imgName;\r
+}\r
+\r
+\r
--- /dev/null
+<html xmlns="http://www.w3.org/1999/xhtml">\r
+<head>\r
+<script type="text/javascript">\r
+ function setupImage() {\r
+ document.PlotImage.src = getParam() + "?" + (new Date().getMilliseconds());\r
+ document.PlotImage.style.display = "block"\r
+ }\r
+ function getParam() {\r
+ return location.href.substring(location.href.indexOf('?') + 1, location.href.length);\r
+ }\r
+</script>\r
+</head>\r
+<body onload='try{setupImage()}catch(err){};'>\r
+ <img name="PlotImage" id="PlotImage" title="Data by cycle" style="display:none" src="#" alt="No data"/>\r
+</body>\r
+</html>\r
+\r
+\r
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">\r
+<head>\r
+ <link rel="stylesheet" href="./Status.css" type="text/css" media="screen"/>\r
+ <script src="./Status.js" type="text/javascript"></script>\r
+ <script src="./ByLane.js" type="text/javascript"></script>\r
+ <title>Status</title>\r
+</head>\r
+ \r
+<body>\r
+ <table style="border:none"><tr>\r
+ <td><img alt="Refresh" title="Refresh" name="RefreshBtn" height="25" width="25" src="./RefreshBtn/r1.png" onmouseout="this.src='./RefreshBtn/r1.png'" onmouseover="this.src='./RefreshBtn/r2.png'" onmousedown="this.src='./RefreshBtn/r3.png'" onmouseup="this.src='./RefreshBtn/r2.png'" onclick="window.location.reload(true)" /> </td>\r
+ <td id="StatUpdateDiv" >\r
+ <table class="StatusTable"><tr>\r
+ <th>Total:</th><td>0</td><th>Extracted:</th><td>0</td><th>Called:</th><td>0</td>\r
+ <th>Scored:</th><td>0</td><th>Copied:</th><td>0</td><th>Err.Rated:</th><td>0</td>\r
+ </tr></table></td> \r
+ <td id="RunNameTD">Loading Run Data ...</td>\r
+ </tr></table>\r
+ <script type="text/javascript">\r
+ loadXSLTable('../reports/StatusUpdate.xml', './StatusUpdate.xsl', 'StatUpdateDiv');\r
+ var runName = xslTransform(loadXMLDoc('../reports/Status.xml'), loadXMLDoc('./RunName.xsl'));\r
+ document.getElementById("RunNameTD").innerHTML = runName;\r
+ document.title = runName + " Status";\r
+ </script>\r
+\r
+<ul id="tabmenu">\r
+ <li><a href="./RunInfo.htm">Run Info</a></li>\r
+ <li><a href="../Status.htm">Tile Status</a></li>\r
+ <li><a href="./Charts.htm">Charts</a></li>\r
+ <li><a href="./Summary.htm">Summary</a></li>\r
+ <li><a class="space">Plots:</a></li>\r
+ <li><a class="selected" href="./ByLane.htm">Cluster Density</a></li>\r
+ <li><a href="./ByCycle.htm">Data By Cycle</a></li>\r
+\r
+</ul>\r
+ \r
+<div id="container">\r
+ <p style="margin: 0px 0px 0px 120px;">\r
+ <input type="checkbox" name="PFOnlyBox" id="PFOnlyBox" title="Show only PF clusters" onclick="loadClustersByLane()"/>\r
+ Show PF only\r
+ </p>\r
+ <img class="Chart" alt="No Data" id="NumClustersImg" src="../reports/NumClusters By Lane.png"/>\r
+ <table class="DataTable" style="margin: 0px 0px 0px 20px" id="NumClustersTbl"></table >\r
+ <script type="text/javascript">loadClustersByLane();</script>\r
+</div>\r
+</body>\r
+</html>\r
+\r
--- /dev/null
+window.onerror = function() {\r
+ parent.location = './Error.htm';\r
+}\r
+\r
+function loadClustersByLane() {\r
+ name = name0 = '../reports/NumClusters By Lane';\r
+ if (document.getElementById('PFOnlyBox').checked) {\r
+ name = name0 + " PF";\r
+ try {\r
+ xmlDoc = loadXMLDoc(name + '.xml');\r
+ } catch (e) { xmlDoc = null; };\r
+ if (xmlDoc == null || xmlDoc.getElementsByTagName('Data') == null) {\r
+ name = name0;\r
+ alert("No data available!");\r
+ document.getElementById('PFOnlyBox').checked = false;\r
+ }\r
+ }\r
+ document.getElementById('NumClustersImg').src = name + ".png";\r
+ imgRefresh('NumClustersImg');\r
+ loadNumClustersTable(name + '.xml', 'NumClustersTbl', 'Lane');\r
+}\r
+\r
+function loadNumClustersTable(xmlName, tblName, tagsName) {\r
+ tbl = document.getElementById(tblName);\r
+ xmlDoc = loadXMLDoc(xmlName);\r
+ if (xmlDoc == null) return;\r
+ xmlRows = xmlDoc.getElementsByTagName(tagsName);\r
+ if (xmlRows == null) return;\r
+ while (tbl.rows.length > 0) tbl.deleteRow(tbl.rows.length - 1);\r
+ if (xmlRows.length > 0 && xmlRows[0].attributes.length > 0) {\r
+ tbl.insertRow(0);\r
+ for (j = xmlRows[0].attributes.length - 1; j >= 1; j--)\r
+ tbl.insertRow(0);\r
+ for (i = xmlRows.length - 1; i >= 0; i--) {\r
+ for (j = xmlRows[i].attributes.length - 1; j >= 1; j--) {\r
+ tbl.rows[j].insertCell(0);\r
+ val = new Number(xmlRows[i].attributes[j].value);\r
+ if (val < 1000) strVal = val.toFixed(0);\r
+ else strVal = (val / 1000).toFixed(0) + "K";\r
+ tbl.rows[j].cells[0].innerHTML = strVal;\r
+ }\r
+ }\r
+ for (j = xmlRows[0].attributes.length - 1; j >= 1; j--) {\r
+ tbl.rows[j].insertCell(0);\r
+ tbl.rows[j].cells[0].innerHTML = xmlRows[0].attributes[j].name.toUpperCase();\r
+ //tbl.rows[j].insertCell(0); tbl.rows[j].insertCell(0);\r
+ }\r
+ for (i = xmlRows.length - 1; i >= 0; i--) {\r
+ tbl.rows[0].insertCell(0);\r
+ tbl.rows[j].cells[0].innerHTML = tagsName + " " + xmlRows[i].attributes[0].value;\r
+ }\r
+ tbl.rows[0].insertCell(0); //tbl.rows[0].insertCell(0); tbl.rows[0].insertCell(0);\r
+ }\r
+}\r
+\r
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">\r
+<head>\r
+ <link rel="stylesheet" href="./Status.css" type="text/css" media="screen"/>\r
+ <script src="./Status.js" type="text/javascript"></script>\r
+ <script src="./Charts.js" type="text/javascript"></script>\r
+ <title>Status</title>\r
+</head>\r
+ \r
+<body>\r
+ <table style="border:none"><tr>\r
+ <td><img alt="Refresh" title="Refresh" name="RefreshBtn" height="25" width="25" src="./RefreshBtn/r1.png" onmouseout="this.src='./RefreshBtn/r1.png'" onmouseover="this.src='./RefreshBtn/r2.png'" onmousedown="this.src='./RefreshBtn/r3.png'" onmouseup="this.src='./RefreshBtn/r2.png'" onclick="window.location.reload(true)" /> </td>\r
+ <td id="StatUpdateDiv" >\r
+ <table class="StatusTable"><tr>\r
+ <th>Total:</th><td>0</td><th>Extracted:</th><td>0</td><th>Called:</th><td>0</td>\r
+ <th>Scored:</th><td>0</td><th>Copied:</th><td>0</td><th>Err.Rated:</th><td>0</td>\r
+ </tr></table></td> \r
+ <td id="RunNameTD">Loading Run Data ...</td>\r
+ </tr></table>\r
+ <script type="text/javascript">\r
+ loadXSLTable('../reports/StatusUpdate.xml', './StatusUpdate.xsl', 'StatUpdateDiv');\r
+ var runName = xslTransform(loadXMLDoc('../reports/Status.xml'), loadXMLDoc('./RunName.xsl'));\r
+ document.getElementById("RunNameTD").innerHTML = runName;\r
+ document.title = runName + " Status";\r
+ </script>\r
+ <map name="tileMap" id = "tileMap"></map> \r
+ <script type="text/javascript">\r
+ var tilesPerLane = xslTransform(loadXMLDoc('../reports/Status.xml'), loadXMLDoc('./TilesPerLane.xsl'));\r
+ var tileMap = new TileMap(tilesPerLane);\r
+ var imgCycle = document.getElementById("ImgCycle");\r
+ if (imgCycle != null) imgCycle = imgCycle.innerHTML;\r
+ else imgCycle = 0;\r
+ </script>\r
+\r
+<ul id="tabmenu">\r
+ <li><a href="./RunInfo.htm">Run Info</a></li>\r
+ <li><a href="../Status.htm">Tile Status</a></li>\r
+ <li><a class="selected" href="./Charts.htm">Charts</a></li>\r
+ <li><a href="./Summary.htm">Summary</a></li>\r
+ <li><a class="space">Plots:</a></li>\r
+ <li><a href="./ByLane.htm">Cluster Density</a></li>\r
+ <li><a href="./ByCycle.htm">Data By Cycle</a></li>\r
+</ul>\r
+ \r
+<div id="container">\r
+ <table class="GreenLife" ><tr>\r
+ <td><form name="imgChartForm1" action="">\r
+ <select size="1" name="QCOptDropDown" onchange="changeImage(this.form)">\r
+ <option value="NumClusters" selected="selected">Cluster Density</option>\r
+ <option value="PassedFilter25">%Cluster PF</option>\r
+ <option value="NumPassedFilter25">Cluster PF Density</option>\r
+ </select> \r
+      <label id="autoscale1lbl" for='autoscale1'>Autoscale </label><input type="checkbox" name="autoscale" id="autoscale1" title="Autoscale" onclick="changeImage(this.form)"/>\r
+ <img name="Chart" class="Chart" id="imgChart1" src="../reports/NumClusters_Chart.png" usemap="#tileMap" onmouseover="tileMap.resetMap(this)" onerror="try{{if(this.src.indexOf('blank.png') == -1)showBlank('imgChart1'); /*setTimeout('imgReload(\'imgChart1\')',20000)*/}}catch(err){{errorPrint(err)}}" alt= "No Data"/>\r
+ </form ></td>\r
+ <td><form name="imgChartForm2" action=""> \r
+ <select size="1" name="QCOptDropDown" onchange="changeImage(this.form)">\r
+ <option value="Intensity" selected="selected">Intensity </option>\r
+ <option value="FWHM">Focus Quality</option>\r
+ <option value="NumGT30">%Q>=30</option>\r
+ <option value="ErrorRate">Error Rate</option>\r
+ </select> \r
+ <select size="1" name="cyDropDown" onchange="changeImage(this.form)"></select>\r
+ <script type="text/javascript">\r
+ fillCycles(document.imgChartForm2.cyDropDown, imgCycle);\r
+ </script>\r
+ <select size="1" name="baseDropDown" onchange="changeImage(this.form)">\r
+ <option value="A" selected="selected">Base A</option>\r
+ <option value="C">Base C</option>\r
+ <option value="G">Base G</option>\r
+ <option value="T">Base T</option>\r
+ </select>\r
+   <label id="autoscale2lbl" for='autoscale2' style ="display :none ">Autoscale </label><input type="checkbox" name="autoscale" id="autoscale2" title="Autoscale" onclick="changeImage(this.form)"/>\r
+ <img name="Chart" class="Chart" id="imgChart2" src="../reports/Intensity/Chart_1_a.png" usemap="#tileMap" onmouseover="tileMap.resetMap(this)" onerror="try{{if(this.src.indexOf('blank.png') == -1)showBlank('imgChart2'); /*setTimeout('imgReload(\'imgChart2\')',20000)*/}}catch(err){{errorPrint(err)}}" alt ="No Data"/>\r
+ </form ></td>\r
+ <td><form name="imgChartForm3" action=""> \r
+ <select size="1" name="QCOptDropDown" onchange="changeImage(this.form)">\r
+ <option value="Intensity">Intensity </option>\r
+ <option value="FWHM" selected="selected">Focus Quality</option>\r
+ <option value="NumGT30">%Q>=30</option>\r
+ <option value="ErrorRate">Error Rate</option>\r
+ </select> \r
+ <select size="1" name="cyDropDown" onchange="changeImage(this.form)"></select>\r
+ <script type="text/javascript">\r
+ fillCycles(document.imgChartForm3.cyDropDown, imgCycle);\r
+ </script>\r
+ <select size="1" name="baseDropDown" onchange="changeImage(this.form)">\r
+ <option value="A" selected="selected">Base A</option>\r
+ <option value="C">Base C</option>\r
+ <option value="G">Base G</option>\r
+ <option value="T">Base T</option>\r
+ </select>\r
+   <label id="autoscale3lbl" for='autoscale3' style ="display :none">Autoscale</label><input type="checkbox" name="autoscale" id="autoscale3" title="Autoscale" onclick="changeImage(this.form)"/>\r
+ <img name="Chart" class="Chart" id="imgChart3" src="../reports/FWHM/Chart_1_a.png" usemap="#tileMap" onmouseover="tileMap.resetMap(this)" onerror="try{{if(this.src.indexOf('blank.png') == -1)showBlank('imgChart3'); /*setTimeout('imgReload(\'imgChart3\')',20000)*/}}catch(err){{errorPrint(err)}}" alt ="No Data"/>\r
+ </form></td>\r
+ </tr></table>\r
+</div> \r
+</body>\r
+</html>\r
+\r
--- /dev/null
+window.onerror = function() {\r
+ parent.location = './Error.htm';\r
+}\r
+\r
+var imageOnFocusId = null;\r
+function TileMap(nTiles) {\r
+ var numLanes = 8;\r
+ var numTiles = nTiles;\r
+ var width = 200;\r
+ var height = 750;\r
+ var X0 = 18;\r
+ var Y0 = 26;\r
+ var dL = width / numLanes;\r
+ var numCols = 2;\r
+ var numRows = numTiles / numCols;\r
+ var dX = width / (numCols * numLanes);\r
+ var dY = height / numRows;\r
+ var map = document.getElementById("tileMap");\r
+ var tileMapXML;\r
+ this.changeLayout = function(layoutNode) {\r
+ nCols = layoutNode.getAttribute("ColsPerLane");\r
+ if (nCols > 0) numCols = nCols;\r
+ nRows = layoutNode.getAttribute("RowsPerLane");\r
+ if (nRows > 0) numRows = nRows;\r
+ dX = width / (numCols * numLanes);\r
+ dY = height / numRows;\r
+ }\r
+ this.newToolTip = function(lane, idx) {\r
+ var area = document.createElement("area");\r
+ area.shape = "rect";\r
+ var col = Math.floor((idx - 1) / numRows);\r
+ var row = (idx - 1) % numRows;\r
+ if (idx - numRows <= 0) row = numRows - row - 1;\r
+ var X1 = Math.round(X0 + dX * col + (lane - 1) * dL);\r
+ var Y1 = Math.round(Y0 + dY * row);\r
+ var X2 = Math.round(X1 + dX);\r
+ var Y2 = Math.round(Y1 + dY);\r
+ area.coords = "'" + X1 + "," + Y1 + "," + X2 + "," + Y2 + "'";\r
+ area.title = "L:" + lane + " T:" + idx;\r
+ map.appendChild(area);\r
+ }\r
+\r
+ this.newToolTipVal = function(tile, base) {\r
+ var area = document.createElement("area");\r
+ area.shape = "rect";\r
+ key = tile.getAttribute("Key");\r
+ if (base == null) base = "Val";\r
+ val = tile.getAttribute(base);\r
+ lane = key.substring(0, 1);\r
+ idx = key.substring(2);\r
+ var col = Math.floor((idx - 1) / numRows);\r
+ var row = (idx - 1) % numRows;\r
+ if (idx - numRows <= 0) row = numRows - row - 1;\r
+ var X1 = Math.round(X0 + dX * col + (lane - 1) * dL);\r
+ var Y1 = Math.round(Y0 + dY * row);\r
+ var X2 = Math.round(X1 + dX);\r
+ var Y2 = Math.round(Y1 + dY);\r
+ area.coords = "'" + X1 + "," + Y1 + "," + X2 + "," + Y2 + "'";\r
+ area.title = "L:" + lane + " T:" + idx + "\n" + "Val= " + val;\r
+ map.appendChild(area);\r
+ }\r
+ this.resetMap = function(image) {\r
+ if (image.id == imageOnFocusId) return;\r
+ xmlName = image.src;\r
+ xmlName = xmlName.replace("@.png", ".png");\r
+ xmlName = xmlName.substring(0, xmlName.lastIndexOf('.')) + ".xml";\r
+ var base = null;\r
+ if (xmlName.lastIndexOf('_a.xml') > 0) base = 'A';\r
+ else if (xmlName.lastIndexOf('_c.xml') > 0) base = 'C';\r
+ else if (xmlName.lastIndexOf('_g.xml') > 0) base = 'G';\r
+ else if (xmlName.lastIndexOf('_t.xml') > 0) base = 'T';\r
+ if (base != null) xmlName = xmlName.substring(0, xmlName.lastIndexOf('_')) + ".xml";\r
+ try {\r
+ this.tileMapXML = loadXMLDoc(xmlName);\r
+ layout = this.tileMapXML.getElementsByTagName("Layout");\r
+ if (layout != null && layout.length > 0) this.changeLayout(layout[0]);\r
+ tiles = this.tileMapXML.getElementsByTagName("TL");\r
+ while (map.lastChild != null) map.removeChild(map.lastChild);\r
+ for (i = 0; i < tiles.length; i++) tileMap.newToolTipVal(tiles[i], base);\r
+ } catch (e) { this.blankMap(); }\r
+ imageOnFocusId = image.id;\r
+ }\r
+\r
+\r
+ this.blankMap = function() {\r
+ while (map.lastChild != null) map.removeChild(map.lastChild);\r
+ for (var l = 1; l <= numLanes; l++) {\r
+ for (var i = 1; i <= numTiles; i++) {\r
+ this.newToolTip(l, i);\r
+ }\r
+ }\r
+ }\r
+}\r
+\r
+function fillCycles(CyBox, maxCy) {\r
+ for (var cy = 1; cy <= maxCy; cy++) {\r
+ var option = document.createElement('option');\r
+ option.setAttribute('value', cy);\r
+ option.appendChild(document.createTextNode(cy));\r
+ CyBox.appendChild(option);\r
+ }\r
+}\r
+\r
+function changeImage(form) {\r
+ var qc = form.QCOptDropDown.value;\r
+ var base = "";\r
+ var cycle = "";\r
+ //alert(form.autoscale.id);\r
+ //return;\r
+ if (form.baseDropDown != null) {\r
+ if (qc == "ErrorRate" || qc == "NumGT30") {\r
+ form.baseDropDown.style.display = 'none';\r
+ document.getElementById(form.autoscale.id.toString() + 'lbl').style.display = 'inline';\r
+ }\r
+ else {\r
+ form.baseDropDown.style.display = 'inline';\r
+ base = "_" + form.baseDropDown.value.toLowerCase();\r
+ document.getElementById(form.autoscale.id.toString() + 'lbl').style.display = 'none';\r
+\r
+ }\r
+ }\r
+ if (form.cyDropDown != null) {\r
+ form.cyDropDown.disabled = false;\r
+ if (form.cyDropDown != null && !form.cyDropDown.disabled) {\r
+ cycle = "_" + form.cyDropDown.value.toLowerCase();\r
+ qc = qc + "/";\r
+ }\r
+ } else qc = qc + "_";\r
+ auto = "";\r
+ if (form.autoscale.checked) auto = "@";\r
+ var suff = cycle + base + auto + ".png";\r
+ form.Chart.src = "../reports/" + qc + "Chart" + suff;\r
+ form.Chart.lowsrc = form.Chart.src;\r
+ imageOnFocusId = null;\r
+}\r
+\r
+function showBlank(imgId) {\r
+ document.getElementById(imgId).lowsrc = document.getElementById(imgId).src;\r
+ document.getElementById(imgId).src = "../reports/blank.png";\r
+}\r
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">\r
+<head>\r
+ <link rel="stylesheet" href="./Status.css" type="text/css" media="screen"/>\r
+ <script src="./Status.js" type="text/javascript"></script>\r
+ <script src="./Controls.js" type="text/javascript"></script>\r
+ <title>Status</title>\r
+</head>\r
+ \r
+<body>\r
+ <table style="border:none"><tr>\r
+ <td><img alt="Refresh" title="Refresh" name="RefreshBtn" height="25" width="25" src="./RefreshBtn/r1.png" onmouseout="this.src='./RefreshBtn/r1.png'" onmouseover="this.src='./RefreshBtn/r2.png'" onmousedown="this.src='./RefreshBtn/r3.png'" onmouseup="this.src='./RefreshBtn/r2.png'" onclick="window.location.reload(true)" /> </td>\r
+ <td id="StatUpdateDiv" >\r
+ <table class="StatusTable"><tr>\r
+ <th>Total:</th><td>0</td><th>Extracted:</th><td>0</td><th>Called:</th><td>0</td>\r
+ <th>Scored:</th><td>0</td><th>Copied:</th><td>0</td><th>Err.Rated:</th><td>0</td>\r
+ </tr></table></td> \r
+ <td id="RunNameTD">Loading Run Data ...</td>\r
+ </tr></table>\r
+ <script type="text/javascript">\r
+ loadXSLTable('../reports/StatusUpdate.xml', './StatusUpdate.xsl', 'StatUpdateDiv');\r
+ runName = xslTransform(loadXMLDoc('../reports/Status.xml'), loadXMLDoc('./RunName.xsl'));\r
+ document.getElementById("RunNameTD").innerHTML = runName;\r
+ document.title = runName + " Status";\r
+ </script>\r
+<ul id="tabmenu">\r
+ <li><a href="./RunInfo.htm">Run Info</a></li>\r
+ <li><a href="../Status.htm">Tile Status</a></li>\r
+ <li><a href="./Charts.htm">Charts</a></li>\r
+ <li><a href="./Summary.htm">Summary</a></li>\r
+ <li><a class="selected" href="./Controls.htm">Controls</a></li>\r
+ <li><a class="space">Plots:</a></li>\r
+ <li><a href="./ByLane.htm">Cluster Density</a></li>\r
+ <li><a href="./ByCycle.htm">Data By Cycle</a></li>\r
+</ul>\r
+ \r
+<div id="container">\r
+ <div id="ControlsTbl" ><p> No data available yet.</p></div>\r
+ <script type="text/javascript">loadControls()</script>\r
+</div>\r
+ \r
+</body>\r
+</html>\r
+\r
--- /dev/null
+window.onerror = function() {\r
+ parent.location = './Error.htm';\r
+}\r
+\r
+function loadControls() {\r
+ loadXSLTable('../reports/controls.xml', './controls.xsl', 'ControlsTbl');\r
+}
\ No newline at end of file
--- /dev/null
+<?xml version="1.0"?> \r
+<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" \r
+version="1.0"> \r
+<xsl:output method="html" indent="yes" omit-xml-declaration="yes"/>\r
+<xsl:template match="/">\r
+ <table class="DataTable" >\r
+ <tr>\r
+ <th>Control</th>\r
+ <th >Lane 1</th><th >Lane 2</th><th >Lane 3</th><th >Lane 4</th>\r
+ <th >Lane 5</th><th >Lane 6</th><th >Lane 7</th><th >Lane 8</th>\r
+ </tr>\r
+ <xsl:for-each select="Controls/ctl"><tr>\r
+ <td><xsl:value-of select="@Key"/></td> \r
+ <td><xsl:value-of select="@L1"/></td> \r
+ <td><xsl:value-of select="@L2"/></td> \r
+ <td><xsl:value-of select="@L3"/></td> \r
+ <td><xsl:value-of select="@L4"/></td> \r
+ <td><xsl:value-of select="@L5"/></td> \r
+ <td><xsl:value-of select="@L6"/></td> \r
+ <td><xsl:value-of select="@L7"/></td> \r
+ <td><xsl:value-of select="@L8"/></td>\r
+ </tr></xsl:for-each>\r
+ </table >\r
+</xsl:template>\r
+</xsl:stylesheet>\r
--- /dev/null
+<html xmlns="http://www.w3.org/1999/xhtml" >\r
+<head></head> \r
+<body>\r
+<p>There was a problem loading the file.</p>\r
+<p>Please click a link below to try again</p>\r
+<p><a href="..\Status.htm">Status.htm</a></p>\r
+</body>\r
+</html>\r
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">\r
+<head>\r
+ <link rel="stylesheet" href="./Status.css" type="text/css" media="screen"/>\r
+ <script src="./Status.js" type="text/javascript"></script>\r
+ <title>Status</title>\r
+</head>\r
+ \r
+<body>\r
+ <table style="border:none"><tr>\r
+ <td><img alt="Refresh" title="Refresh" name="RefreshBtn" height="25" width="25" src="./RefreshBtn/r1.png" onmouseout="this.src='./RefreshBtn/r1.png'" onmouseover="this.src='./RefreshBtn/r2.png'" onmousedown="this.src='./RefreshBtn/r3.png'" onmouseup="this.src='./RefreshBtn/r2.png'" onclick="window.location.reload(true)" /> </td>\r
+ <td id="StatUpdateDiv" >\r
+ <table class="StatusTable"><tr>\r
+ <th>Total:</th><td>0</td><th>Extracted:</th><td>0</td><th>Called:</th><td>0</td>\r
+ <th>Scored:</th><td>0</td><th>Copied:</th><td>0</td><th>Err.Rated:</th><td>0</td>\r
+ </tr></table></td> \r
+ <td id="RunNameTD">Loading Run Data ...</td>\r
+ </tr></table>\r
+ <script type="text/javascript">\r
+ loadXSLTable('../reports/StatusUpdate.xml', './StatusUpdate.xsl', 'StatUpdateDiv');\r
+ runName = xslTransform(loadXMLDoc('../reports/Status.xml'), loadXMLDoc('./RunName.xsl'));\r
+ document.getElementById("RunNameTD").innerHTML = runName;\r
+ document.title = runName + " Status";\r
+ </script>\r
+<ul id="tabmenu">\r
+ <li><a class="selected" href="./RunInfo.htm">Run Info</a></li>\r
+ <li><a href="../Status.htm">Tile Status</a></li>\r
+ <li><a href="./Charts.htm">Charts</a></li>\r
+ <li><a href="./Summary.htm">Summary</a></li>\r
+ <li><a class="space">Plots:</a></li>\r
+ <li><a href="./ByLane.htm">Cluster Density</a></li>\r
+ <li><a href="./ByCycle.htm">Data By Cycle</a></li>\r
+</ul>\r
+ \r
+<div id="container">\r
+ <script type="text/javascript" >\r
+ loadXSLTable('../reports/Status.xml', './RunInfo.xsl', 'container');\r
+ </script>\r
+</div>\r
+ \r
+</body>\r
+</html>\r
+\r
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>\r
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"\r
+ xmlns:msxsl="urn:schemas-microsoft-com:xslt" exclude-result-prefixes="msxsl"\r
+ xmlns:lxslt="http://xml.apache.org/xslt">\r
+<xsl:output method="html" indent="yes"/>\r
+ <xsl:template match="/">\r
+ <table class="InfoTable">\r
+ <tr style="text-align: center;">Run Description<p/></tr>\r
+ <tr><th>Software:</th><td><xsl:value-of select="/Status/Software"/></td></tr>\r
+ <tr><th>Run name:</th><td><xsl:value-of select="/Status/RunName"/></td></tr>\r
+ <tr><th>Cycles:</th><td><xsl:value-of select="/Status/NumCycles"/></td></tr>\r
+ <tr><th>Instrument name:</th><td><xsl:value-of select="/Status/InstrumentName"/></td></tr>\r
+ <tr><th>Run Started (Estimated):</th><td><xsl:value-of select="/Status/RunStarted"/></td></tr>\r
+ <tr><th>Input Directory:</th><td><xsl:value-of select="/Status/InputDir"/></td></tr>\r
+ <tr><th>Output Directory:</th><td><xsl:value-of select="/Status/OutputDir"/></td></tr>\r
+ <tr><p/></tr>\r
+ </table >\r
+ <p/>\r
+ <table class="InfoTable">\r
+ <tr style="text-align: center;">Configuration Settings<p/></tr>\r
+ <tr><th><li type="square">Copy all run files:</li></th><td><xsl:value-of select="/Status/Configuration/CopyAllFiles"/></td></tr>\r
+ <tr><th><li type="square">Copy images:</li></th><td><xsl:value-of select="/Status/Configuration/CopyImages"/></td></tr>\r
+ <tr><th><li type="square">Delete image files:</li></th><td><xsl:value-of select="/Status/Configuration/DeleteImages"/></td></tr>\r
+ <tr><th><li type="square">Delete intensity files:</li></th><td><xsl:value-of select="/Status/Configuration/DeleteIntensity"/></td></tr>\r
+ <tr><th><li type="square">Run info file exists:</li></th><td><xsl:value-of select="/Status/Configuration/RunInfoExists"/></td></tr>\r
+ <tr><th><li type="square">Is this a paired end run:</li></th><td><xsl:value-of select="/Status/Configuration/IsPairedEndRun"/></td></tr>\r
+ <tr><th><li type="square">Total number of reads:</li></th><td><xsl:value-of select="/Status/Configuration/NumberOfReads"/></td></tr>\r
+ <tr><th><li type="square">Number of lanes:</li></th><td><xsl:value-of select="/Status/Configuration/NumberOfLanes"/></td></tr>\r
+ <tr><th><li type="square">Number of tiles per lane:</li></th><td><xsl:value-of select="/Status/Configuration/TilesPerLane"/></td></tr>\r
+ <tr><th><li type="square">Control lane:</li></th>\r
+ <td>\r
+ <xsl:if test="/Status/Configuration/ControlLane = 0"> None</xsl:if>\r
+ <xsl:if test="/Status/Configuration/ControlLane > 0 ">\r
+ <xsl:value-of select="/Status/Configuration/ControlLane"/>\r
+ </xsl:if>\r
+ </td>\r
+ </tr> \r
+ </table>\r
+ </xsl:template>\r
+</xsl:stylesheet>\r
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>\r
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"\r
+ xmlns:msxsl="urn:schemas-microsoft-com:xslt" exclude-result-prefixes="msxsl"\r
+ xmlns:lxslt="http://xml.apache.org/xslt">\r
+<xsl:output method="html" indent="yes"/>\r
+ <xsl:template match="/">\r
+ <xsl:value-of select="/Status/RunName"/>\r
+ </xsl:template>\r
+</xsl:stylesheet>\r
--- /dev/null
+body\r
+{\r
+ margin: 0px;\r
+ font-family: Arial, Helvetica, sans-serif;\r
+ background-color: #F4F5F5;\r
+ border-top-style: solid;\r
+ border-top-color: #FF9900;\r
+ border-top-width: 10px;\r
+ padding-top: 3px;\r
+ background-image: url('../Status_Files/illumina.png');\r
+ background-repeat: no-repeat;\r
+ background-position: top right;\r
+ color: #555;\r
+ font-weight: bold;\r
+}\r
+\r
+#tabmenu\r
+{\r
+ font: normal 14px Arial, Helvetica, sans-serif;\r
+ list-style-type: none;\r
+ border-bottom: 1px solid #BB5500;\r
+ margin: 12px 0px 0px 0px;\r
+ padding-left: 0;\r
+ padding-right: 0;\r
+ padding-bottom: 26px;\r
+ font-weight: bold;\r
+}\r
+\r
+#tabmenu li\r
+{\r
+ display: inline;\r
+ float: left;\r
+ height: 24px;\r
+ min-width: 80px;\r
+ text-align: center;\r
+ padding: 0;\r
+}\r
+\r
+#tabmenu li a\r
+{\r
+ float: left;\r
+ color: #777;\r
+ text-decoration: none;\r
+ padding: 4px;\r
+ text-align: center;\r
+ background-color: #ddd;\r
+ min-width: 80px;\r
+ border: 1px solid gray;\r
+ border-bottom: none;\r
+ margin: 0px 1px 0px 1px;\r
+\r
+}\r
+\r
+#tabmenu li a.selected\r
+{\r
+ background-color: #F7F8f8;\r
+ color: #000;\r
+ font-size: 100%;\r
+ border: 1px solid #BB5500;\r
+ border-bottom: 2px solid #F7F8f8;\r
+\r
+}\r
+\r
+#tabmenu li a:hover\r
+{\r
+ color: #BB5500;\r
+ font-size :120%;\r
+ border: 1px solid #BB5500;\r
+}\r
+#tabmenu li a.selected:hover\r
+{\r
+ border-bottom: 2px solid #F7F8f8;\r
+}\r
+\r
+#container\r
+{\r
+ border: 1px solid #BB5500;\r
+ border-top: none;\r
+ padding: 10px;\r
+ left: 0;\r
+ top: 0;\r
+ background-color: #F7F8f8;\r
+ min-width: 1100px;\r
+}\r
+\r
+\r
+\r
+#tabmenu li a.space\r
+{\r
+ font-weight: normal;\r
+ font-size :100%;\r
+ color: #000;\r
+ background-color: #F5F5F5;\r
+ border: none;\r
+ text-align: right;\r
+}\r
+\r
+table.DataTable\r
+{\r
+ border-collapse: collapse;\r
+ background-color: #e0e0e0;\r
+ border: 1px dotted #BB5500;\r
+ padding: 10px;\r
+ padding:50px;\r
+\r
+}\r
+\r
+table.DataTable td, table.DataTable th\r
+{\r
+ font-family: Arial, Helvetica, sans-serif;\r
+ font-size: smaller;\r
+ font-weight: bold;\r
+ font-variant: normal;\r
+ text-transform: none;\r
+ padding: 3px; \r
+ border-right: dotted 1px #BB5500;\r
+ border-left: dotted 1px #BB5500;\r
+ color: #555555;\r
+}\r
+\r
+table.DataTable tr:hover td, table.DataTable tr:hover td a, table.DataTable tr:hover th a\r
+{\r
+ color: #BB5500;\r
+}\r
+\r
+table.DataTable th\r
+{\r
+ padding: 5px;\r
+ border: dotted 1px #BB5500;\r
+ color: #000000;\r
+}\r
+\r
+table.InfoTable\r
+{\r
+ margin: 20px;\r
+ border-style: none;\r
+ border-collapse: collapse;\r
+ background-color: #e0e0e0;\r
+ padding: 50px;\r
+ outline-style: solid;\r
+ outline-color: #e0e0e0;\r
+ outline-width: 10px;\r
+}\r
+\r
+table.InfoTable td, table.InfoTable th\r
+{\r
+ border-style: none;\r
+ font-family: Arial, Helvetica, sans-serif;\r
+ font-size: smaller;\r
+ font-weight: bold;\r
+ font-variant: normal;\r
+ text-transform: none;\r
+ padding: 5px 30px 5px 20px;\r
+ color: #555555;\r
+ text-align: left;\r
+}\r
+\r
+table.InfoTable tr:hover td, table.InfoTable tr:hover td a, table.InfoTable tr:hover th a\r
+{\r
+ color: #BB5500;\r
+}\r
+\r
+table.InfoTable th\r
+{\r
+ color: #000000;\r
+}\r
+\r
+table.StatusTable\r
+{\r
+ margin: 0px 0px 0px 0px;\r
+ border-collapse: collapse;\r
+ background-color: #e0e0e0;\r
+ padding: 1px;\r
+ /*outline-style: solid;\r
+ outline-color: #e0e0e0;\r
+ outline-width: 2px;*/\r
+ border: 1px dotted #BB5500;\r
+\r
+}\r
+\r
+table.StatusTable td, table.StatusTable th\r
+{\r
+ border: 1px dotted #BB5500;\r
+ font-family: Arial, Helvetica, sans-serif;\r
+ font-size: small;\r
+ font-weight: bold;\r
+ font-variant: normal;\r
+ text-transform: none;\r
+ color: #555555;\r
+ text-align: left;\r
+}\r
+table.StatusTable th\r
+{\r
+ border-right: none;\r
+ padding-right: 5px;\r
+}\r
+\r
+table.StatusTable td\r
+{\r
+ border-left: none;\r
+ padding-right: 5px;\r
+ color: #BB5500;\r
+}\r
+\r
+table.StatusTable tr:hover td, table.StatusTable tr:hover td a, table.StatusTable tr:hover th a\r
+{\r
+ color: #ff8800;\r
+}\r
+\r
+label\r
+{\r
+ font-size: smaller;\r
+ font-weight: normal;\r
+ color: #000000;\r
+}\r
+\r
+image.Chart\r
+{\r
+ border: 1px solid #BB5500;\r
+ margin: 5px 0px 0px 0px;\r
+}\r
+\r
+iframe\r
+{ \r
+ margin: 5px 0px 0px 0px;\r
+ border: 1px solid #BB5500;\r
+}\r
+\r
+#RunNameTD\r
+{font-size :100%; padding-left: 20px}
\ No newline at end of file
--- /dev/null
+window.onerror = function() {\r
+ parent.location = "./Status_Files/StatusError.htm"\r
+}\r
+\r
+//Reading XML file\r
+var xmlhttp = false;\r
+/* running locally on IE5.5, IE6, IE7 */; /*@cc_on\r
+if (location.protocol == "file:") {\r
+ if (!xmlhttp) try { xmlhttp = new ActiveXObject("MSXML2.XMLHTTP"); } catch (e) { xmlhttp = false; }\r
+ if (!xmlhttp) try { xmlhttp = new ActiveXObject("Microsoft.XMLHTTP"); } catch (e) { xmlhttp = false; }\r
+}\r
+/* IE7, Firefox, Safari, Opera... */\r
+if (!xmlhttp) try { xmlhttp = new XMLHttpRequest(); } catch (e) { xmlhttp = false; }\r
+/* IE6 */\r
+if (typeof ActiveXObject != "undefined") {\r
+ if (!xmlhttp) try { xmlhttp = new ActiveXObject("MSXML2.XMLHTTP"); } catch (e) { xmlhttp = false; }\r
+ if (!xmlhttp) try { xmlhttp = new ActiveXObject("Microsoft.XMLHTTP"); } catch (e) { xmlhttp = false; }\r
+}\r
+/* IceBrowser */\r
+if (!xmlhttp) try { xmlhttp = createRequest(); } catch (e) { xmlhttp = false; }\r
+\r
+function loadXMLDoc(dname) {\r
+ var xmlDoc = null;\r
+ try {\r
+ if (!xmlhttp) return "Your browser doesn't seem to support XMLHttpRequests.";\r
+ xmlhttp.open("GET", dname, false); //make sure open appears before onreadystatechange lest IE will encounter issues beyond the first request\r
+ xmlhttp.send(null);\r
+ var parser = false;\r
+ try {\r
+ parser = new DOMParser();\r
+ xmlDoc = parser.parseFromString(xmlhttp.responseText, "text/xml");\r
+ } catch (e) { parser = false }\r
+ if (!parser) {\r
+ xmlDoc = new ActiveXObject("Microsoft.XMLDOM");\r
+ //xmlDoc = new ActiveXObject("Msxml2.DOMDocument.6.0");\r
+ xmlDoc.async = "false";\r
+ xmlDoc.loadXML(xmlhttp.responseText);\r
+ }\r
+ if(xmlDoc.childNodes.length == 0)xmlDoc= null;\r
+ } catch(e){};\r
+ return xmlDoc;\r
+}\r
+//End of reading XML file\r
+\r
+\r
+function errorPrint(err) {\r
+ document.writeln(err.description);\r
+ document.writeln("<p>There was a problem loading the file.</p>");\r
+ document.writeln("<p>Please click a link below to try again</p>");\r
+ document.writeln("<p><a href='Status.htm'>Status.htm</a></p>");\r
+ }\r
+\r
+function imgRefresh(imgId) {\r
+ var s = document.getElementById(imgId).src;\r
+ if (s.indexOf('?') > 0) s = s.substring(0, s.indexOf('?'));\r
+ document.getElementById(imgId).src = s + "?" + (new Date().getMilliseconds());\r
+}\r
+\r
+function imgReload(imgId) {\r
+ document.getElementById(imgId).src = document.getElementById(imgId).lowsrc;\r
+}\r
+\r
+function getNodeText(node) {\r
+ var txt = "";\r
+ if (node.textContent != undefined) txt = node.textContent;\r
+ else if (node.text != undefined) txt = node.text;\r
+ return txt;\r
+}\r
+\r
+// Cookie functions\r
+function setCookie(name, value, expires, path, domain, secure) {\r
+ document.cookie = name + "=" + escape(value) +\r
+ ((expires) ? "; expires=" + expires.toGMTString() : "") +\r
+ ((path) ? "; path=" + path : "") +\r
+ ((domain) ? "; domain=" + domain : "") +\r
+ ((secure) ? "; secure" : "");\r
+}\r
+\r
+function getCookie(name) {\r
+ var dc = document.cookie;\r
+ var prefix = name + "=";\r
+ var begin = dc.indexOf("; " + prefix);\r
+ if (begin == -1) {\r
+ begin = dc.indexOf(prefix);\r
+ if (begin != 0) return null;\r
+ } else {\r
+ begin += 2;\r
+ }\r
+ var end = document.cookie.indexOf(";", begin);\r
+ if (end == -1) {\r
+ end = dc.length;\r
+ }\r
+ return unescape(dc.substring(begin + prefix.length, end));\r
+}\r
+\r
+function deleteCookie(name, path, domain) {\r
+ if (getCookie(name)) {\r
+ document.cookie = name + "=" +\r
+ ((path) ? "; path=" + path : "") +\r
+ ((domain) ? "; domain=" + domain : "") +\r
+ "; expires=Thu, 01-Jan-70 00:00:01 GMT";\r
+ }\r
+}\r
+\r
+function loadNumClustersTableByLane(xmlName, tblName, tagsName) {\r
+ tbl = document.getElementById(tblName);\r
+ xmlDoc = loadXMLDoc(xmlName);\r
+ if (xmlDoc == null) return;\r
+ xmlRows = xmlDoc.getElementsByTagName(tagsName);\r
+ while (tbl.rows.length > 0) tbl.deleteRow(tbl.rows.length - 1);\r
+ if (xmlRows.length > 0 && xmlRows[0].attributes.length > 0) {\r
+ for (i = 0; i < xmlRows.length; i++) {\r
+ tbl.insertRow(0);\r
+ for (j = xmlRows[i].attributes.length - 1; j >= 0; j--) {\r
+ tbl.rows[0].insertCell(0);\r
+ tbl.rows[0].cells[0].innerHTML = xmlRows[i].attributes[j].value;\r
+ }\r
+ //create column titles\r
+ tbl.insertRow(0);\r
+ }\r
+ for (j = xmlRows[0].attributes.length - 1; j >= 0; j--) {\r
+ tbl.rows[0].insertCell(0);\r
+ tbl.rows[0].cells[0].innerHTML = xmlRows[0].attributes[j].name;\r
+ }\r
+ tbl.rows[0].cells[0].innerHTML = tagsName + "#"\r
+ }\r
+}\r
+\r
+function loadXSLTable(xmlName, xslName, tblName) {\r
+ tbl = document.getElementById(tblName);\r
+ xmlDoc = loadXMLDoc(xmlName);\r
+ xslDoc = loadXMLDoc(xslName);\r
+ if (xmlDoc == null || xslDoc == null) return false;\r
+ // code for IE\r
+ if (window.ActiveXObject) {\r
+ ex = xmlDoc.transformNode(xslDoc);\r
+ tbl.innerHTML = ex;\r
+ }\r
+ // code for Mozilla, Firefox, Opera, etc.\r
+ else if (document.implementation && document.implementation.createDocument) {\r
+ xsltProcessor = new XSLTProcessor();\r
+ xsltProcessor.importStylesheet(xslDoc);\r
+ resultDocument = xsltProcessor.transformToFragment(xmlDoc, document);\r
+ if ( tbl.hasChildNodes() )\r
+ while ( tbl.childNodes.length >= 1 ) \r
+ tbl.removeChild( tbl.firstChild );\r
+ tbl.appendChild(resultDocument);\r
+ return true;\r
+ }\r
+}\r
+\r
+function xslTransform(xmlDoc, xslDoc) {\r
+ resultDocument = null;\r
+ if (xmlDoc != null && xslDoc != null) {\r
+ // code for IE\r
+ if (window.ActiveXObject) {\r
+ ex = xmlDoc.transformNode(xslDoc);\r
+ resultDocument = ex;\r
+ }\r
+ // code for Mozilla, Firefox, Opera, etc.\r
+ else if (document.implementation && document.implementation.createDocument) {\r
+ xsltProcessor = new XSLTProcessor();\r
+ xsltProcessor.importStylesheet(xslDoc);\r
+ resultDocument = xsltProcessor.transformToFragment(xmlDoc, document).textContent;\r
+ }\r
+ }\r
+ return resultDocument;\r
+}\r
--- /dev/null
+<html xmlns="http://www.w3.org/1999/xhtml" >\r
+<head></head> \r
+<body>\r
+<p>There was a problem loading the file.</p>\r
+<p>Please click a link below to try again</p>\r
+<p><a href=".\Status.htm">Status.htm</a></p>\r
+</body>\r
+</html>\r
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>\r
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"\r
+ xmlns:msxsl="urn:schemas-microsoft-com:xslt" exclude-result-prefixes="msxsl"\r
+ xmlns:lxslt="http://xml.apache.org/xslt">\r
+<xsl:output method="html" indent="yes"/>\r
+ <xsl:template match="/">\r
+ <table class="StatusTable"><tr>\r
+ <th>Total:</th><td id="NumCycles"><xsl:value-of select="/Status/NumCycles"/></td>\r
+ <th>Extracted:</th><td id="ImgCycle"><xsl:value-of select="/Status/ImgCycle"/></td>\r
+ <th>Called:</th><td id="CallCycle"><xsl:value-of select="/Status/CallCycle"/></td>\r
+ <th>Scored:</th><td id="ScoreCycle"><xsl:value-of select="/Status/ScoreCycle"/></td>\r
+ <th>Copied:</th><td id="CopyCycle"><xsl:value-of select="/Status/CopyCycle"/></td>\r
+ </tr></table>\r
+ </xsl:template>\r
+</xsl:stylesheet>\r
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">\r
+<head>\r
+ <link rel="stylesheet" href="./Status.css" type="text/css" media="screen"/>\r
+ <script src="./Status.js" type="text/javascript"></script>\r
+ <script src="./Summary.js" type="text/javascript"></script>\r
+ <title>Status</title>\r
+</head>\r
+ \r
+<body>\r
+ <table style="border:none"><tr>\r
+ <td><img alt="Refresh" title="Refresh" name="RefreshBtn" height="25" width="25" src="./RefreshBtn/r1.png" onmouseout="this.src='./RefreshBtn/r1.png'" onmouseover="this.src='./RefreshBtn/r2.png'" onmousedown="this.src='./RefreshBtn/r3.png'" onmouseup="this.src='./RefreshBtn/r2.png'" onclick="window.location.reload(true)" /> </td>\r
+ <td id="StatUpdateDiv" >\r
+ <table class="StatusTable"><tr>\r
+ <th>Total:</th><td>0</td><th>Extracted:</th><td>0</td><th>Called:</th><td>0</td>\r
+ <th>Scored:</th><td>0</td><th>Copied:</th><td>0</td><th>Err.Rated:</th><td>0</td>\r
+ </tr></table></td> \r
+ <td id="RunNameTD">Loading Run Data ...</td>\r
+ </tr></table>\r
+ <script type="text/javascript">\r
+ loadXSLTable('../reports/StatusUpdate.xml', './StatusUpdate.xsl', 'StatUpdateDiv');\r
+ runName = xslTransform(loadXMLDoc('../reports/Status.xml'), loadXMLDoc('./RunName.xsl'));\r
+ document.getElementById("RunNameTD").innerHTML = runName;\r
+ document.title = runName + " Status";\r
+ </script>\r
+<ul id="tabmenu">\r
+ <li><a href="./RunInfo.htm">Run Info</a></li>\r
+ <li><a href="../Status.htm">Tile Status</a></li>\r
+ <li><a href="./Charts.htm">Charts</a></li>\r
+ <li><a class="selected" href="./Summary.htm">Summary</a></li>\r
+ <li><a class="space">Plots:</a></li>\r
+ <li><a href="./ByLane.htm">Cluster Density</a></li>\r
+ <li><a href="./ByCycle.htm">Data By Cycle</a></li>\r
+</ul>\r
+ \r
+<div id="container">\r
+ <div id="SumTbl1" ><p> No data available yet.</p></div>\r
+ <div id="SumTbl2"></div>\r
+ <div id="SumTbl3"></div>\r
+ <div id="SumTbl4"></div>\r
+ <div id="SumTbl5"></div>\r
+ <div id="SumTbl6"></div>\r
+ <div id="SumTbl7"></div>\r
+ <div id="SumTbl8"></div>\r
+ <div id="SumTbl9"></div>\r
+ <div id="SumTbl10"></div>\r
+ <div id="SumTbl11"></div>\r
+ <script type="text/javascript">loadSumTable()</script>\r
+</div>\r
+ \r
+</body>\r
+</html>\r
+\r
--- /dev/null
+window.onerror = function() {\r
+ parent.location = './Error.htm';\r
+}\r
+\r
+function loadSumTable() {\r
+ for (i = 1; i < 12; i++)\r
+ loadXSLTable('../reports/Summary/read' + i + '.xml', './Summary.xsl', 'SumTbl' + i);\r
+}
\ No newline at end of file
--- /dev/null
+<?xml version="1.0"?> \r
+<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" \r
+version="1.0"> \r
+<xsl:output method="html" indent="yes" omit-xml-declaration="yes"/>\r
+<xsl:template match="/">\r
+ <p/>   <b>Read #<xsl:value-of select="Summary/@Read"/></b>\r
+ <i><xsl:value-of select="Summary/@ReadType"/></i>\r
+ <table class="DataTable" >\r
+ <tr>\r
+ <th >Lane</th> <th>Tiles</th> <th>Clu.Dens. (#/mm<sup>2</sup>)</th>\r
+ <th>% PF Clusters </th> <th>Clusters PF (#/mm<sup>2</sup>)</th> <th>% Phas./Preph.</th>\r
+ <th>Cycles<br/>Err Rated</th> <th>% Aligned</th> <th>% Error Rate</th> \r
+ <th>% Error Rate<br/> 35 cycle</th > <th>% Error Rate<br/> 75 cycle</th > <th>% Error Rate<br/> 100 cycle</th > <th>1<sup>st</sup> Cycle Int</th>\r
+ <th>% Intensity<br/> Cycle 20</th>\r
+ </tr>\r
+ <xsl:variable name="densityRatio" select="Summary/@densityRatio"/>\r
+ <xsl:for-each select="Summary/Lane">\r
+ <tr>\r
+ <td><xsl:value-of select="@key"/></td> \r
+ <td><xsl:value-of select="@TileCount"/></td> \r
+ <td><xsl:value-of select="format-number(@ClustersRaw * $densityRatio div 1000,'#')"/>K +/- \r
+ <xsl:value-of select="format-number(@ClustersRawSD * $densityRatio div 1000,'#.0')"/>K</td> \r
+ <td><xsl:value-of select="@PrcPFClusters"/> +/- \r
+ <xsl:value-of select="@PrcPFClustersSD"/></td> \r
+ <td><xsl:value-of select="format-number(@ClustersPF* $densityRatio div 1000,'#.0')"/>K +/- \r
+ <xsl:value-of select="format-number(@ClustersPFSD* $densityRatio div 1000,'#.00')"/>K</td> \r
+ <td><xsl:value-of select="@Phasing"/> /\r
+ <xsl:value-of select="@Prephasing"/></td>\r
+ <td><xsl:value-of select="@CalledCyclesMin"/>\r
+ <xsl:if test="@CalledCyclesMax > @CalledCyclesMin">-<xsl:value-of select="@CalledCyclesMax"/></xsl:if></td>\r
+ <td><xsl:value-of select="@PrcAlign"/> +/-\r
+ <xsl:value-of select="@PrcAlignSD"/></td> \r
+ <td><xsl:value-of select="@ErrRatePhiX"/> +/-\r
+ <xsl:value-of select="@ErrRatePhiXSD"/></td>\r
+ <td><xsl:value-of select="@ErrRate35"/> +/-\r
+ <xsl:value-of select="@ErrRate35SD"/></td>\r
+ <td><xsl:value-of select="@ErrRate75"/> +/-\r
+ <xsl:value-of select="@ErrRate75SD"/></td>\r
+ <td><xsl:value-of select="@ErrRate100"/> +/-\r
+ <xsl:value-of select="@ErrRate100SD"/></td>\r
+ <td><xsl:value-of select="format-number(@FirstCycleIntPF,'#')"/> +/-\r
+ <xsl:value-of select="format-number(@FirstCycleIntPFSD,'#.0')"/></td>\r
+ <td><xsl:value-of select="format-number(@PrcIntensityAfter20CyclesPF,'#.0')"/> +/-\r
+ <xsl:value-of select="format-number(@PrcIntensityAfter20CyclesPFSD,'#.00')"/></td>\r
+ </tr>\r
+ </xsl:for-each>\r
+ </table >\r
+</xsl:template>\r
+</xsl:stylesheet>\r
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>\r
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"\r
+ xmlns:msxsl="urn:schemas-microsoft-com:xslt" exclude-result-prefixes="msxsl"\r
+ xmlns:lxslt="http://xml.apache.org/xslt">\r
+<xsl:output method="html" indent="yes"/>\r
+ <xsl:template match="/">\r
+ <xsl:value-of select="/Status/Configuration/TilesPerLane"/>\r
+ </xsl:template>\r
+</xsl:stylesheet>\r
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">\r
+<head>\r
+ <link rel="stylesheet" href="./Status.css" type="text/css" media="screen"/>\r
+ <script src="./Status.js" type="text/javascript"></script>\r
+ <script src="./Summary.js" type="text/javascript"></script>\r
+ <title>Status</title>\r
+</head>\r
+ \r
+<body>\r
+ <table style="border:none"><tr>\r
+ <td><img alt="Refresh" title="Refresh" name="RefreshBtn" height="25" width="25" src="./RefreshBtn/r1.png" onmouseout="this.src='./RefreshBtn/r1.png'" onmouseover="this.src='./RefreshBtn/r2.png'" onmousedown="this.src='./RefreshBtn/r3.png'" onmouseup="this.src='./RefreshBtn/r2.png'" onclick="window.location.reload(true)" /> </td>\r
+ <td id="StatUpdateDiv" >\r
+ <table class="StatusTable"><tr>\r
+ <th>Total:</th><td>0</td><th>Extracted:</th><td>0</td><th>Called:</th><td>0</td>\r
+ <th>Scored:</th><td>0</td><th>Copied:</th><td>0</td><th>Err.Rated:</th><td>0</td>\r
+ </tr></table></td> \r
+ <td id="RunNameTD">Loading Run Data ...</td>\r
+ </tr></table>\r
+ <script type="text/javascript">\r
+ loadXSLTable('../reports/StatusUpdate.xml', './StatusUpdate.xsl', 'StatUpdateDiv');\r
+ runName = xslTransform(loadXMLDoc('../reports/Status.xml'), loadXMLDoc('./RunName.xsl'));\r
+ document.getElementById("RunNameTD").innerHTML = runName;\r
+ document.title = runName + " Status";\r
+ </script>\r
+<ul id="tabmenu">\r
+ <li><a href="./RunInfo.htm">Run Info</a></li>\r
+ <li><a href="../Status.htm">Tile Status</a></li>\r
+ <li><a href="./Charts.htm">Charts</a></li>\r
+ <li><a class="selected" href="./Summary.htm">Summary</a></li>\r
+ <li><a class="space">Plots:</a></li>\r
+ <li><a href="./ByLane.htm">Cluster Density</a></li>\r
+ <li><a href="./ByCycle.htm">Data By Cycle</a></li>\r
+</ul>\r
+ \r
+<div id="container">\r
+ <div id="SumTbl1" ><p> No data available yet.</p></div>\r
+ <div id="SumTbl2"></div>\r
+ <div id="SumTbl3"></div>\r
+ <div id="SumTbl4"></div>\r
+ <div id="SumTbl5"></div>\r
+ <div id="SumTbl6"></div>\r
+ <div id="SumTbl7"></div>\r
+ <div id="SumTbl8"></div>\r
+ <div id="SumTbl9"></div>\r
+ <div id="SumTbl10"></div>\r
+ <div id="SumTbl11"></div>\r
+ <script type="text/javascript">loadSumTable()</script>\r
+</div>\r
+ \r
+</body>\r
+</html>\r
+\r
--- /dev/null
+<?xml version="1.0"?>
+<RunParameters>
+ <Barcodes>
+ </Barcodes>
+ <Defaults>
+ <ANALYSIS>none</ANALYSIS>
+ <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
+ <CHROM_NAME_VALIDATION>on</CHROM_NAME_VALIDATION>
+ <CMDPREFIX></CMDPREFIX>
+ <DATASET_POST_RUN_COMMAND></DATASET_POST_RUN_COMMAND>
+ <ELAND_EXTENDED_MULTI_READS>off</ELAND_EXTENDED_MULTI_READS>
+ <ELAND_FASTQ_FILES_PER_PROCESS>3</ELAND_FASTQ_FILES_PER_PROCESS>
+ <ELAND_GENOME></ELAND_GENOME>
+ <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
+ <ELAND_MAX_MATCHES></ELAND_MAX_MATCHES>
+ <ELAND_PARAMS></ELAND_PARAMS>
+ <ELAND_REPEAT></ELAND_REPEAT>
+ <ELAND_RNA_GENE_MD_GROUP_LABEL></ELAND_RNA_GENE_MD_GROUP_LABEL>
+ <ELAND_RNA_GENOME_ANNOTATION></ELAND_RNA_GENOME_ANNOTATION>
+ <ELAND_RNA_GENOME_CONTAM></ELAND_RNA_GENOME_CONTAM>
+ <ELAND_RNA_GENOME_CONTAM_MASK>*.fa</ELAND_RNA_GENOME_CONTAM_MASK>
+ <ELAND_RNA_MULTI_READS>off</ELAND_RNA_MULTI_READS>
+ <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
+ <ELAND_SEED_LENGTH2></ELAND_SEED_LENGTH2>
+ <EMAIL_DOMAIN>domain.com</EMAIL_DOMAIN>
+ <EMAIL_LIST>${logName}</EMAIL_LIST>
+ <EMAIL_SERVER>localhost:25</EMAIL_SERVER>
+ <EXPT_DIR>/mmjggl/nicodemus/data01/sequencer/110815_SN787_0101_AD07K6ACXX/Unaligned_1MM</EXPT_DIR>
+ <FLAT_TXT_GZ_SUFFIX>Flat.txt.gz</FLAT_TXT_GZ_SUFFIX>
+ <FLOWCELL>D07K6ACXX</FLOWCELL>
+ <GENE_MD_GZ_SUFFIX>_gene.md.gz</GENE_MD_GZ_SUFFIX>
+ <INCREASED_SENSITIVITY></INCREASED_SENSITIVITY>
+ <KAGU_PAIR_PARAMS>--muf 0</KAGU_PAIR_PARAMS>
+ <KAGU_PARAMS>--mmaq 4</KAGU_PARAMS>
+ <NUM_LEADING_DIRS_TO_STRIP>2</NUM_LEADING_DIRS_TO_STRIP>
+ <OA_SUFFIX>.oa</OA_SUFFIX>
+ <ORIGINAL_READS>1</ORIGINAL_READS>
+ <ORIGINAL_READ_LENGTH1>50</ORIGINAL_READ_LENGTH1>
+ <ORPHAN_ALIGNER_PARAMS>2</ORPHAN_ALIGNER_PARAMS>
+ <OUT_DIR>/mmjggl/nicodemus/data01/sequencer/110815_SN787_0101_AD07K6ACXX/Aligned_1MM</OUT_DIR>
+ <PAS_PARAMS></PAS_PARAMS>
+ <RAMM_REPORT_TYPE></RAMM_REPORT_TYPE>
+ <READS>1</READS>
+ <READ_LENGTH1>49</READ_LENGTH1>
+ <RNAQC_COUNT_CLUSTERS_CMD>$(WC) -l</RNAQC_COUNT_CLUSTERS_CMD>
+ <RNAQC_COUNT_CLUSTERS_NAME>totalClusters</RNAQC_COUNT_CLUSTERS_NAME>
+ <RNAQC_COUNT_GENOME_CMD>($(GREP) -cvE '^((NM|QC|RM|[0-9]+:[0-9]+:[0-9]+)$$|splice_sites)' || exit 0)</RNAQC_COUNT_GENOME_CMD>
+ <RNAQC_COUNT_GENOME_NAME>genomeUsable</RNAQC_COUNT_GENOME_NAME>
+ <RNAQC_COUNT_NM_CMD>($(FGREP) -wc NM || exit 0)</RNAQC_COUNT_NM_CMD>
+ <RNAQC_COUNT_NM_NAME>noMatch</RNAQC_COUNT_NM_NAME>
+ <RNAQC_COUNT_PF_CMD>$(WC) -l</RNAQC_COUNT_PF_CMD>
+ <RNAQC_COUNT_PF_NAME>PFClusters</RNAQC_COUNT_PF_NAME>
+ <RNAQC_COUNT_QC_CMD>($(FGREP) -wc QC || exit 0)</RNAQC_COUNT_QC_CMD>
+ <RNAQC_COUNT_QC_NAME>QC</RNAQC_COUNT_QC_NAME>
+ <RNAQC_COUNT_RM_CMD>($(FGREP) -wc RM || exit 0)</RNAQC_COUNT_RM_CMD>
+ <RNAQC_COUNT_RM_NAME>repeatMasked</RNAQC_COUNT_RM_NAME>
+ <RNAQC_COUNT_SPLICE_CMD>($(FGREP) -c splice_sites || exit 0)</RNAQC_COUNT_SPLICE_CMD>
+ <RNAQC_COUNT_SPLICE_NAME>spliceUsable</RNAQC_COUNT_SPLICE_NAME>
+ <RNAQC_COUNT_USABLE_CMD>$(CUT) -f13 |($(EGREP) [0-9] || exit 0)|$(WC) -l</RNAQC_COUNT_USABLE_CMD>
+ <RNAQC_COUNT_USABLE_NAME>usable</RNAQC_COUNT_USABLE_NAME>
+ <RNAQC_FIND_CONTAMS_CMD>($(GREP) -vE '^(NM|QC|RM|[0-9]+:[0-9]+:[0-9]+)$$' || exit 0)</RNAQC_FIND_CONTAMS_CMD>
+ <SAMTOOLS_GENOME></SAMTOOLS_GENOME>
+ <SEQGENEMD2REFFLAT_PARAMS></SEQGENEMD2REFFLAT_PARAMS>
+ <SINGLESEED></SINGLESEED>
+ <SPLCSTS_PARAMS>-v $(CASAVA_LOG_LEVEL)</SPLCSTS_PARAMS>
+ <SQUASH_GENOME_PARAMS></SQUASH_GENOME_PARAMS>
+ <UNGAPPED></UNGAPPED>
+ <USE_BASES>y*n</USE_BASES>
+ <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
+ <WEB_DIR_ROOT>http://host.domain.com/yourshare/</WEB_DIR_ROOT>
+ <WITH_ORPHAN_ALIGNER>true</WITH_ORPHAN_ALIGNER>
+ </Defaults>
+ <Lanes>
+ <Lane index="1">
+ <Barcodes></Barcodes>
+ <Defaults>
+ <ANALYSIS>eland_extended</ANALYSIS>
+ <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
+ <ELAND_GENOME>/mmjggl/nicodemus/data01/genomes/elegans190/chromosomes/</ELAND_GENOME>
+ <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
+ <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
+ <READS>1</READS>
+ <READ_LENGTH1>49</READ_LENGTH1>
+ <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
+ <USE_BASES>Y*n</USE_BASES>
+ <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
+ </Defaults>
+ <Projects></Projects>
+ <References></References>
+ <Samples></Samples>
+ </Lane>
+ <Lane index="2">
+ <Barcodes></Barcodes>
+ <Defaults>
+ <ANALYSIS>eland_extended</ANALYSIS>
+ <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
+ <ELAND_GENOME>/mmjggl/nicodemus/data01/genomes/elegans190/chromosomes/</ELAND_GENOME>
+ <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
+ <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
+ <READS>1</READS>
+ <READ_LENGTH1>49</READ_LENGTH1>
+ <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
+ <USE_BASES>Y*n</USE_BASES>
+ <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
+ </Defaults>
+ <Projects></Projects>
+ <References></References>
+ <Samples></Samples>
+ </Lane>
+ <Lane index="4">
+ <Barcodes></Barcodes>
+ <Defaults>
+ <ANALYSIS>eland_extended</ANALYSIS>
+ <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
+ <ELAND_GENOME>/mmjggl/nicodemus/data01/genomes/hg18/chromosomes/</ELAND_GENOME>
+ <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
+ <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
+ <READS>1</READS>
+ <READ_LENGTH1>49</READ_LENGTH1>
+ <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
+ <USE_BASES>Y*n</USE_BASES>
+ <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
+ </Defaults>
+ <Projects></Projects>
+ <References></References>
+ <Samples></Samples>
+ </Lane>
+ <Lane index="5">
+ <Barcodes></Barcodes>
+ <Defaults>
+ <ANALYSIS>eland_extended</ANALYSIS>
+ <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
+ <ELAND_GENOME>/mmjggl/nicodemus/data01/genomes/hg18/chromosomes/</ELAND_GENOME>
+ <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
+ <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
+ <READS>1</READS>
+ <READ_LENGTH1>49</READ_LENGTH1>
+ <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
+ <USE_BASES>Y*n</USE_BASES>
+ <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
+ </Defaults>
+ <Projects></Projects>
+ <References></References>
+ <Samples></Samples>
+ </Lane>
+ <Lane index="6">
+ <Barcodes></Barcodes>
+ <Defaults>
+ <ANALYSIS>eland_extended</ANALYSIS>
+ <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
+ <ELAND_GENOME>/mmjggl/nicodemus/data01/genomes/hg18/chromosomes/</ELAND_GENOME>
+ <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
+ <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
+ <READS>1</READS>
+ <READ_LENGTH1>49</READ_LENGTH1>
+ <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
+ <USE_BASES>Y*n</USE_BASES>
+ <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
+ </Defaults>
+ <Projects></Projects>
+ <References></References>
+ <Samples></Samples>
+ </Lane>
+ <Lane index="7">
+ <Barcodes></Barcodes>
+ <Defaults>
+ <ANALYSIS>none</ANALYSIS>
+ <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
+ </Defaults>
+ <Projects></Projects>
+ <References></References>
+ <Samples></Samples>
+ </Lane>
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+ <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
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+ <Defaults>
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+ <Samples></Samples>
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+ </Lanes>
+ <Projects>
+ <Project name="12383">
+ <ANALYSIS>eland_extended</ANALYSIS>
+ <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
+ <ELAND_GENOME>/mmjggl/nicodemus/data01/genomes/hg18/chromosomes/</ELAND_GENOME>
+ <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
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+ <READS>1</READS>
+ <READ_LENGTH1>49</READ_LENGTH1>
+ <USE_BASES>Y*n</USE_BASES>
+ <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
+ </Project>
+ <Project name="Undetermined_indices">
+ <ANALYSIS>none</ANALYSIS>
+ </Project>
+ </Projects>
+ <References>
+ <Reference name="mm9">
+ <ANALYSIS>eland_extended</ANALYSIS>
+ <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
+ <ELAND_GENOME>/mmjggl/nicodemus/data01/genomes/mm9/chromosomes/</ELAND_GENOME>
+ <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
+ <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
+ <READS>1</READS>
+ <READ_LENGTH1>49</READ_LENGTH1>
+ <USE_BASES>Y*n</USE_BASES>
+ <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
+ </Reference>
+ </References>
+ <Samples>
+ </Samples>
+ <Software CmdAndArgs="/mmjggl/nicodemus/data01/casava-v1.8.1/bin/configureAlignment.pl config.txt --EXPT_DIR /mmjggl/nicodemus/data01/sequencer/110815_SN787_0101_AD07K6ACXX/Unaligned_1MM/ --OUT_DIR /mmjggl/nicodemus/data01/sequencer/110815_SN787_0101_AD07K6ACXX/Aligned_1MM -make" Name="configureAlignment.pl" Version="CASAVA-1.8.1">
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+ <Software Name="RTA" Version="1.12.4.2">
+ <Software Name="HiSeq Control Software" Platform="HiSeq" Version="1.4.8" />
+ </Software>
+ </Software>
+ </Software>
+ </Software>
+</RunParameters>
--- /dev/null
+<DemultiplexConfig>
+ <Software Version="CASAVA-1.8.1" CmdAndArgs="/mmjggl/nicodemus/data01/casava-v1.8.1/bin/configureBclToFastq.pl --input-dir Data/Intensities/BaseCalls/ --output-dir Unaligned --sample-sheet Data/Intensities/BaseCalls/SampleSheet.csv" Name="configureBclToFastq.pl">
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+ <Software Version="1.12.4.2" Name="RTA">
+ <Software Version="1.4.8" Platform="HiSeq" Name="HiSeq Control Software" />
+ </Software>
+ </Software>
+ </Software>
+ <FlowcellInfo ID="D07K6ACXX" Operator="Lorian" Recipe="SR_indexing" Desc="">
+ <Lane Number="1">
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+ </Lane>
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+ </Lane>
+ <Lane Number="3">
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+ </Lane>
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+ <Lane Number="5">
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+ </Lane>
+ <Lane Number="6">
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+ <Lane Number="7">
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+ </FlowcellInfo>
+</DemultiplexConfig>
--- /dev/null
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+ <SmtFilter>failed-chastity</SmtFilter>
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+ </BaseCallParameters>
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+ <Barcode>
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+ </Lane>
+ <Lane Index="7">
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+ </Lane>
+ <Lane Index="8">
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+ </Lane>
+ </TileSelection>
+ </Run>
+</BaseCallAnalysis>
--- /dev/null
+<?xml version="1.0"?>
+<BustardSummary>
+ <ChipResultsSummary>
+ <clusterCountPF>454185731</clusterCountPF>
+ <clusterCountRaw>781064977</clusterCountRaw>
+ <yield>25888586667</yield>
+ </ChipResultsSummary>
+ <ChipSummary>
+ <ChipID>unknown</ChipID>
+ <Machine>HWI-ST0787</Machine>
+ <RunFolder>110815_SN787_0101_AD07K6ACXX</RunFolder>
+ </ChipSummary>
+ <Date>2011-08-18 20:18:19</Date>
+ <ExpandedLaneSummary>
+ <Read>
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+ </ExpandedLaneSummary>
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+ </LaneResultsSummary>
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+ <percentClustersPF>89.93</percentClustersPF>
+ <signal20AsPctOf1>90.66</signal20AsPctOf1>
+ <tileNumber>2103</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>4219627</clusterCountPF>
+ <clusterCountRaw>4681613</clusterCountRaw>
+ <oneSig>1403.97</oneSig>
+ <percentClustersPF>90.13</percentClustersPF>
+ <signal20AsPctOf1>90.49</signal20AsPctOf1>
+ <tileNumber>2104</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>4414065</clusterCountPF>
+ <clusterCountRaw>4956383</clusterCountRaw>
+ <oneSig>1386.15</oneSig>
+ <percentClustersPF>89.06</percentClustersPF>
+ <signal20AsPctOf1>89.95</signal20AsPctOf1>
+ <tileNumber>2105</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>4579204</clusterCountPF>
+ <clusterCountRaw>5232590</clusterCountRaw>
+ <oneSig>1365.53</oneSig>
+ <percentClustersPF>87.51</percentClustersPF>
+ <signal20AsPctOf1>89.26</signal20AsPctOf1>
+ <tileNumber>2106</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>4682961</clusterCountPF>
+ <clusterCountRaw>5469205</clusterCountRaw>
+ <oneSig>1333.32</oneSig>
+ <percentClustersPF>85.62</percentClustersPF>
+ <signal20AsPctOf1>89.03</signal20AsPctOf1>
+ <tileNumber>2107</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>3928926</clusterCountPF>
+ <clusterCountRaw>5870004</clusterCountRaw>
+ <oneSig>1286.80</oneSig>
+ <percentClustersPF>66.93</percentClustersPF>
+ <signal20AsPctOf1>87.34</signal20AsPctOf1>
+ <tileNumber>2108</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>3556282</clusterCountPF>
+ <clusterCountRaw>3852699</clusterCountRaw>
+ <oneSig>1457.50</oneSig>
+ <percentClustersPF>92.31</percentClustersPF>
+ <signal20AsPctOf1>88.49</signal20AsPctOf1>
+ <tileNumber>2201</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>3741136</clusterCountPF>
+ <clusterCountRaw>4072130</clusterCountRaw>
+ <oneSig>1441.42</oneSig>
+ <percentClustersPF>91.87</percentClustersPF>
+ <signal20AsPctOf1>89.42</signal20AsPctOf1>
+ <tileNumber>2202</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>3842742</clusterCountPF>
+ <clusterCountRaw>4212391</clusterCountRaw>
+ <oneSig>1415.97</oneSig>
+ <percentClustersPF>91.22</percentClustersPF>
+ <signal20AsPctOf1>89.95</signal20AsPctOf1>
+ <tileNumber>2203</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>4140127</clusterCountPF>
+ <clusterCountRaw>4577001</clusterCountRaw>
+ <oneSig>1387.43</oneSig>
+ <percentClustersPF>90.46</percentClustersPF>
+ <signal20AsPctOf1>89.88</signal20AsPctOf1>
+ <tileNumber>2204</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>4372303</clusterCountPF>
+ <clusterCountRaw>4862284</clusterCountRaw>
+ <oneSig>1384.77</oneSig>
+ <percentClustersPF>89.92</percentClustersPF>
+ <signal20AsPctOf1>88.76</signal20AsPctOf1>
+ <tileNumber>2205</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>4531801</clusterCountPF>
+ <clusterCountRaw>5119662</clusterCountRaw>
+ <oneSig>1367.26</oneSig>
+ <percentClustersPF>88.52</percentClustersPF>
+ <signal20AsPctOf1>88.81</signal20AsPctOf1>
+ <tileNumber>2206</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>4148375</clusterCountPF>
+ <clusterCountRaw>5301292</clusterCountRaw>
+ <oneSig>1326.28</oneSig>
+ <percentClustersPF>78.25</percentClustersPF>
+ <signal20AsPctOf1>89.46</signal20AsPctOf1>
+ <tileNumber>2207</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>3747919</clusterCountPF>
+ <clusterCountRaw>5523881</clusterCountRaw>
+ <oneSig>1328.04</oneSig>
+ <percentClustersPF>67.85</percentClustersPF>
+ <signal20AsPctOf1>85.54</signal20AsPctOf1>
+ <tileNumber>2208</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>3685991</clusterCountPF>
+ <clusterCountRaw>4034260</clusterCountRaw>
+ <oneSig>1437.04</oneSig>
+ <percentClustersPF>91.37</percentClustersPF>
+ <signal20AsPctOf1>88.87</signal20AsPctOf1>
+ <tileNumber>2301</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>3894450</clusterCountPF>
+ <clusterCountRaw>4285846</clusterCountRaw>
+ <oneSig>1425.73</oneSig>
+ <percentClustersPF>90.87</percentClustersPF>
+ <signal20AsPctOf1>89.86</signal20AsPctOf1>
+ <tileNumber>2302</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>3941822</clusterCountPF>
+ <clusterCountRaw>4382141</clusterCountRaw>
+ <oneSig>1397.98</oneSig>
+ <percentClustersPF>89.95</percentClustersPF>
+ <signal20AsPctOf1>90.41</signal20AsPctOf1>
+ <tileNumber>2303</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>4299760</clusterCountPF>
+ <clusterCountRaw>4825173</clusterCountRaw>
+ <oneSig>1380.92</oneSig>
+ <percentClustersPF>89.11</percentClustersPF>
+ <signal20AsPctOf1>89.99</signal20AsPctOf1>
+ <tileNumber>2304</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>4523197</clusterCountPF>
+ <clusterCountRaw>5101827</clusterCountRaw>
+ <oneSig>1374.81</oneSig>
+ <percentClustersPF>88.66</percentClustersPF>
+ <signal20AsPctOf1>89.72</signal20AsPctOf1>
+ <tileNumber>2305</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>4658536</clusterCountPF>
+ <clusterCountRaw>5357124</clusterCountRaw>
+ <oneSig>1362.66</oneSig>
+ <percentClustersPF>86.96</percentClustersPF>
+ <signal20AsPctOf1>88.93</signal20AsPctOf1>
+ <tileNumber>2306</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>4706753</clusterCountPF>
+ <clusterCountRaw>5569616</clusterCountRaw>
+ <oneSig>1336.27</oneSig>
+ <percentClustersPF>84.51</percentClustersPF>
+ <signal20AsPctOf1>89.15</signal20AsPctOf1>
+ <tileNumber>2307</tileNumber>
+ </Tile>
+ <Tile>
+ <clusterCountPF>2196707</clusterCountPF>
+ <clusterCountRaw>3787138</clusterCountRaw>
+ <oneSig>1265.29</oneSig>
+ <percentClustersPF>58.00</percentClustersPF>
+ <signal20AsPctOf1>89.55</signal20AsPctOf1>
+ <tileNumber>2308</tileNumber>
+ </Tile>
+ <readNumber>1</readNumber>
+ </Read>
+
+ <laneNumber>8</laneNumber>
+ </Lane>
+ </TileResultsByLane>
+</BustardSummary>
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>\r
+<!--Illumina RTA Status Report-->\r
+<Status>\r
+ <Software>Illumina RTA 1.12.4.2</Software>\r
+ <RunName>110815_SN787_0101_AD07K6ACXX</RunName>\r
+ <InstrumentName>HWI-ST0787</InstrumentName>\r
+ <RunStarted>Thursday, August 18, 2011 12:33 PM</RunStarted>\r
+ <NumCycles>57</NumCycles>\r
+ <ImgCycle>57</ImgCycle>\r
+ <ScoreCycle>57</ScoreCycle>\r
+ <CallCycle>57</CallCycle>\r
+ <InputDir>D:\Illumina\HiSeqTemp\110815_SN787_0101_AD07K6ACXX</InputDir>\r
+ <OutputDir>\\NICODEMUS\volvox\110815_SN787_0101_AD07K6ACXX</OutputDir>\r
+ <Configuration>\r
+ <CopyAllFiles>true</CopyAllFiles>\r
+ <CopyImages>False</CopyImages>\r
+ <DeleteImages>True</DeleteImages>\r
+ <RunInfoExists>True</RunInfoExists>\r
+ <IsPairedEndRun>False</IsPairedEndRun>\r
+ <NumberOfReads>2</NumberOfReads>\r
+ <NumberOfLanes>8</NumberOfLanes>\r
+ <TilesPerLane>48</TilesPerLane>\r
+ <ControlLane>0</ControlLane>\r
+ </Configuration>\r
+</Status>
\ No newline at end of file
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?><!--Illumina RTA Status Report--><Status><NumCycles>57</NumCycles><ImgCycle>57</ImgCycle><ScoreCycle>57</ScoreCycle><CopyCycle>57</CopyCycle><CallCycle>57</CallCycle><ErrRateCycle>57</ErrRateCycle></Status>
\ No newline at end of file
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?><!--Illumina RTA Data--><Summary Read="1" densityRatio="0.173619792"><Lane key="1" TileCount="48" ClustersRaw="3878755" ClustersRawSD="579626.0" ClustersPF="1040253" ClustersPFSD="1059982.5" PrcPFClusters="27.8" PrcPFClustersSD="27.72" Phasing="0.381" Prephasing="0.084" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="707" FirstCycleIntPFSD="2076.1" PrcIntensityAfter20CyclesPF="60.0" PrcIntensityAfter20CyclesPFSD="6.61" /><Lane key="2" TileCount="48" ClustersRaw="3920639" ClustersRawSD="1027332.4" ClustersPF="474380" ClustersPFSD="739312.7" PrcPFClusters="13.4" PrcPFClustersSD="17.58" Phasing="0.369" Prephasing="0.251" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="2617" FirstCycleIntPFSD="3391.7" PrcIntensityAfter20CyclesPF="60.0" PrcIntensityAfter20CyclesPFSD="5.30" /><Lane key="3" TileCount="48" ClustersRaw="5713049" ClustersRawSD="876187.3" ClustersPF="376501" ClustersPFSD="895452.3" PrcPFClusters="6.0" PrcPFClustersSD="14.30" Phasing="0.247" Prephasing="0.200" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="5279" FirstCycleIntPFSD="1974.8" PrcIntensityAfter20CyclesPF="21.8" PrcIntensityAfter20CyclesPFSD="35.10" /><Lane key="4" TileCount="48" ClustersRaw="5852907" ClustersRawSD="538640.6" ClustersPF="329831" ClustersPFSD="758370.9" PrcPFClusters="5.4" PrcPFClustersSD="12.52" Phasing="0.210" Prephasing="0.180" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="4181" FirstCycleIntPFSD="1283.3" PrcIntensityAfter20CyclesPF="29.0" PrcIntensityAfter20CyclesPFSD="45.34" /><Lane key="5" TileCount="48" ClustersRaw="4006751" ClustersRawSD="1265247.4" ClustersPF="52186" ClustersPFSD="233275.6" PrcPFClusters="0.9" PrcPFClustersSD="4.22" Phasing="0.000" Prephasing="0.000" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="2579" FirstCycleIntPFSD="2952.5" PrcIntensityAfter20CyclesPF="16.0" PrcIntensityAfter20CyclesPFSD="29.57" /><Lane key="6" TileCount="48" ClustersRaw="5678021" ClustersRawSD="627070.7" ClustersPF="1490900" ClustersPFSD="1624380.0" PrcPFClusters="25.5" PrcPFClustersSD="26.81" Phasing="0.267" Prephasing="0.212" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="6221" FirstCycleIntPFSD="675.5" PrcIntensityAfter20CyclesPF="76.9" PrcIntensityAfter20CyclesPFSD="4.87" /><Lane key="7" TileCount="48" ClustersRaw="1854131" ClustersRawSD="429053.2" ClustersPF="1585131" ClustersPFSD="693768.5" PrcPFClusters="85.0" PrcPFClustersSD="30.78" Phasing="0.133" Prephasing="0.241" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="6584" FirstCycleIntPFSD="455.9" PrcIntensityAfter20CyclesPF="109.1" PrcIntensityAfter20CyclesPFSD="4.78" /><Lane key="8" TileCount="48" ClustersRaw="4777517" ClustersRawSD="592904.0" ClustersPF="4113021" ClustersPFSD="439623.7" PrcPFClusters="86.5" PrcPFClustersSD="7.36" Phasing="0.219" Prephasing="0.235" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="6314" FirstCycleIntPFSD="760.7" PrcIntensityAfter20CyclesPF="37.3" PrcIntensityAfter20CyclesPFSD="9.19" /></Summary>
\ No newline at end of file
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?><!--Illumina RTA Data--><Summary Read="2" ReadType=" (Index)" densityRatio="0.173619792"><Lane key="1" TileCount="48" ClustersRaw="3878755" ClustersRawSD="579626.0" ClustersPF="1040253" ClustersPFSD="1059982.5" PrcPFClusters="27.8" PrcPFClustersSD="27.72" Phasing="0.000" Prephasing="0.000" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="991" FirstCycleIntPFSD="2165.9" PrcIntensityAfter20CyclesPF="0.0" PrcIntensityAfter20CyclesPFSD="0.00" /><Lane key="2" TileCount="48" ClustersRaw="3920639" ClustersRawSD="1027332.4" ClustersPF="474380" ClustersPFSD="739312.7" PrcPFClusters="13.4" PrcPFClustersSD="17.58" Phasing="0.000" Prephasing="0.000" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="925" FirstCycleIntPFSD="2096.4" PrcIntensityAfter20CyclesPF="0.0" PrcIntensityAfter20CyclesPFSD="0.00" /><Lane key="3" TileCount="48" ClustersRaw="5713049" ClustersRawSD="876187.3" ClustersPF="376501" ClustersPFSD="895452.3" PrcPFClusters="6.0" PrcPFClustersSD="14.30" Phasing="0.000" Prephasing="0.000" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="1181" FirstCycleIntPFSD="1800.6" PrcIntensityAfter20CyclesPF="0.0" PrcIntensityAfter20CyclesPFSD="0.00" /><Lane key="4" TileCount="48" ClustersRaw="5852907" ClustersRawSD="538640.6" ClustersPF="329831" ClustersPFSD="758370.9" PrcPFClusters="5.4" PrcPFClustersSD="12.52" Phasing="0.000" Prephasing="0.000" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="483" FirstCycleIntPFSD="1007.8" PrcIntensityAfter20CyclesPF="0.0" PrcIntensityAfter20CyclesPFSD="0.00" /><Lane key="5" TileCount="48" ClustersRaw="4006751" ClustersRawSD="1265247.4" ClustersPF="52186" ClustersPFSD="233275.6" PrcPFClusters="0.9" PrcPFClustersSD="4.22" Phasing="0.000" Prephasing="0.000" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="1592" FirstCycleIntPFSD="1930.7" PrcIntensityAfter20CyclesPF="0.0" PrcIntensityAfter20CyclesPFSD="0.00" /><Lane key="6" TileCount="48" ClustersRaw="5678021" ClustersRawSD="627070.7" ClustersPF="1490900" ClustersPFSD="1624380.0" PrcPFClusters="25.5" PrcPFClustersSD="26.81" Phasing="0.000" Prephasing="0.000" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="2308" FirstCycleIntPFSD="2746.0" PrcIntensityAfter20CyclesPF="0.0" PrcIntensityAfter20CyclesPFSD="0.00" /><Lane key="7" TileCount="48" ClustersRaw="1854131" ClustersRawSD="429053.2" ClustersPF="1585131" ClustersPFSD="693768.5" PrcPFClusters="85.0" PrcPFClustersSD="30.78" Phasing="0.000" Prephasing="0.000" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="5761" FirstCycleIntPFSD="3328.6" PrcIntensityAfter20CyclesPF="0.0" PrcIntensityAfter20CyclesPFSD="0.00" /><Lane key="8" TileCount="48" ClustersRaw="4777517" ClustersRawSD="592904.0" ClustersPF="4113021" ClustersPFSD="439623.7" PrcPFClusters="86.5" PrcPFClustersSD="7.36" Phasing="0.000" Prephasing="0.000" CalledCyclesMin="0" CalledCyclesMax="0" PrcAlign="0.00" PrcAlignSD="0.000" ErrRatePhiX="0.00" ErrRatePhiXSD="0.000" ErrRate35="0.00" ErrRate35SD="0.000" ErrRate75="0.00" ErrRate75SD="0.000" ErrRate100="0.00" ErrRate100SD="0.000" FirstCycleIntPF="2791" FirstCycleIntPFSD="3369.4" PrcIntensityAfter20CyclesPF="0.0" PrcIntensityAfter20CyclesPFSD="0.00" /></Summary>
\ No newline at end of file
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>\r
+<BaseCallAnalysis xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema">\r
+ <Run Name="BaseCalls">\r
+ <BaseCallParameters>\r
+ <ChastityThreshold>0.6</ChastityThreshold>\r
+ <Matrix Path="">\r
+ <AutoFlag>2</AutoFlag>\r
+ <AutoLane>0</AutoLane>\r
+ <Cycle>1</Cycle>\r
+ <CycleOffset>0</CycleOffset>\r
+ <FirstCycle>1</FirstCycle>\r
+ <LastCycle>50</LastCycle>\r
+ <Read>1</Read>\r
+ </Matrix>\r
+ <Matrix Path="">\r
+ <AutoFlag>2</AutoFlag>\r
+ <AutoLane>0</AutoLane>\r
+ <Cycle>51</Cycle>\r
+ <CycleOffset>0</CycleOffset>\r
+ <FirstCycle>51</FirstCycle>\r
+ <LastCycle>57</LastCycle>\r
+ <Read>2</Read>\r
+ </Matrix>\r
+ <Phasing Path="">\r
+ <AutoFlag>2</AutoFlag>\r
+ <AutoLane>0</AutoLane>\r
+ <Cycle>2</Cycle>\r
+ <CycleOffset>1</CycleOffset>\r
+ <FirstCycle>1</FirstCycle>\r
+ <LastCycle>50</LastCycle>\r
+ <Read>1</Read>\r
+ <PhasingRate>0</PhasingRate>\r
+ <PrephasingRate>0</PrephasingRate>\r
+ </Phasing>\r
+ <Phasing Path="">\r
+ <AutoFlag>2</AutoFlag>\r
+ <AutoLane>0</AutoLane>\r
+ <Cycle>52</Cycle>\r
+ <CycleOffset>1</CycleOffset>\r
+ <FirstCycle>51</FirstCycle>\r
+ <LastCycle>57</LastCycle>\r
+ <Read>2</Read>\r
+ <PhasingRate>0</PhasingRate>\r
+ <PrephasingRate>0</PrephasingRate>\r
+ </Phasing>\r
+ <PureBases>0</PureBases>\r
+ <SmtFilter>failed-chastity</SmtFilter>\r
+ <SmtRelation>le</SmtRelation>\r
+ <SmtThreshold>1.0</SmtThreshold>\r
+ </BaseCallParameters>\r
+ <Cycles First="1" Last="57" Number="57" />\r
+ <Input />\r
+ <RunParameters>\r
+ <AutoCycleFlag>0</AutoCycleFlag>\r
+ <BasecallFlag>0</BasecallFlag>\r
+ <Deblocked>0</Deblocked>\r
+ <DebugFlag>0</DebugFlag>\r
+ <FirstRunOnlyFlag>0</FirstRunOnlyFlag>\r
+ <ImagingReads Index="1">\r
+ <FirstCycle>1</FirstCycle>\r
+ <LastCycle>50</LastCycle>\r
+ </ImagingReads>\r
+ <ImagingReads Index="2">\r
+ <FirstCycle>51</FirstCycle>\r
+ <LastCycle>57</LastCycle>\r
+ <RunFolder>110815_SN787_0101_AD07K6ACXX</RunFolder>\r
+ </ImagingReads>\r
+ <Instrument>HWI-ST0787</Instrument>\r
+ <IterativeMatrixFlag>0</IterativeMatrixFlag>\r
+ <MakeFlag>0</MakeFlag>\r
+ <MaxCycle>0</MaxCycle>\r
+ <MinCycle>0</MinCycle>\r
+ <Reads Index="1">\r
+ <FirstCycle>1</FirstCycle>\r
+ <LastCycle>50</LastCycle>\r
+ </Reads>\r
+ <Reads Index="2">\r
+ <FirstCycle>51</FirstCycle>\r
+ <LastCycle>57</LastCycle>\r
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\ No newline at end of file
+++ /dev/null
-<?xml version="1.0"?>
-<RunParameters>
- <Barcodes>
- </Barcodes>
- <Defaults>
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- <CHROM_NAME_VALIDATION>on</CHROM_NAME_VALIDATION>
- <CMDPREFIX></CMDPREFIX>
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- <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
- <ELAND_SEED_LENGTH2></ELAND_SEED_LENGTH2>
- <EMAIL_DOMAIN>domain.com</EMAIL_DOMAIN>
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- </Software>
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+++ /dev/null
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+++ /dev/null
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+++ /dev/null
-<?xml version="1.0"?>
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\ No newline at end of file
+++ /dev/null
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- <RunFolder>110815_SN787_0101_AD07K6ACXX</RunFolder>\r
- </Reads>\r
- <RunFolder>110815_SN787_0101_AD07K6ACXX</RunFolder>\r
- <RunFolderDate>110815</RunFolderDate>\r
- <RunFolderId>0101</RunFolderId>\r
- <RunFlowcellId>D07K6ACXX</RunFlowcellId>\r
- <Barcode>\r
- <Cycle Use="true">51</Cycle>\r
- <Cycle Use="true">52</Cycle>\r
- <Cycle Use="true">53</Cycle>\r
- <Cycle Use="true">54</Cycle>\r
- <Cycle Use="true">55</Cycle>\r
- <Cycle Use="true">56</Cycle>\r
- <Cycle Use="true">57</Cycle>\r
- </Barcode>\r
- <QTableVersion>New6</QTableVersion>\r
- </RunParameters>\r
- <Software Name="RTA" Version="1.12.4.2" />\r
- <TileSelection>\r
- <Lane Index="1">\r
- <Sample>s</Sample>\r
- <Tile>1101</Tile>\r
- <Tile>1102</Tile>\r
- <Tile>1104</Tile>\r
- <Tile>1103</Tile>\r
- <Tile>1106</Tile>\r
- <Tile>1105</Tile>\r
- <Tile>1108</Tile>\r
- <Tile>1107</Tile>\r
- <Tile>1201</Tile>\r
- <Tile>1204</Tile>\r
- <Tile>1202</Tile>\r
- <Tile>1205</Tile>\r
- <Tile>1206</Tile>\r
- <Tile>1208</Tile>\r
- <Tile>1301</Tile>\r
- <Tile>1302</Tile>\r
- <Tile>1304</Tile>\r
- <Tile>1203</Tile>\r
- <Tile>1305</Tile>\r
- <Tile>1306</Tile>\r
- <Tile>1308</Tile>\r
- <Tile>2102</Tile>\r
- <Tile>2101</Tile>\r
- <Tile>1207</Tile>\r
- <Tile>2105</Tile>\r
- <Tile>2106</Tile>\r
- <Tile>2104</Tile>\r
- <Tile>1303</Tile>\r
- <Tile>2201</Tile>\r
- <Tile>2202</Tile>\r
- <Tile>1307</Tile>\r
- <Tile>2206</Tile>\r
- <Tile>2205</Tile>\r
- <Tile>2108</Tile>\r
- <Tile>2302</Tile>\r
- <Tile>2103</Tile>\r
- <Tile>2301</Tile>\r
- <Tile>2204</Tile>\r
- <Tile>2305</Tile>\r
- <Tile>2107</Tile>\r
- <Tile>2203</Tile>\r
- <Tile>2208</Tile>\r
- <Tile>2306</Tile>\r
- <Tile>2207</Tile>\r
- <Tile>2304</Tile>\r
- <Tile>2303</Tile>\r
- <Tile>2308</Tile>\r
- <Tile>2307</Tile>\r
- </Lane>\r
- <Lane Index="2">\r
- <Sample>s</Sample>\r
- <Tile>1101</Tile>\r
- <Tile>1105</Tile>\r
- <Tile>1102</Tile>\r
- <Tile>1106</Tile>\r
- <Tile>1201</Tile>\r
- <Tile>1103</Tile>\r
- <Tile>1104</Tile>\r
- <Tile>1202</Tile>\r
- <Tile>1205</Tile>\r
- <Tile>1107</Tile>\r
- <Tile>1206</Tile>\r
- <Tile>1108</Tile>\r
- <Tile>1203</Tile>\r
- <Tile>1302</Tile>\r
- <Tile>1204</Tile>\r
- <Tile>1301</Tile>\r
- <Tile>1208</Tile>\r
- <Tile>1207</Tile>\r
- <Tile>1305</Tile>\r
- <Tile>1306</Tile>\r
- <Tile>1304</Tile>\r
- <Tile>2101</Tile>\r
- <Tile>1303</Tile>\r
- <Tile>2102</Tile>\r
- <Tile>1308</Tile>\r
- <Tile>2105</Tile>\r
- <Tile>1307</Tile>\r
- <Tile>2106</Tile>\r
- <Tile>2201</Tile>\r
- <Tile>2104</Tile>\r
- <Tile>2103</Tile>\r
- <Tile>2202</Tile>\r
- <Tile>2205</Tile>\r
- <Tile>2107</Tile>\r
- <Tile>2108</Tile>\r
- <Tile>2206</Tile>\r
- <Tile>2301</Tile>\r
- <Tile>2203</Tile>\r
- <Tile>2204</Tile>\r
- <Tile>2208</Tile>\r
- <Tile>2207</Tile>\r
- <Tile>2302</Tile>\r
- <Tile>2305</Tile>\r
- <Tile>2303</Tile>\r
- <Tile>2304</Tile>\r
- <Tile>2306</Tile>\r
- <Tile>2307</Tile>\r
- <Tile>2308</Tile>\r
- </Lane>\r
- <Lane Index="3">\r
- <Sample>s</Sample>\r
- <Tile>1101</Tile>\r
- <Tile>1103</Tile>\r
- <Tile>1102</Tile>\r
- <Tile>1104</Tile>\r
- <Tile>1105</Tile>\r
- <Tile>1106</Tile>\r
- <Tile>1107</Tile>\r
- <Tile>1108</Tile>\r
- <Tile>1201</Tile>\r
- <Tile>1204</Tile>\r
- <Tile>1202</Tile>\r
- <Tile>1203</Tile>\r
- <Tile>1205</Tile>\r
- <Tile>1206</Tile>\r
- <Tile>1207</Tile>\r
- <Tile>1208</Tile>\r
- <Tile>1302</Tile>\r
- <Tile>1301</Tile>\r
- <Tile>1303</Tile>\r
- <Tile>1304</Tile>\r
- <Tile>1306</Tile>\r
- <Tile>1305</Tile>\r
- <Tile>1308</Tile>\r
- <Tile>2101</Tile>\r
- <Tile>2102</Tile>\r
- <Tile>2105</Tile>\r
- <Tile>1307</Tile>\r
- <Tile>2104</Tile>\r
- <Tile>2106</Tile>\r
- <Tile>2201</Tile>\r
- <Tile>2108</Tile>\r
- <Tile>2103</Tile>\r
- <Tile>2107</Tile>\r
- <Tile>2202</Tile>\r
- <Tile>2205</Tile>\r
- <Tile>2204</Tile>\r
- <Tile>2301</Tile>\r
- <Tile>2206</Tile>\r
- <Tile>2305</Tile>\r
- <Tile>2203</Tile>\r
- <Tile>2208</Tile>\r
- <Tile>2302</Tile>\r
- <Tile>2207</Tile>\r
- <Tile>2304</Tile>\r
- <Tile>2306</Tile>\r
- <Tile>2303</Tile>\r
- <Tile>2308</Tile>\r
- <Tile>2307</Tile>\r
- </Lane>\r
- <Lane Index="4">\r
- <Sample>s</Sample>\r
- <Tile>1101</Tile>\r
- <Tile>1105</Tile>\r
- <Tile>1201</Tile>\r
- <Tile>1102</Tile>\r
- <Tile>1106</Tile>\r
- <Tile>1205</Tile>\r
- <Tile>1104</Tile>\r
- <Tile>1202</Tile>\r
- <Tile>1103</Tile>\r
- <Tile>1301</Tile>\r
- <Tile>1206</Tile>\r
- <Tile>1108</Tile>\r
- <Tile>1107</Tile>\r
- <Tile>1305</Tile>\r
- <Tile>1302</Tile>\r
- <Tile>2101</Tile>\r
- <Tile>1203</Tile>\r
- <Tile>1306</Tile>\r
- <Tile>1204</Tile>\r
- <Tile>1207</Tile>\r
- <Tile>2102</Tile>\r
- <Tile>1208</Tile>\r
- <Tile>2105</Tile>\r
- <Tile>1303</Tile>\r
- <Tile>2106</Tile>\r
- <Tile>1304</Tile>\r
- <Tile>2201</Tile>\r
- <Tile>1307</Tile>\r
- <Tile>1308</Tile>\r
- <Tile>2202</Tile>\r
- <Tile>2103</Tile>\r
- <Tile>2104</Tile>\r
- <Tile>2205</Tile>\r
- <Tile>2206</Tile>\r
- <Tile>2302</Tile>\r
- <Tile>2108</Tile>\r
- <Tile>2301</Tile>\r
- <Tile>2107</Tile>\r
- <Tile>2305</Tile>\r
- <Tile>2306</Tile>\r
- <Tile>2204</Tile>\r
- <Tile>2203</Tile>\r
- <Tile>2208</Tile>\r
- <Tile>2207</Tile>\r
- <Tile>2303</Tile>\r
- <Tile>2304</Tile>\r
- <Tile>2308</Tile>\r
- <Tile>2307</Tile>\r
- </Lane>\r
- <Lane Index="5">\r
- <Sample>s</Sample>\r
- <Tile>1102</Tile>\r
- <Tile>1101</Tile>\r
- <Tile>1106</Tile>\r
- <Tile>1105</Tile>\r
- <Tile>1202</Tile>\r
- <Tile>1201</Tile>\r
- <Tile>1205</Tile>\r
- <Tile>1206</Tile>\r
- <Tile>1301</Tile>\r
- <Tile>1104</Tile>\r
- <Tile>1302</Tile>\r
- <Tile>1103</Tile>\r
- <Tile>1108</Tile>\r
- <Tile>1305</Tile>\r
- <Tile>1306</Tile>\r
- <Tile>1107</Tile>\r
- <Tile>2102</Tile>\r
- <Tile>1203</Tile>\r
- <Tile>1204</Tile>\r
- <Tile>2101</Tile>\r
- <Tile>2106</Tile>\r
- <Tile>1207</Tile>\r
- <Tile>2202</Tile>\r
- <Tile>1303</Tile>\r
- <Tile>1208</Tile>\r
- <Tile>2105</Tile>\r
- <Tile>2201</Tile>\r
- <Tile>1304</Tile>\r
- <Tile>1307</Tile>\r
- <Tile>2206</Tile>\r
- <Tile>2103</Tile>\r
- <Tile>2205</Tile>\r
- <Tile>2302</Tile>\r
- <Tile>2107</Tile>\r
- <Tile>1308</Tile>\r
- <Tile>2301</Tile>\r
- <Tile>2203</Tile>\r
- <Tile>2104</Tile>\r
- <Tile>2305</Tile>\r
- <Tile>2207</Tile>\r
- <Tile>2108</Tile>\r
- <Tile>2306</Tile>\r
- <Tile>2303</Tile>\r
- <Tile>2204</Tile>\r
- <Tile>2307</Tile>\r
- <Tile>2208</Tile>\r
- <Tile>2304</Tile>\r
- <Tile>2308</Tile>\r
- </Lane>\r
- <Lane Index="6">\r
- <Sample>s</Sample>\r
- <Tile>1101</Tile>\r
- <Tile>1102</Tile>\r
- <Tile>1103</Tile>\r
- <Tile>1106</Tile>\r
- <Tile>1105</Tile>\r
- <Tile>1107</Tile>\r
- <Tile>1202</Tile>\r
- <Tile>1201</Tile>\r
- <Tile>1203</Tile>\r
- <Tile>1207</Tile>\r
- <Tile>1205</Tile>\r
- <Tile>1206</Tile>\r
- <Tile>1301</Tile>\r
- <Tile>1303</Tile>\r
- <Tile>1302</Tile>\r
- <Tile>1104</Tile>\r
- <Tile>1305</Tile>\r
- <Tile>1306</Tile>\r
- <Tile>2101</Tile>\r
- <Tile>1108</Tile>\r
- <Tile>2102</Tile>\r
- <Tile>1307</Tile>\r
- <Tile>2103</Tile>\r
- <Tile>2105</Tile>\r
- <Tile>1204</Tile>\r
- <Tile>2106</Tile>\r
- <Tile>2107</Tile>\r
- <Tile>2201</Tile>\r
- <Tile>2202</Tile>\r
- <Tile>1208</Tile>\r
- <Tile>2203</Tile>\r
- <Tile>2206</Tile>\r
- <Tile>2205</Tile>\r
- <Tile>1304</Tile>\r
- <Tile>2302</Tile>\r
- <Tile>2207</Tile>\r
- <Tile>2301</Tile>\r
- <Tile>1308</Tile>\r
- <Tile>2306</Tile>\r
- <Tile>2303</Tile>\r
- <Tile>2305</Tile>\r
- <Tile>2307</Tile>\r
- <Tile>2104</Tile>\r
- <Tile>2108</Tile>\r
- <Tile>2204</Tile>\r
- <Tile>2208</Tile>\r
- <Tile>2304</Tile>\r
- <Tile>2308</Tile>\r
- </Lane>\r
- <Lane Index="7">\r
- <Sample>s</Sample>\r
- <Tile>1102</Tile>\r
- <Tile>1106</Tile>\r
- <Tile>1101</Tile>\r
- <Tile>1105</Tile>\r
- <Tile>1202</Tile>\r
- <Tile>1201</Tile>\r
- <Tile>1206</Tile>\r
- <Tile>1205</Tile>\r
- <Tile>1103</Tile>\r
- <Tile>1302</Tile>\r
- <Tile>1301</Tile>\r
- <Tile>1107</Tile>\r
- <Tile>1306</Tile>\r
- <Tile>1305</Tile>\r
- <Tile>1203</Tile>\r
- <Tile>2101</Tile>\r
- <Tile>2102</Tile>\r
- <Tile>2105</Tile>\r
- <Tile>1207</Tile>\r
- <Tile>2106</Tile>\r
- <Tile>2201</Tile>\r
- <Tile>2202</Tile>\r
- <Tile>2205</Tile>\r
- <Tile>1303</Tile>\r
- <Tile>1307</Tile>\r
- <Tile>2206</Tile>\r
- <Tile>2301</Tile>\r
- <Tile>2103</Tile>\r
- <Tile>2305</Tile>\r
- <Tile>2302</Tile>\r
- <Tile>2107</Tile>\r
- <Tile>2306</Tile>\r
- <Tile>2203</Tile>\r
- <Tile>2207</Tile>\r
- <Tile>2303</Tile>\r
- <Tile>2307</Tile>\r
- <Tile>1104</Tile>\r
- <Tile>1108</Tile>\r
- <Tile>1204</Tile>\r
- <Tile>1208</Tile>\r
- <Tile>1304</Tile>\r
- <Tile>1308</Tile>\r
- <Tile>2104</Tile>\r
- <Tile>2108</Tile>\r
- <Tile>2204</Tile>\r
- <Tile>2208</Tile>\r
- <Tile>2304</Tile>\r
- <Tile>2308</Tile>\r
- </Lane>\r
- <Lane Index="8">\r
- <Sample>s</Sample>\r
- <Tile>1101</Tile>\r
- <Tile>1102</Tile>\r
- <Tile>1105</Tile>\r
- <Tile>1106</Tile>\r
- <Tile>1201</Tile>\r
- <Tile>1202</Tile>\r
- <Tile>1103</Tile>\r
- <Tile>1205</Tile>\r
- <Tile>1206</Tile>\r
- <Tile>1107</Tile>\r
- <Tile>1301</Tile>\r
- <Tile>1302</Tile>\r
- <Tile>1203</Tile>\r
- <Tile>1306</Tile>\r
- <Tile>1305</Tile>\r
- <Tile>1207</Tile>\r
- <Tile>2101</Tile>\r
- <Tile>1303</Tile>\r
- <Tile>2102</Tile>\r
- <Tile>1307</Tile>\r
- <Tile>2105</Tile>\r
- <Tile>2103</Tile>\r
- <Tile>2106</Tile>\r
- <Tile>2201</Tile>\r
- <Tile>2107</Tile>\r
- <Tile>2205</Tile>\r
- <Tile>2202</Tile>\r
- <Tile>2206</Tile>\r
- <Tile>2203</Tile>\r
- <Tile>2301</Tile>\r
- <Tile>2305</Tile>\r
- <Tile>2302</Tile>\r
- <Tile>2306</Tile>\r
- <Tile>1104</Tile>\r
- <Tile>2207</Tile>\r
- <Tile>1108</Tile>\r
- <Tile>1204</Tile>\r
- <Tile>2303</Tile>\r
- <Tile>2307</Tile>\r
- <Tile>1208</Tile>\r
- <Tile>1304</Tile>\r
- <Tile>1308</Tile>\r
- <Tile>2104</Tile>\r
- <Tile>2108</Tile>\r
- <Tile>2204</Tile>\r
- <Tile>2208</Tile>\r
- <Tile>2304</Tile>\r
- <Tile>2308</Tile>\r
- </Lane>\r
- </TileSelection>\r
- <Time />\r
- <User />\r
- </Run>\r
-</ImageAnalysis>
\ No newline at end of file
fromTypedNode
from htsworkflow.util.hashfile import make_md5sum
-logger = logging.getLogger(__name__)
+LOGGER = logging.getLogger(__name__)
DAF_VARIABLE_NAMES = ("variables", "extraVariables")
VARIABLES_TERM_NAME = 'variables'
if view_name is not None:
attributes['views'][view_name] = view_attributes
- logger.debug("DAF Attributes" + pformat(attributes))
+ LOGGER.debug("DAF Attributes" + pformat(attributes))
return attributes
otherwise specifies model to use
"""
if daf_file is None and model is None:
- logger.error("We need a DAF or Model containing a DAF to work")
+ LOGGER.error("We need a DAF or Model containing a DAF to work")
self.name = name
self.submissionSet = get_submission_uri(self.name)
"""Examine files in our result directory
"""
for lib_id, result_dir in result_map.items():
- logger.info("Importing %s from %s" % (lib_id, result_dir))
+ LOGGER.info("Importing %s from %s" % (lib_id, result_dir))
try:
self.import_submission_dir(result_dir, lib_id)
except MetadataLookupException, e:
- logger.error("Skipping %s: %s" % (lib_id, str(e)))
+ LOGGER.error("Skipping %s: %s" % (lib_id, str(e)))
def import_submission_dir(self, submission_dir, library_id):
"""Import a submission directories and update our model as needed
"""
path, filename = os.path.split(pathname)
- logger.debug("Searching for view")
+ LOGGER.debug("Searching for view")
view = self.find_view(filename)
if view is None:
- logger.warn("Unrecognized file: {0}".format(pathname))
+ LOGGER.warn("Unrecognized file: {0}".format(pathname))
return None
if str(view) == str(libraryOntology['ignore']):
return None
dafTermOntology['name']))
if view_name is None:
errmsg = 'Could not find view name for {0}'
- logger.warning(errmsg.format(str(view)))
+ LOGGER.warning(errmsg.format(str(view)))
return
view_name = str(view_name)
RDF.Statement(self.submissionSet,
dafTermOntology['has_submission'],
submissionNode))
- logger.debug("Adding statements to {0}".format(str(submissionNode)))
+ LOGGER.debug("Adding statements to {0}".format(str(submissionNode)))
self.model.add_statement(RDF.Statement(submissionNode,
submissionOntology['has_view'],
submissionView))
submissionOntology['library'],
libNode))
- logger.debug("Adding statements to {0}".format(str(submissionView)))
+ LOGGER.debug("Adding statements to {0}".format(str(submissionView)))
# add track specific information
self.model.add_statement(
RDF.Statement(submissionView, dafTermOntology['view'], view))
# add file specific information
self.create_file_attributes(filename, submissionView, submission_uri, submission_dir)
- logger.debug("Done.")
+ LOGGER.debug("Done.")
def create_file_attributes(self, filename, submissionView, submission_uri, submission_dir):
# add file specific information
- logger.debug("Updating file md5sum")
+ LOGGER.debug("Updating file md5sum")
fileNode = RDF.Node(RDF.Uri(submission_uri + '/' + filename))
submission_pathname = os.path.join(submission_dir, filename)
self.model.add_statement(
md5 = make_md5sum(submission_pathname)
if md5 is None:
errmsg = "Unable to produce md5sum for {0}"
- logger.warning(errmsg.format(submission_pathname))
+ LOGGER.warning(errmsg.format(submission_pathname))
else:
self.model.add_statement(
RDF.Statement(fileNode, dafTermOntology['md5sum'], md5))
else:
msg = "Found wrong number of view names for {0} len = {1}"
msg = msg.format(str(view), len(names))
- logger.error(msg)
+ LOGGER.error(msg)
raise RuntimeError(msg)
def _get_filename_view_map(self):
for s in self.model.find_statements(filename_query):
view_name = s.subject
literal_re = s.object.literal_value['string']
- logger.debug("Found: %s" % (literal_re,))
+ LOGGER.debug("Found: %s" % (literal_re,))
try:
filename_re = re.compile(literal_re)
except re.error, e:
- logger.error("Unable to compile: %s" % (literal_re,))
+ LOGGER.error("Unable to compile: %s" % (literal_re,))
patterns[literal_re] = view_name
return patterns
import logging
+import os
import RDF
from htsworkflow.util.rdfhelp import \
fromTypedNode, \
+ geoSoftNS, \
+ simplifyUri, \
submissionOntology
from django.conf import settings
def make_soft(self, result_map):
samples = []
+ platform = self.get_platform_metadata()
+ platform_attribs = dict(platform)
+ platform_id = platform_attribs['^platform']
+ series = self.get_series_metadata()
+ series_attribs = dict(series)
+ series_id = series_attribs['^series']
for lib_id, result_dir in result_map.items():
an_analysis = self.get_submission_node(result_dir)
- samples.append(self.get_sample_metadata(an_analysis))
+ metadata = self.get_sample_metadata(an_analysis)
+ if len(metadata) > 1:
+ errmsg = 'Confused there are more than one samples for %s'
+ LOGGER.debug(errmsg % (str(an_analysis,)))
+ metadata = metadata[0]
+ metadata['raw'] = self.get_sample_files(an_analysis,
+ geoSoftNS['raw'])
+ metadata['supplimental'] = self.get_sample_files(
+ an_analysis,
+ geoSoftNS['supplemental'])
+ samples.append(metadata)
soft_template = loader.get_template('geo_submission.soft')
context = Context({
- 'samples': samples
+ 'platform': platform,
+ 'series': series,
+ 'samples': samples,
+ 'platform_id': platform_id,
+ 'series_id': series_id,
})
print str(soft_template.render(context))
else:
return True
+ def get_platform_metadata(self):
+ """Gather information for filling out sample section of a SOFT file
+ """
+ query_template = loader.get_template('geo_platform.sparql')
+ submission = str(self.submissionSetNS[''].uri)
+ context = Context({
+ 'submission': submission,
+ })
+
+ results = self.execute_query(query_template, context)
+ return self.query_to_soft_dictionary(results, 'platform')
+
+ def get_series_metadata(self):
+ """Gather information for filling out sample section of a SOFT file
+ """
+ query_template = loader.get_template('geo_series.sparql')
+ submission = str(self.submissionSetNS[''].uri)
+ context = Context({
+ 'submission': submission,
+ })
+
+ results = self.execute_query(query_template, context)
+ return self.query_to_soft_dictionary(results, 'series')
+
def get_sample_metadata(self, analysis_node):
"""Gather information for filling out sample section of a SOFT file
"""
- query_template = loader.get_template('geo_submission.sparql')
+ query_template = loader.get_template('geo_samples.sparql')
context = Context({
'submission': str(analysis_node.uri),
+ 'submissionSet': str(self.submissionSetNS[''].uri),
})
- formatted_query = query_template.render(context)
- query = RDF.SPARQLQuery(str(formatted_query))
- rdfstream = query.execute(self.model)
- results = []
- for r in rdfstream:
- results.append(r)
+ results = self.execute_query(query_template, context)
+ for r in results:
+
+ r['dataProtocol'] = str(r['dataProtocol']).replace('\n', ' ')
return results
+
+ def get_sample_files(self, analysis_node, file_class):
+ """Gather files
+ """
+ query_template = loader.get_template('geo_files.sparql')
+
+ context = Context({
+ 'submission': str(analysis_node.uri),
+ 'file_class': str(file_class)
+ })
+
+ return self.execute_query(query_template, context)
+
+ def query_to_soft_dictionary(self, results, heading):
+ attributes = []
+ for r in results:
+ name = simplifyUri(geoSoftNS, r['name'])
+ if name is not None:
+ if name.lower() == heading.lower():
+ name = '^' + name
+ else:
+ name = '!' + name
+ for v in fromTypedNode(r['value']).split(os.linesep):
+ v = v.strip()
+ if len(v) > 0:
+ attributes.append((name, v))
+ return attributes
MetadataLookupException, \
get_submission_uri
-logger = logging.getLogger(__name__)
+LOGGER = logging.getLogger(__name__)
class Submission(object):
def __init__(self, name, model):
self.model = model
self.submissionSet = get_submission_uri(self.name)
- self.submissionSetNS = RDF.NS(str(self.submissionSet) + '/')
+ self.submissionSetNS = RDF.NS(str(self.submissionSet) + '#')
self.libraryNS = RDF.NS('http://jumpgate.caltech.edu/library/')
self.__view_map = None
"""Examine files in our result directory
"""
for lib_id, result_dir in result_map.items():
- logger.info("Importing %s from %s" % (lib_id, result_dir))
+ LOGGER.info("Importing %s from %s" % (lib_id, result_dir))
try:
self.import_analysis_dir(result_dir, lib_id)
except MetadataLookupException, e:
- logger.error("Skipping %s: %s" % (lib_id, str(e)))
+ LOGGER.error("Skipping %s: %s" % (lib_id, str(e)))
def import_analysis_dir(self, analysis_dir, library_id):
"""Import a submission directories and update our model as needed
"""
path, filename = os.path.split(pathname)
- logger.debug("Searching for view")
- file_classification = self.find_best_match(filename)
- if file_classification is None:
- logger.warn("Unrecognized file: {0}".format(pathname))
+ LOGGER.debug("Searching for view")
+ file_type = self.find_best_match(filename)
+ if file_type is None:
+ LOGGER.warn("Unrecognized file: {0}".format(pathname))
return None
- if str(file_classification) == str(libraryOntology['ignore']):
+ if str(file_type) == str(libraryOntology['ignore']):
return None
an_analysis_name = self.make_submission_name(analysis_dir)
an_analysis = self.get_submission_node(analysis_dir)
an_analysis_uri = str(an_analysis.uri)
+ file_classification = self.model.get_target(file_type,
+ rdfNS['type'])
+ if file_classification is None:
+ errmsg = 'Could not find class for {0}'
+ logger.warning(errmsg.format(str(file_type)))
+ return
+ self.model.add_statement(
+ RDF.Statement(self.submissionSetNS[''],
+ submissionOntology['has_submission'],
+ an_analysis))
self.model.add_statement(RDF.Statement(an_analysis,
submissionOntology['name'],
toTypedNode(an_analysis_name)))
submissionOntology['library'],
libNode))
- logger.debug("Adding statements to {0}".format(str(an_analysis)))
+ LOGGER.debug("Adding statements to {0}".format(str(an_analysis)))
# add track specific information
self.model.add_statement(
RDF.Statement(an_analysis,
an_analysis_uri,
analysis_dir)
self.add_md5s(filename, fileNode, analysis_dir)
-
- logger.debug("Done.")
+ self.model.add_statement(
+ RDF.Statement(fileNode,
+ rdfNS['type'],
+ file_type))
+ LOGGER.debug("Done.")
def link_file_to_classes(self, filename, submissionNode, submission_uri, analysis_dir):
# add file specific information
return fileNode
def add_md5s(self, filename, fileNode, analysis_dir):
- logger.debug("Updating file md5sum")
+ LOGGER.debug("Updating file md5sum")
submission_pathname = os.path.join(analysis_dir, filename)
md5 = make_md5sum(submission_pathname)
if md5 is None:
errmsg = "Unable to produce md5sum for {0}"
- logger.warning(errmsg.format(submission_pathname))
+ LOGGER.warning(errmsg.format(submission_pathname))
else:
self.model.add_statement(
RDF.Statement(fileNode, dafTermOntology['md5sum'], md5))
for s in self.model.find_statements(filename_query):
view_name = s.subject
literal_re = s.object.literal_value['string']
- logger.debug("Found: %s" % (literal_re,))
+ LOGGER.debug("Found: %s" % (literal_re,))
try:
filename_re = re.compile(literal_re)
except re.error, e:
- logger.error("Unable to compile: %s" % (literal_re,))
+ LOGGER.error("Unable to compile: %s" % (literal_re,))
patterns[literal_re] = view_name
return patterns
"Unrecognized library type %s for %s" % \
(library_type, str(libNode)))
+ def execute_query(self, template, context):
+ """Execute the query, returning the results
+ """
+ formatted_query = template.render(context)
+ LOGGER.debug(formatted_query)
+ query = RDF.SPARQLQuery(str(formatted_query))
+ rdfstream = query.execute(self.model)
+ results = []
+ for r in rdfstream:
+ results.append(r)
+ return results
--- /dev/null
+PREFIX libraryOntology: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
+PREFIX submissionOntology: <http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#>
+PREFIX ucscDaf: <http://jumpgate.caltech.edu/wiki/UcscDaf#>
+PREFIX ncbiTaxon: <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=>
+PREFIX geoSoft: <http://www.ncbi.nlm.nih.gov/geo/info/soft2.html#>
+
+select distinct ?filename, ?md5sum, ?file_type ?file_type_label
+WHERE {
+ <{{submission}}> ucscDaf:has_file ?file ;
+ a submissionOntology:submission .
+
+ ?file ucscDaf:filename ?filename ;
+ ucscDaf:md5sum ?md5sum ;
+ a ?file_type .
+ ?file_type a <{{file_class}}> ;
+ geoSoft:fileTypeLabel ?file_type_label .
+
+}
\ No newline at end of file
--- /dev/null
+PREFIX libraryOntology: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
+PREFIX submissionOntology: <http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#>
+PREFIX ucscDaf: <http://jumpgate.caltech.edu/wiki/UcscDaf#>
+PREFIX ncbiTaxon: <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=>
+PREFIX geoSoft: <http://www.ncbi.nlm.nih.gov/geo/info/soft2.html#>
+
+
+select distinct ?name ?value
+WHERE {
+ <{{submission}}> submissionOntology:has_platform ?platform .
+ ?platform a geoSoft:platform .
+
+ ?platform ?name ?value .
+}
--- /dev/null
+PREFIX libraryOntology: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
+PREFIX submissionOntology: <http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#>
+PREFIX ucscDaf: <http://jumpgate.caltech.edu/wiki/UcscDaf#>
+PREFIX ncbiTaxon: <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=>
+PREFIX geoSoft: <http://www.ncbi.nlm.nih.gov/geo/info/soft2.html#>
+PREFIX cells: <http://encodewiki.ucsc.edu/EncodeDCC/index.php/Cell_lines#>
+
+select distinct ?name ?cell ?antibody ?sex ?control ?strain ?controlId ?library_id ?treatment ?protocol ?readType ?insertLength ?replicate, ?mapAlgorithm ?species_name ?taxon_id ?extractMolecule ?growthProtocol ?extractProtocol ?dataProtocol ?experiment_type ?library_selection ?library_source
+WHERE {
+ <{{submission}}> a submissionOntology:submission .
+
+ OPTIONAL { <{{submission}}> ucscDaf:control ?control }
+ OPTIONAL { <{{submission}}> ucscDaf:controlId ?controlId }
+ OPTIONAL { ?library libraryOntology:antibody ?antibody }
+ OPTIONAL { ?library libraryOntology:cell_line ?cell .
+ ?cell_line cells:cell ?cell ;
+ cells:documents ?growthProtocol . }
+ OPTIONAL { ?library ucscDaf:sex ?sex }
+ OPTIONAL { ?library libraryOntology:library_id ?library_id }
+ OPTIONAL { ?library libraryOntology:replicate ?replicate }
+ OPTIONAL { ?library libraryOntology:species ?species_name }
+ OPTIONAL { ?library libraryOntology:condition_term ?treatment }
+ OPTIONAL { ?library libraryOntology:experiment_type ?experiment_type }
+ OPTIONAL { ?library libraryOntology:librarySelection ?library_selection }
+ OPTIONAL { ?library libraryOntology:librarySource ?library_source }
+ OPTIONAL { <{{submissionSet}}> geoSoft:data_processing ?dataProtocol }
+ OPTIONAL { ?library libraryOntology:extractMolecule ?extractMolecule }
+ OPTIONAL { ?library libraryOntology:extractProtocol ?extractProtocol }
+ OPTIONAL { ?library ucscDaf:protocol ?protocol }
+ OPTIONAL { ?library ucscDaf:readType ?readType }
+ OPTIONAL { ?library ucscDaf:strain ?strain }
+ OPTIONAL { ?library libraryOntology:insert_size ?insertLength }
+ OPTIONAL { ?library ucscDaf:mapAlgorithm ?mapAlgorithm }
+
+ <{{submission}}> submissionOntology:library ?library ;
+ submissionOntology:name ?name .
+ ?species libraryOntology:species ?species_name ;
+ libraryOntology:taxon_id ?taxon_id .
+
+
+}
\ No newline at end of file
--- /dev/null
+PREFIX libraryOntology: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
+PREFIX submissionOntology: <http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#>
+PREFIX ucscDaf: <http://jumpgate.caltech.edu/wiki/UcscDaf#>
+PREFIX ncbiTaxon: <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=>
+PREFIX geoSoft: <http://www.ncbi.nlm.nih.gov/geo/info/soft2.html#>
+
+
+select distinct ?name ?value
+WHERE {
+ <{{submission}}> submissionOntology:has_series ?series.
+ ?series a geoSoft:series .
+
+ ?series ?name ?value .
+}
-Soft template
-!Platform_title = Illumina Genome Analyzer (Homo sapiens)
-!Platform_geo_accession = GPL9052
-{% for sample in samples %}{% for row in sample %}{%if forloop.first %}
+{% for name, value in series %}{{name}} = {{value}}
+{% endfor %}!Series_platform_id = {{ platform_id }}
+{% for row in samples %}
^SAMPLE={{row.name}}
+!Sample_type=SRA
!Sample_title={{row.name}}
+!Sample_series_id = {{ series_id }}
+!Sample_instrument_model = Illumina Genome Analyzer
+!Sample_instrument_model = Illumina Genome Analyzer II
+!Sample_instrument_model = Illumina Genome Analyzer IIx
+!Sample_instrument_model = Illumina HiSeq 2000
+!Sample_channel_count = 1
!Sample_organism_ch1 = {{ row.species_name }}
!Sample_taxid_ch1 = {{ row.taxon_id }}
-{% spaceless %}{% if row.cell %}!Sample_characteristics_ch1 = cell: {{ row.cell }}
-{% endif %}{% endspaceless %}{% endif %}
-!Sample_supplementary_file_{{forloop.counter}}={{row.filename}}{% endfor %}{% endfor %}
\ No newline at end of file
+!Sample_platform_id = {{ platform_id }}
+!Sample_source_name_ch1={{row.cell}}
+!Sample_library_strategy={{ row.experiment_type }}
+!Sample_library_source={{row.library_source}}
+!Sample_library_selection={{ row.library_selection }}
+!Sample_growth_protocol_ch1={{ row.growthProtocol|safe }}
+!Sample_extract_protocol={{ row.extractProtocol|safe }}
+!Sample_data_processing={{ row.dataProtocol|safe }}
+!Sample_molecule_ch1 = {{ row.extractMolecule }}
+!Sample_characteristics_ch1 = labExpId: {{ row.library_id }}
+!Sample_characteristics_ch1 = replicate: {{ row.replicate }}
+{% if row.cell %}{% spaceless %}
+!Sample_characteristics_ch1 = cell: {{ row.cell }}
+{% endspaceless %}{% endif %}
+{% if row.readType %}{% spaceless %}
+!Sample_characteristics_ch1 = readType: {{ row.readType }}
+{% endspaceless %}{% endif %}{% if row.antibody %}{% spaceless %}
+!Sample_characteristics_ch1 = cell: {{ row.antibody }}
+{% endspaceless %}{% endif %}{% for raw in row.raw %}
+!Sample_raw_file_{{forloop.counter}}={{raw.filename}}
+!Sample_raw_file_type_{{forloop.counter}}={{raw.file_type_label}}
+!Sample_raw_file_checksum_{{forloop.counter}}={{raw.md5sum}}{% endfor %}{% for sup in row.supplimental %}
+!Sample_supplementary_file_{{forloop.counter}}={{sup.filename}}
+!Sample_supplementary_file_checksum_{{forloop.counter}}={{sup.md5sum}}
+{% endfor %}{% endfor %}
\ No newline at end of file
+++ /dev/null
-PREFIX libraryOntology: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
-PREFIX submissionOntology: <http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#>
-PREFIX ucscDaf: <http://jumpgate.caltech.edu/wiki/UcscDaf#>
-PREFIX ncbiTaxon: <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=>
-
-select distinct ?name ?filename ?md5sum ?cell ?antibody ?sex ?control ?strain ?controlId ?labExpId ?labVersion ?treatment ?protocol ?readType ?insertLength ?replicate, ?mapAlgorithm ?species_name ?taxon_id
-WHERE {
- <{{submission}}> a submissionOntology:submission .
-
- OPTIONAL { ?submission ucscDaf:control ?control }
- #OPTIONAL { ?submission ucscDaf:controlId ?controlId }
- #OPTIONAL { ?library libraryOntology:antibody ?antibody }
- OPTIONAL { ?library libraryOntology:cell_line ?cell } .
- #OPTIONAL { ?library ucscDaf:sex ?sex }
- OPTIONAL { ?library libraryOntology:library_id ?labExpId }
- OPTIONAL { ?library libraryOntology:library_id ?labVersion }
- OPTIONAL { ?library libraryOntology:replicate ?replicate }
- OPTIONAL { ?library libraryOntology:species ?species_name }
-
- #OPTIONAL { ?library libraryOntology:condition_term ?treatment }
- #OPTIONAL { ?library ucscDaf:protocol ?protocol }
- #OPTIONAL { ?library ucscDaf:readType ?readType }
- #OPTIONAL { ?library ucscDaf:strain ?strain }
- #OPTIONAL { ?library libraryOntology:insert_size ?insertLength }
- #OPTIONAL { ?library ucscDaf:mapAlgorithm ?mapAlgorithm }
-
- <{{submission}}> submissionOntology:library ?library ;
- ucscDaf:has_file ?file ;
- submissionOntology:name ?name .
- ?species libraryOntology:species ?species_name ;
- libraryOntology:taxon_id ?taxon_id .
- ?file ucscDaf:filename ?filename .
-}
--- /dev/null
+<!DOCTYPE html>
+<html>
+ <head>
+ <title>Report</title>
+ <style>
+table {
+ border-spacing: 0;
+}
+
+table, td {
+ border-style: solid;
+}
+
+td { margin: 0;
+ border-width: 1px 1px 0 0;
+ padding: 4px;
+} </style>
+ </head>
+ <body>
+ <table>
+ <thead>
+ <tr>{% for k in results.0 %}
+ <td>{{k}}</td>{% endfor %}
+ </tr>
+ </thead>
+ <tbody>
+ {% for row in results %}<tr>{% for value in row.values %}
+ <td>{% spaceless %}
+ {% if value.url %}<a href="{{ value.url }}">{% endif%}
+ {{value.simple}}
+ {% if value.url %}</a>{% endif %}</td>{% endspaceless %}{% endfor %}
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+ </body>
+</html>
return a list of numbers and non-numeric substrings of +str+
the numeric substrings are converted to integer, non-numeric are left as is
"""
- if type(str) in types.StringTypes:
+ if type(str) in types.StringTypes:
chunks = re.findall("(\d+|\D+)",str)
#convert numeric strings to numbers
- chunks = [re.match('\d',x) and int(x) or x for x in chunks]
+ chunks = [re.match('\d',x) and int(x) or x for x in chunks]
return chunks
elif type(str) in [types.IntType, types.LongType, types.FloatType]:
return [str]
bChunks = chunkify(b)
return cmp(aChunks,bChunks) #built in comparison works once data is prepared
-
-
-
-if __name__ == "__main__":
- unsorted = ["1000X Radonius Maximus","10X Radonius","200X Radonius","20X Radonius","20X Radonius Prime","30X Radonius","40X Radonius","Allegia 50 Clasteron","Allegia 500 Clasteron","Allegia 51 Clasteron","Allegia 51B Clasteron","Allegia 52 Clasteron","Allegia 60 Clasteron","Alpha 100","Alpha 2","Alpha 200","Alpha 2A","Alpha 2A-8000","Alpha 2A-900","Callisto Morphamax","Callisto Morphamax 500","Callisto Morphamax 5000","Callisto Morphamax 600","Callisto Morphamax 700","Callisto Morphamax 7000","Callisto Morphamax 7000 SE","Callisto Morphamax 7000 SE2","QRS-60 Intrinsia Machine","QRS-60F Intrinsia Machine","QRS-62 Intrinsia Machine","QRS-62F Intrinsia Machine","Xiph Xlater 10000","Xiph Xlater 2000","Xiph Xlater 300","Xiph Xlater 40","Xiph Xlater 5","Xiph Xlater 50","Xiph Xlater 500","Xiph Xlater 5000","Xiph Xlater 58"]
- sorted = unsorted[:]
- sorted.sort(alphanum)
- print '+++++Sorted...++++'
- print '\n'.join(sorted)
"""Helper features for working with librdf
"""
+import collections
from datetime import datetime
+from urlparse import urlparse, urlunparse
+from urllib2 import urlopen
import logging
import os
import types
+import lxml.html
+import lxml.html.clean
import RDF
logger = logging.getLogger(__name__)
owlNS = RDF.NS('http://www.w3.org/2002/07/owl#')
dublinCoreNS = RDF.NS("http://purl.org/dc/elements/1.1/")
rdfNS = RDF.NS("http://www.w3.org/1999/02/22-rdf-syntax-ns#")
-rdfsNS= RDF.NS("http://www.w3.org/2000/01/rdf-schema#")
+rdfsNS = RDF.NS("http://www.w3.org/2000/01/rdf-schema#")
xsdNS = RDF.NS("http://www.w3.org/2001/XMLSchema#")
# internal ontologies
-submissionOntology = RDF.NS("http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#")
+submissionOntology = RDF.NS(
+ "http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#")
dafTermOntology = RDF.NS("http://jumpgate.caltech.edu/wiki/UcscDaf#")
libraryOntology = RDF.NS("http://jumpgate.caltech.edu/wiki/LibraryOntology#")
-inventoryOntology = RDF.NS("http://jumpgate.caltech.edu/wiki/InventoryOntology#")
+inventoryOntology = RDF.NS(
+ "http://jumpgate.caltech.edu/wiki/InventoryOntology#")
submissionLog = RDF.NS("http://jumpgate.caltech.edu/wiki/SubmissionsLog/")
+geoSoftNS = RDF.NS('http://www.ncbi.nlm.nih.gov/geo/info/soft2.html#')
ISOFORMAT_MS = "%Y-%m-%dT%H:%M:%S.%f"
ISOFORMAT_SHORT = "%Y-%m-%dT%H:%M:%S"
-def sparql_query(model, query_filename):
+
+def sparql_query(model, query_filename, output_format='text'):
"""Execute sparql query from file
"""
logger.info("Opening: %s" % (query_filename,))
- query_body = open(query_filename,'r').read()
+ query_body = open(query_filename, 'r').read()
query = RDF.SPARQLQuery(query_body)
results = query.execute(model)
- display_query_results(results)
+ if output_format == 'html':
+ html_query_results(results)
+ else:
+ display_query_results(results)
+
def display_query_results(results):
+ """A very simple display of sparql query results showing name value pairs
+ """
for row in results:
- output = []
- for k,v in row.items()[::-1]:
- print "{0}: {1}".format(k,v)
+ for k, v in row.items()[::-1]:
+ print "{0}: {1}".format(k, v)
print
+def html_query_results(result_stream):
+ from django.conf import settings
+ from django.template import Context, loader
+
+ # I did this because I couldn't figure out how to
+ # get simplify_rdf into the django template as a filter
+ class Simplified(object):
+ def __init__(self, value):
+ self.simple = simplify_rdf(value)
+ if value.is_resource():
+ self.url = value
+ else:
+ self.url = None
+
+ template = loader.get_template('rdf_report.html')
+ results = []
+ for row in result_stream:
+ new_row = collections.OrderedDict()
+ row_urls = []
+ for k,v in row.items():
+ new_row[k] = Simplified(v)
+ results.append(new_row)
+ context = Context({'results': results,})
+ print template.render(context)
def blankOrUri(value=None):
+ """Return a blank node for None or a resource node for strings.
+ """
node = None
if value is None:
node = RDF.Node()
def toTypedNode(value):
+ """Convert a python variable to a RDF Node with its closest xsd type
+ """
if type(value) == types.BooleanType:
value_type = xsdNS['boolean'].uri
if value:
node = RDF.Node(literal=unicode(value).encode('utf-8'))
return node
+
def fromTypedNode(node):
+ """Convert a typed RDF Node to its closest python equivalent
+ """
if node is None:
return None
- value_type = str(node.literal_value['datatype'])
- # chop off xml schema declaration
- value_type = value_type.replace(str(xsdNS[''].uri),'')
+ value_type = get_node_type(node)
literal = node.literal_value['string']
literal_lower = literal.lower()
elif value_type in ('dateTime'):
try:
return datetime.strptime(literal, ISOFORMAT_MS)
- except ValueError, e:
+ except ValueError, _:
return datetime.strptime(literal, ISOFORMAT_SHORT)
return literal
+def get_node_type(node):
+ """Return just the base name of a XSD datatype:
+ e.g. http://www.w3.org/2001/XMLSchema#integer -> integer
+ """
+ # chop off xml schema declaration
+ value_type = node.literal_value['datatype']
+ if value_type is None:
+ return "string"
+ else:
+ value_type = str(value_type)
+ return value_type.replace(str(xsdNS[''].uri), '')
+
+
+def simplify_rdf(value):
+ """Return a short name for a RDF object
+ e.g. The last part of a URI or an untyped string.
+ """
+ if isinstance(value, RDF.Node):
+ if value.is_resource():
+ name = simplify_uri(str(value.uri))
+ elif value.is_blank():
+ name = '<BLANK>'
+ else:
+ name = value.literal_value['string']
+ elif isinstance(value, RDF.Uri):
+ name = split_uri(str(value))
+ else:
+ name = value
+ return str(name)
+
+
+def simplify_uri(uri):
+ """Split off the end of a uri
+
+ >>> simplify_uri('http://asdf.org/foo/bar')
+ 'bar'
+ >>> simplify_uri('http://asdf.org/foo/bar#bleem')
+ 'bleem'
+ >>> simplify_uri('http://asdf.org/foo/bar/')
+ 'bar'
+ >>> simplify_uri('http://asdf.org/foo/bar?was=foo')
+ 'was=foo'
+ """
+ parsed = urlparse(uri)
+ if len(parsed.query) > 0:
+ return parsed.query
+ elif len(parsed.fragment) > 0:
+ return parsed.fragment
+ elif len(parsed.path) > 0:
+ for element in reversed(parsed.path.split('/')):
+ if len(element) > 0:
+ return element
+ raise ValueError("Unable to simplify %s" % (uri,))
+
+def simplifyUri(namespace, term):
+ """Remove the namespace portion of a term
+
+ returns None if they aren't in common
+ """
+ if isinstance(term, RDF.Node):
+ if term.is_resource():
+ term = term.uri
+ else:
+ raise ValueError("This works on resources")
+ elif not isinstance(term, RDF.Uri):
+ raise ValueError("This works on resources")
+ term_s = str(term)
+ if not term_s.startswith(namespace._prefix):
+ return None
+ return term_s.replace(namespace._prefix, "")
+
+
def get_model(model_name=None, directory=None):
if directory is None:
directory = os.getcwd()
return model
-def load_into_model(model, parser_name, filename, ns=None):
- if not os.path.exists(filename):
- raise IOError("Can't find {0}".format(filename))
-
- data = open(filename, 'r').read()
+def load_into_model(model, parser_name, path, ns=None):
+ url_parts = list(urlparse(path))
+ if len(url_parts[0]) == 0:
+ url_parts[0] = 'file'
+ url_parts[2] = os.path.abspath(url_parts[2])
+ url = urlunparse(url_parts)
+ logger.info("Opening %s" % (url,))
+ req = urlopen(url)
+ logger.debug("request status: %s" % (req.code,))
+ if parser_name is None:
+ content_type = req.headers.get('Content-Type', None)
+ parser_name = guess_parser(content_type, path)
+ logger.debug("Guessed parser: %s" % (parser_name,))
+ data = req.read()
load_string_into_model(model, parser_name, data, ns)
def load_string_into_model(model, parser_name, data, ns=None):
if ns is None:
- ns = "http://localhost/"
-
+ ns = RDF.NS("http://localhost/")
+ imports = owlNS['imports']
rdf_parser = RDF.Parser(name=parser_name)
- rdf_parser.parse_string_into_model(model, data, ns)
+ for s in rdf_parser.parse_string_as_stream(data, ns):
+ if s.predicate == imports:
+ obj = str(s.object)
+ logger.info("Importing %s" % (obj,))
+ load_into_model(model, None, obj, ns)
+ if s.object.is_literal():
+ value_type = get_node_type(s.object)
+ if value_type == 'string':
+ s.object = sanitize_literal(s.object)
+ model.add_statement(s)
+
+
+def sanitize_literal(node):
+ """Clean up a literal string
+ """
+ if not isinstance(node, RDF.Node):
+ raise ValueError("sanitize_literal only works on RDF.Nodes")
+ element = lxml.html.fromstring(node.literal_value['string'])
+ cleaner = lxml.html.clean.Cleaner(page_structure=False)
+ element = cleaner.clean_html(element)
+ text = lxml.html.tostring(element)
+ p_len = 3
+ slash_p_len = 4
+
+ args = {'literal': text[p_len:-slash_p_len]}
+ datatype = node.literal_value['datatype']
+ if datatype is not None:
+ args['datatype'] = datatype
+ language = node.literal_value['language']
+ if language is not None:
+ args['language'] = language
+ return RDF.Node(**args)
+
+
+def guess_parser(content_type, pathname):
+ if content_type in ('application/rdf+xml'):
+ return 'rdfxml'
+ elif content_type in ('application/x-turtle'):
+ return 'turtle'
+ elif content_type in ('text/html'):
+ return 'rdfa'
+ elif content_type is None:
+ _, ext = os.path.splitext(pathname)
+ if ext in ('xml', 'rdf'):
+ return 'rdfxml'
+ elif ext in ('html'):
+ return 'rdfa'
+ elif ext in ('turtle'):
+ return 'turtle'
+ return 'guess'
def get_serializer(name='turtle'):
"""Return a serializer with our standard prefixes loaded
writer.set_namespace('ucscDaf', dafTermOntology._prefix)
return writer
+
def dump_model(model):
serializer = get_serializer()
print serializer.serialize_model_to_string(model)
--- /dev/null
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+
+<http://jumpgate.caltech.edu/wiki/TestCase>
+ rdfs:label "TestCase" .
\ No newline at end of file
for i in xrange(len(scratch)):
self.failUnlessEqual(scratch[i], sorted[i])
+ def test_long_names(self):
+ unsorted = ["1000X Radonius Maximus","10X Radonius","200X Radonius","20X Radonius","20X Radonius Prime","30X Radonius","40X Radonius","Allegia 50 Clasteron","Allegia 500 Clasteron","Allegia 51 Clasteron","Allegia 51B Clasteron","Allegia 52 Clasteron","Allegia 60 Clasteron","Alpha 100","Alpha 2","Alpha 200","Alpha 2A","Alpha 2A-8000","Alpha 2A-900","Callisto Morphamax","Callisto Morphamax 500","Callisto Morphamax 5000","Callisto Morphamax 600","Callisto Morphamax 700","Callisto Morphamax 7000","Callisto Morphamax 7000 SE","Callisto Morphamax 7000 SE2","QRS-60 Intrinsia Machine","QRS-60F Intrinsia Machine","QRS-62 Intrinsia Machine","QRS-62F Intrinsia Machine","Xiph Xlater 10000","Xiph Xlater 2000","Xiph Xlater 300","Xiph Xlater 40","Xiph Xlater 5","Xiph Xlater 50","Xiph Xlater 500","Xiph Xlater 5000","Xiph Xlater 58"]
+ expected = ['10X Radonius', '20X Radonius', '20X Radonius Prime', '30X Radonius', '40X Radonius', '200X Radonius', '1000X Radonius Maximus', 'Allegia 50 Clasteron', 'Allegia 51 Clasteron', 'Allegia 51B Clasteron', 'Allegia 52 Clasteron', 'Allegia 60 Clasteron', 'Allegia 500 Clasteron', 'Alpha 2', 'Alpha 2A', 'Alpha 2A-900', 'Alpha 2A-8000', 'Alpha 100', 'Alpha 200', 'Callisto Morphamax', 'Callisto Morphamax 500', 'Callisto Morphamax 600', 'Callisto Morphamax 700', 'Callisto Morphamax 5000', 'Callisto Morphamax 7000', 'Callisto Morphamax 7000 SE', 'Callisto Morphamax 7000 SE2', 'QRS-60 Intrinsia Machine', 'QRS-60F Intrinsia Machine', 'QRS-62 Intrinsia Machine', 'QRS-62F Intrinsia Machine', 'Xiph Xlater 5', 'Xiph Xlater 40', 'Xiph Xlater 50', 'Xiph Xlater 58', 'Xiph Xlater 300', 'Xiph Xlater 500', 'Xiph Xlater 2000', 'Xiph Xlater 5000', 'Xiph Xlater 10000']
+
+ s = unsorted[:]
+ s.sort(alphanum)
+ self.failUnlessEqual(s, expected)
+
+ def test_bad_input(self):
+ unsorted = [object(), (1,3j)]
+ s = unsorted[:]
+ self.failUnlessRaises(ValueError, s.sort, alphanum)
+
def suite():
return unittest.makeSuite(testAlphanum, 'test')
+import os
import unittest
import types
+
from datetime import datetime
from htsworkflow.util.rdfhelp import \
blankOrUri, \
- toTypedNode, \
+ dump_model, \
fromTypedNode, \
+ get_model, \
+ load_string_into_model, \
+ rdfsNS, \
+ toTypedNode, \
+ simplifyUri, \
+ sanitize_literal, \
xsdNS
try:
- import RDF
-
- class TestRDFHelp(unittest.TestCase):
- def test_typed_node_boolean(self):
- node = toTypedNode(True)
- self.failUnlessEqual(node.literal_value['string'], u'1')
- self.failUnlessEqual(str(node.literal_value['datatype']),
- 'http://www.w3.org/2001/XMLSchema#boolean')
-
- def test_typed_node_string(self):
- node = toTypedNode('hello')
- self.failUnlessEqual(node.literal_value['string'], u'hello')
- self.failUnless(node.literal_value['datatype'] is None)
-
- def test_blank_or_uri_blank(self):
- node = blankOrUri()
- self.failUnlessEqual(node.is_blank(), True)
-
- def test_blank_or_uri_url(self):
- s = 'http://google.com'
- node = blankOrUri(s)
- self.failUnlessEqual(node.is_resource(), True)
- self.failUnlessEqual(str(node.uri), s)
-
- def test_blank_or_uri_node(self):
- s = RDF.Node(RDF.Uri('http://google.com'))
- node = blankOrUri(s)
- self.failUnlessEqual(node.is_resource(), True)
- self.failUnlessEqual(node, s)
-
- def test_unicode_node_roundtrip(self):
- literal = u'\u5927'
- roundtrip = fromTypedNode(toTypedNode(literal))
- self.failUnlessEqual(roundtrip, literal)
- self.failUnlessEqual(type(roundtrip), types.UnicodeType)
-
- def test_datetime_no_microsecond(self):
- dateTimeType = xsdNS['dateTime'].uri
- short_isostamp = '2011-12-20T11:44:25'
- short_node = RDF.Node(literal=short_isostamp,
- datatype=dateTimeType)
- short_datetime = datetime(2011,12,20,11,44,25)
-
- self.assertEqual(fromTypedNode(short_node), short_datetime)
- self.assertEqual(toTypedNode(short_datetime), short_node)
- self.assertEqual(fromTypedNode(toTypedNode(short_datetime)),
- short_datetime)
-
- def test_datetime_with_microsecond(self):
- dateTimeType = xsdNS['dateTime'].uri
- long_isostamp = '2011-12-20T11:44:25.081776'
- long_node = RDF.Node(literal=long_isostamp,
- datatype=dateTimeType)
- long_datetime = datetime(2011,12,20,11,44,25,81776)
-
- self.assertEqual(fromTypedNode(long_node), long_datetime)
- self.assertEqual(toTypedNode(long_datetime), long_node)
- self.assertEqual(fromTypedNode(toTypedNode(long_datetime)),
- long_datetime)
-
- def suite():
- return unittest.makeSuite(testRdfHelp, 'test')
+ import RDF
+
+ class TestRDFHelp(unittest.TestCase):
+ def test_from_none(self):
+ self.failUnlessEqual(fromTypedNode(None), None)
+
+ def test_typed_node_boolean(self):
+ node = toTypedNode(True)
+ self.failUnlessEqual(node.literal_value['string'], u'1')
+ self.failUnlessEqual(str(node.literal_value['datatype']),
+ 'http://www.w3.org/2001/XMLSchema#boolean')
+
+ def test_bad_boolean(self):
+ node = RDF.Node(literal='bad', datatype=xsdNS['boolean'].uri)
+ self.failUnlessRaises(ValueError, fromTypedNode, node)
+
+ def test_typed_node_string(self):
+ node = toTypedNode('hello')
+ self.failUnlessEqual(node.literal_value['string'], u'hello')
+ self.failUnless(node.literal_value['datatype'] is None)
+
+ def test_typed_real_like(self):
+ num = 3.14
+ node = toTypedNode(num)
+ self.failUnlessEqual(fromTypedNode(node), num)
+
+ def test_typed_integer(self):
+ num = 3
+ node = toTypedNode(num)
+ self.failUnlessEqual(fromTypedNode(node), num)
+ self.failUnlessEqual(type(fromTypedNode(node)), type(num))
+
+ def test_typed_node_string(self):
+ s = "Argh matey"
+ node = toTypedNode(s)
+ self.failUnlessEqual(fromTypedNode(node), s)
+ self.failUnlessEqual(type(fromTypedNode(node)), types.UnicodeType)
+
+ def test_blank_or_uri_blank(self):
+ node = blankOrUri()
+ self.failUnlessEqual(node.is_blank(), True)
+
+ def test_blank_or_uri_url(self):
+ s = 'http://google.com'
+ node = blankOrUri(s)
+ self.failUnlessEqual(node.is_resource(), True)
+ self.failUnlessEqual(str(node.uri), s)
+
+ def test_blank_or_uri_node(self):
+ s = RDF.Node(RDF.Uri('http://google.com'))
+ node = blankOrUri(s)
+ self.failUnlessEqual(node.is_resource(), True)
+ self.failUnlessEqual(node, s)
+
+ def test_unicode_node_roundtrip(self):
+ literal = u'\u5927'
+ roundtrip = fromTypedNode(toTypedNode(literal))
+ self.failUnlessEqual(roundtrip, literal)
+ self.failUnlessEqual(type(roundtrip), types.UnicodeType)
+
+ def test_datetime_no_microsecond(self):
+ dateTimeType = xsdNS['dateTime'].uri
+ short_isostamp = '2011-12-20T11:44:25'
+ short_node = RDF.Node(literal=short_isostamp,
+ datatype=dateTimeType)
+ short_datetime = datetime(2011,12,20,11,44,25)
+
+ self.assertEqual(fromTypedNode(short_node), short_datetime)
+ self.assertEqual(toTypedNode(short_datetime), short_node)
+ self.assertEqual(fromTypedNode(toTypedNode(short_datetime)),
+ short_datetime)
+
+ def test_datetime_with_microsecond(self):
+ dateTimeType = xsdNS['dateTime'].uri
+ long_isostamp = '2011-12-20T11:44:25.081776'
+ long_node = RDF.Node(literal=long_isostamp,
+ datatype=dateTimeType)
+ long_datetime = datetime(2011,12,20,11,44,25,81776)
+
+ self.assertEqual(fromTypedNode(long_node), long_datetime)
+ self.assertEqual(toTypedNode(long_datetime), long_node)
+ self.assertEqual(fromTypedNode(toTypedNode(long_datetime)),
+ long_datetime)
+
+ def test_simplify_uri(self):
+ nsOrg = RDF.NS('example.org/example#')
+ nsCom = RDF.NS('example.com/example#')
+
+ term = 'foo'
+ node = nsOrg[term]
+ self.failUnlessEqual(simplifyUri(nsOrg, node), term)
+ self.failUnlessEqual(simplifyUri(nsCom, node), None)
+ self.failUnlessEqual(simplifyUri(nsOrg, node.uri), term)
+
+ def test_simplify_uri_exceptions(self):
+ nsOrg = RDF.NS('example.org/example#')
+ nsCom = RDF.NS('example.com/example#')
+
+ node = toTypedNode('bad')
+ self.failUnlessRaises(ValueError, simplifyUri, nsOrg, node)
+ self.failUnlessRaises(ValueError, simplifyUri, nsOrg, nsOrg)
+
+ def test_owl_import(self):
+ path, name = os.path.split(__file__)
+ loc = 'file://'+os.path.abspath(path)+'/'
+ model = get_model()
+ fragment = '''
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+
+_:a owl:imports "{loc}extra.turtle" .
+'''.format(loc=loc)
+ load_string_into_model(model, 'turtle', fragment, loc)
+ tc = RDF.Node(RDF.Uri('http://jumpgate.caltech.edu/wiki/TestCase'))
+ query = RDF.Statement(tc, rdfsNS['label'], None)
+ result = list(model.find_statements(query))
+ self.failUnlessEqual(len(result), 1)
+ self.failUnlessEqual(str(result[0].object), 'TestCase')
+
+ def test_sanitize_literal_text(self):
+ self.failUnlessRaises(ValueError, sanitize_literal, "hi")
+ hello_text = "hello"
+ hello_none = RDF.Node(hello_text)
+ self.failUnlessEqual(str(sanitize_literal(hello_none)),
+ hello_text)
+ hello_str = RDF.Node(literal=hello_text,
+ datatype=xsdNS['string'].uri)
+ hello_clean = sanitize_literal(hello_str)
+ self.failUnlessEqual(hello_clean.literal_value['string'],
+ hello_text)
+
+ def test_sanitize_literal_html(self):
+ hello = "hello <a onload='javascript:alert(\"foo\");' href='http://google.com'>google.com</a>, whats up?"
+ hello_clean = 'hello <a href="http://google.com">google.com</a>, whats up?'
+ hello_node = RDF.Node(literal=hello,
+ datatype=xsdNS['string'].uri)
+ hello_sanitized = sanitize_literal(hello_node)
+ self.failUnlessEqual(hello_sanitized.literal_value['string'],
+ hello_clean)
+
+ hostile = "hi <b>there</b><script type='text/javascript>alert('boo');</script><a href='javascript:alert('poke')>evil</a> scammer"
+ hostile_node = RDF.Node(hostile)
+ hostile_sanitized = sanitize_literal(hostile_node)
+ # so it drops the stuff after the javascript link.
+ # I suppose it could be worse
+ hostile_result = """hi <b>there</b>"""
+ self.failUnlessEqual(str(hostile_sanitized), hostile_result)
+
+
+ def suite():
+ return unittest.makeSuite(TestRDFHelp, 'test')
except ImportError, e:
print "Unable to test rdfhelp"
projects / htsworkflow.git / commitdiff
