matrix_auto_flag = int(matrix.find('AutoFlag').text)
matrix_auto_lane = int(matrix.find('AutoLane').text)
+ crosstalk = None
if matrix_auto_flag:
# we estimated the matrix from something in this run.
# though we don't really care which lane it was
matrix_path = os.path.join(bustard_path, 'Matrix', 's_02_matrix.txt')
- matrix = CrosstalkMatrix(matrix_path)
+ crosstalk = CrosstalkMatrix(matrix_path)
else:
- # the matrix was provided
matrix_elements = call_parameters.find('MatrixElements')
- if matrix_elements is None:
- raise RuntimeError('Expected to find MatrixElements in Bustard BaseCallParameters')
- matrix = CrosstalkMatrix(xml=matrix_elements)
+ # the matrix was provided
+ if matrix_elements is not None:
+ crosstalk = CrosstalkMatrix(xml=matrix_elements)
+ else:
+ # we have no crosstalk matrix?
+ pass
- return matrix
+ return crosstalk
class Bustard(object):
XML_VERSION = 2
def __init__(self, xml=None):
self.version = None
- self.date = date.today()
+ self.date = None
self.user = None
self.phasing = {}
self.crosstalk = None
self.set_elements(xml)
def _get_time(self):
+ if self.date is None:
+ return None
return time.mktime(self.date.timetuple())
time = property(_get_time, doc='return run time as seconds since epoch')
{'version': str(Bustard.XML_VERSION)})
version = ElementTree.SubElement(root, Bustard.SOFTWARE_VERSION)
version.text = self.version
- run_date = ElementTree.SubElement(root, Bustard.DATE)
- run_date.text = str(self.time)
- user = ElementTree.SubElement(root, Bustard.USER)
- user.text = self.user
+ if self.time is not None:
+ run_date = ElementTree.SubElement(root, Bustard.DATE)
+ run_date.text = str(self.time)
+ if self.user is not None:
+ user = ElementTree.SubElement(root, Bustard.USER)
+ user.text = self.user
params = ElementTree.SubElement(root, Bustard.PARAMETERS)
# add phasing parameters
for lane in LANE_LIST:
- params.append(self.phasing[lane].get_elements())
+ if self.phasing.has_key(lane):
+ params.append(self.phasing[lane].get_elements())
# add crosstalk matrix if it exists
if self.crosstalk is not None:
pathname = os.path.abspath(pathname)
path, name = os.path.split(pathname)
groups = name.split("_")
- 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]
+ 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
+
b.pathname = pathname
bustard_config_filename = os.path.join(pathname, 'config.xml')
paramfiles = glob(os.path.join(pathname, "params?.xml"))
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']
return b
xml_version = int(tree.attrib.get('version', 0))
if xml_version > Gerald.XML_VERSION:
logging.warn('XML tree is a higher version than this class')
+ self.eland_results = ELAND()
for element in list(tree):
tag = element.tag.lower()
if tag == Gerald.RUN_PARAMETERS.lower():
else:
logging.warn("Unrecognized tag %s" % (element.tag,))
-
def gerald(pathname):
g = Gerald()
- g.pathname = pathname
- path, name = os.path.split(pathname)
+ g.pathname = os.path.expanduser(pathname)
+ path, name = os.path.split(g.pathname)
logging.info("Parsing gerald config.xml")
- config_pathname = os.path.join(pathname, 'config.xml')
+ config_pathname = os.path.join(g.pathname, 'config.xml')
g.tree = ElementTree.parse(config_pathname).getroot()
# parse Summary.htm file
logging.info("Parsing Summary.htm")
- summary_pathname = os.path.join(pathname, 'Summary.htm')
+ summary_pathname = os.path.join(g.pathname, 'Summary.htm')
g.summary = Summary(summary_pathname)
# parse eland files
g.eland_results = eland(g.pathname, g)
VERSION_RE, \
EUROPEAN_STRPTIME
+SOFTWARE_NAMES = ('IPAR_1.01', 'IPAR_1.3', 'Intensities')
+
class Tiles(object):
def __init__(self, tree):
self.tree = tree.find("TileSelection")
def _get_cycles(self):
if self.tree is None:
- return None
+ raise RuntimeError("get cycles called before xml tree initalized")
cycles = self.tree.find("Cycles")
+ assert cycles is not None
if cycles is None:
return None
return cycles.attrib
tree = ElementTree.parse(paramfile).getroot()
run = tree.find('Run')
- if run.attrib.has_key('Name') and run.attrib['Name'].startswith("IPAR"):
+ if run.attrib.has_key('Name') and run.attrib['Name'] in SOFTWARE_NAMES:
return run
-
- return None
+ else:
+ logging.info("No run found")
+ return None
def ipar(pathname):
"""
Examine the directory at pathname and initalize a IPAR object
"""
- logging.info("Searching IPAR directory")
+ logging.info("Searching IPAR directory %s" % (pathname,))
i = IPAR()
i.pathname = pathname
# parse firecrest directory name
path, name = os.path.split(pathname)
groups = name.split('_')
- if groups[0] != 'IPAR':
+ if not (groups[0] == 'IPAR' or groups[0] == 'Intensities'):
raise ValueError('ipar can only process IPAR directories')
bustard_pattern = os.path.join(pathname, 'Bustard*')
elif glob(bustard_pattern) > 0:
i.matrix = None
# its still live.
- else:
- return None
# look for parameter xml file
- paramfile = os.path.join(path, '.params')
- if os.path.exists(paramfile):
- i.tree = load_ipar_param_tree(paramfile)
- mtime_local = os.stat(paramfile)[stat.ST_MTIME]
- i.time = mtime_local
+ paramfiles = [os.path.join(pathname, 'config.xml'),
+ os.path.join(path, '.params')]
+ for paramfile in paramfiles:
+ if os.path.exists(paramfile):
+ logging.info("Found IPAR Config file at: %s" % ( paramfile, ))
+ i.tree = load_ipar_param_tree(paramfile)
+ mtime_local = os.stat(paramfile)[stat.ST_MTIME]
+ i.time = mtime_local
+ return i
+
return i
def fromxml(tree):
f.set_elements(tree)
return f
-if __name__ == "__main__":
- i = ipar(os.path.expanduser('~/gec/081021_HWI-EAS229_0063_30HKUAAXX/Data/IPAR_1.01'))
- x = i.get_elements()
- j = fromxml(x)
+#if __name__ == "__main__":
+ #i = ipar(os.path.expanduser('~/gec/081021_HWI-EAS229_0063_30HKUAAXX/Data/IPAR_1.01'))
+ #x = i.get_elements()
+ #j = fromxml(x)
#ElementTree.dump(x)
- print j.date
- print j.start
- print j.stop
- print i.tiles.keys()
- print j.tiles.keys()
- print j.tiles.items()
- print j.file_list()
+ #print j.date
+ #print j.start
+ #print j.stop
+ #print i.tiles.keys()
+ #print j.tiles.keys()
+ #print j.tiles.items()
+ #print j.file_list()
VERSION_RE = "([0-9\.]+)"
USER_RE = "([a-zA-Z0-9]+)"
LANES_PER_FLOWCELL = 8
+LANE_LIST = range(1, LANES_PER_FLOWCELL+1)
from htsworkflow.util.alphanum import alphanum
from htsworkflow.util.ethelp import indent, flatten
def scan_post_image_analysis(runs, runfolder, image_analysis, pathname):
logging.info("Looking for bustard directories in %s" % (pathname,))
- bustard_glob = os.path.join(pathname, "Bustard*")
- for bustard_pathname in glob(bustard_glob):
+ bustard_dirs = glob(os.path.join(pathname, "Bustard*"))
+ # RTA BaseCalls looks enough like Bustard.
+ bustard_dirs.extend(glob(os.path.join(pathname, "BaseCalls")))
+ for bustard_pathname in bustard_dirs:
logging.info("Found bustard directory %s" % (bustard_pathname,))
b = bustard.bustard(bustard_pathname)
gerald_glob = os.path.join(bustard_pathname, 'GERALD*')
logging.info('Found firecrest in ' + datadir)
image_analysis = firecrest.firecrest(firecrest_pathname)
if image_analysis is None:
- logging.warn(
+ logging.warn(
"%s is an empty or invalid firecrest directory" % (firecrest_pathname,)
)
- else:
+ else:
scan_post_image_analysis(
runs, runfolder, image_analysis, firecrest_pathname
)
# scan for IPAR directories
- for ipar_pathname in glob(os.path.join(datadir,"IPAR_*")):
+ ipar_dirs = glob(os.path.join(datadir, "IPAR_*"))
+ # The Intensities directory from the RTA software looks a lot like IPAR
+ ipar_dirs.extend(glob(os.path.join(datadir, 'Intensities')))
+ for ipar_pathname in ipar_dirs:
logging.info('Found ipar directories in ' + datadir)
image_analysis = ipar.ipar(ipar_pathname)
if image_analysis is None:
- logging.warn(
+ logging.warn(
"%s is an empty or invalid IPAR directory" %(ipar_pathname,)
)
- else:
+ else:
scan_post_image_analysis(
runs, runfolder, image_analysis, ipar_pathname
)
from htsworkflow.pipelines import bustard
from htsworkflow.pipelines import gerald
+ gerald_dir = os.path.expanduser(gerald_dir)
bustard_dir = os.path.abspath(os.path.join(gerald_dir, '..'))
image_dir = os.path.abspath(os.path.join(gerald_dir, '..', '..'))
image_run = firecrest.firecrest(image_dir)
elif re.search('IPAR', short_image_dir, re.IGNORECASE) is not None:
image_run = ipar.ipar(image_dir)
+ elif re.search('Intensities', short_image_dir, re.IGNORECASE) is not None:
+ image_run = ipar.ipar(image_dir)
+
# if we din't find a run, report the error and return
if image_run is None:
msg = '%s does not contain an image processing step' % (image_dir,)
destination = os.path.join(gerald_dir, 'config.xml')
shutil.copy(source, destination)
+def make_rta_intensities_1460(data_dir, version='1.4.6.0'):
+ """
+ Construct an artificial RTA Intensities parameter file and directory
+ """
+ intensities_dir = os.path.join(data_dir, 'Intensities')
+ if not os.path.exists(intensities_dir):
+ os.mkdir(intensities_dir)
+
+ param_file = os.path.join(TESTDATA_DIR, 'rta_intensities_config.xml')
+ shutil.copy(param_file, os.path.join(intensities_dir, 'config.xml'))
+
+ return intensities_dir
+
+def make_rta_basecalls_1460(intensities_dir):
+ """
+ Construct an artificial RTA Intensities parameter file and directory
+ """
+ basecalls_dir = os.path.join(intensities_dir, 'BaseCalls')
+ if not os.path.exists(basecalls_dir):
+ os.mkdir(basecalls_dir)
+
+ param_file = os.path.join(TESTDATA_DIR, 'rta_basecalls_config.xml')
+ shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
+
+ return basecalls_dir
+
+
def make_matrix(matrix_filename):
contents = """# Auto-generated frequency response matrix
> A
--- /dev/null
+#!/usr/bin/env python
+
+from datetime import datetime, date
+import os
+import tempfile
+import shutil
+import unittest
+
+from htsworkflow.pipelines import eland
+from htsworkflow.pipelines import ipar
+from htsworkflow.pipelines import bustard
+from htsworkflow.pipelines import gerald
+from htsworkflow.pipelines import runfolder
+from htsworkflow.pipelines.runfolder import ElementTree
+
+from htsworkflow.pipelines.test.simulate_runfolder import *
+
+
+def make_runfolder(obj=None):
+ """
+ Make a fake runfolder, attach all the directories to obj if defined
+ """
+ # make a fake runfolder directory
+ temp_dir = tempfile.mkdtemp(prefix='tmp_runfolder_')
+
+ runfolder_dir = os.path.join(temp_dir,
+ '090608_HWI-EAS229_0117_4286GAAXX')
+ os.mkdir(runfolder_dir)
+
+ data_dir = os.path.join(runfolder_dir, 'Data')
+ os.mkdir(data_dir)
+
+ intensities_dir = make_rta_intensities_1460(data_dir)
+
+ basecalls_dir = make_rta_basecalls_1460(intensities_dir)
+
+ #make_phasing_params(bustard_dir)
+ #make_bustard_config132(bustard_dir)
+
+ gerald_dir = os.path.join(basecalls_dir,
+ 'GERALD_16-06-2009_diane')
+ os.mkdir(gerald_dir)
+ make_gerald_config_100(gerald_dir)
+ make_summary_ipar130_htm(gerald_dir)
+ make_eland_multi(gerald_dir, lane_list=[1,2,3,4,5,6,])
+ make_scarf(gerald_dir, lane_list=[7,])
+ make_fastq(gerald_dir, lane_list=[8,])
+
+ if obj is not None:
+ obj.temp_dir = temp_dir
+ obj.runfolder_dir = runfolder_dir
+ obj.data_dir = data_dir
+ obj.image_analysis_dir = intensities_dir
+ obj.bustard_dir = basecalls_dir
+ obj.gerald_dir = gerald_dir
+
+
+class RunfolderTests(unittest.TestCase):
+ """
+ Test components of the runfolder processing code
+ which includes firecrest, bustard, and gerald
+ """
+ def setUp(self):
+ # attaches all the directories to the object passed in
+ make_runfolder(self)
+
+ def tearDown(self):
+ shutil.rmtree(self.temp_dir)
+
+ def test_ipar(self):
+ """
+ Construct a firecrest object
+ """
+ i = ipar.ipar(self.image_analysis_dir)
+ self.failUnlessEqual(i.version, '1.4.6.0')
+ self.failUnlessEqual(i.start, 1)
+ self.failUnlessEqual(i.stop, 38)
+
+ xml = i.get_elements()
+ # just make sure that element tree can serialize the tree
+ xml_str = ElementTree.tostring(xml)
+
+ i2 = ipar.IPAR(xml=xml)
+ self.failUnlessEqual(i.version, i2.version)
+ self.failUnlessEqual(i.start, i2.start)
+ self.failUnlessEqual(i.stop, i2.stop)
+ self.failUnlessEqual(i.date, i2.date)
+
+ def test_bustard(self):
+ """
+ construct a bustard object
+ """
+ b = bustard.bustard(self.bustard_dir)
+ self.failUnlessEqual(b.version, '1.4.6.0')
+ self.failUnlessEqual(b.date, None)
+ self.failUnlessEqual(b.user, None)
+ self.failUnlessEqual(len(b.phasing), 0)
+
+ xml = b.get_elements()
+ b2 = bustard.Bustard(xml=xml)
+ self.failUnlessEqual(b.version, b2.version)
+ self.failUnlessEqual(b.date, b2.date )
+ self.failUnlessEqual(b.user, b2.user)
+
+ def test_gerald(self):
+ # 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(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
+ # instead of pythons default 0..8
+ genomes = [None,
+ '/g/mm9',
+ '/g/mm9',
+ '/g/elegans190',
+ '/g/arabidopsis01222004',
+ '/g/mm9',
+ '/g/mm9',
+ '/g/mm9',
+ '/g/mm9', ]
+
+ # test lane specific parameters from gerald config file
+ for i in range(1,9):
+ cur_lane = g.lanes[i]
+ self.failUnlessEqual(cur_lane.analysis, 'eland_extended')
+ self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
+ self.failUnlessEqual(cur_lane.read_length, '37')
+ self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
+
+ # I want to be able to use a simple iterator
+ for l in g.lanes.values():
+ self.failUnlessEqual(l.analysis, 'eland_extended')
+ self.failUnlessEqual(l.read_length, '37')
+ self.failUnlessEqual(l.use_bases, 'Y'*37)
+
+ # test data extracted from summary file
+ clusters = [None,
+ (126910, 4300), (165739, 6792),
+ (196565, 8216), (153897, 8501),
+ (135536, 3908), (154083, 9315),
+ (159991, 9292), (198479, 17671),]
+
+ self.failUnlessEqual(len(g.summary), 1)
+ for i in range(1,9):
+ summary_lane = g.summary[0][i]
+ self.failUnlessEqual(summary_lane.cluster, clusters[i])
+ self.failUnlessEqual(summary_lane.lane, i)
+
+ xml = g.get_elements()
+ # just make sure that element tree can serialize the tree
+ xml_str = ElementTree.tostring(xml)
+ g2 = gerald.Gerald(xml=xml)
+ return
+
+ # do it all again after extracting from the xml file
+ self.failUnlessEqual(g.version, g2.version)
+ self.failUnlessEqual(g.date, g2.date)
+ self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
+ self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
+
+ # test lane specific parameters from gerald config file
+ for i in range(1,9):
+ g_lane = g.lanes[i]
+ g2_lane = g2.lanes[i]
+ self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
+ self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
+ self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
+ self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
+
+ # test (some) summary elements
+ self.failUnlessEqual(len(g.summary), 1)
+ for i in range(1,9):
+ g_summary = g.summary[0][i]
+ g2_summary = g2.summary[0][i]
+ self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
+ self.failUnlessEqual(g_summary.lane, g2_summary.lane)
+
+ g_eland = g.eland_results
+ g2_eland = g2.eland_results
+ for lane in g_eland.results[0].keys():
+ g_results = g_eland.results[0][lane]
+ g2_results = g2_eland.results[0][lane]
+ self.failUnlessEqual(g_results.reads,
+ g2_results.reads)
+ if isinstance(g_results, eland.ElandLane):
+ self.failUnlessEqual(len(g_results.mapped_reads),
+ len(g2_results.mapped_reads))
+ for k in g_results.mapped_reads.keys():
+ self.failUnlessEqual(g_results.mapped_reads[k],
+ g2_results.mapped_reads[k])
+
+ self.failUnlessEqual(len(g_results.match_codes),
+ len(g2_results.match_codes))
+ for k in g_results.match_codes.keys():
+ self.failUnlessEqual(g_results.match_codes[k],
+ g2_results.match_codes[k])
+
+
+ def test_eland(self):
+ return
+ hg_map = {'Lambda.fa': 'Lambda.fa'}
+ for i in range(1,22):
+ short_name = 'chr%d.fa' % (i,)
+ long_name = 'hg18/chr%d.fa' % (i,)
+ hg_map[short_name] = long_name
+
+ genome_maps = { 1:hg_map, 2:hg_map, 3:hg_map, 4:hg_map,
+ 5:hg_map, 6:hg_map, 7:hg_map, 8:hg_map }
+ eland_container = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
+
+ # I added sequence lanes to the last 2 lanes of this test case
+ for i in range(1,7):
+ lane = eland_container.results[0][i]
+ self.failUnlessEqual(lane.reads, 6)
+ self.failUnlessEqual(lane.sample_name, "s")
+ self.failUnlessEqual(lane.lane_id, i)
+ self.failUnlessEqual(len(lane.mapped_reads), 17)
+ self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
+ self.failUnlessEqual(lane.match_codes['U0'], 3)
+ self.failUnlessEqual(lane.match_codes['R0'], 2)
+ self.failUnlessEqual(lane.match_codes['U1'], 1)
+ self.failUnlessEqual(lane.match_codes['R1'], 9)
+ self.failUnlessEqual(lane.match_codes['U2'], 0)
+ self.failUnlessEqual(lane.match_codes['R2'], 12)
+ self.failUnlessEqual(lane.match_codes['NM'], 1)
+ self.failUnlessEqual(lane.match_codes['QC'], 0)
+
+ # test scarf
+ lane = eland_container.results[0][7]
+ self.failUnlessEqual(lane.reads, 5)
+ self.failUnlessEqual(lane.sample_name, 's')
+ self.failUnlessEqual(lane.lane_id, 7)
+ self.failUnlessEqual(lane.sequence_type, eland.SequenceLane.SCARF_TYPE)
+
+ # test fastq
+ lane = eland_container.results[0][8]
+ self.failUnlessEqual(lane.reads, 3)
+ self.failUnlessEqual(lane.sample_name, 's')
+ self.failUnlessEqual(lane.lane_id, 8)
+ self.failUnlessEqual(lane.sequence_type, eland.SequenceLane.FASTQ_TYPE)
+
+ xml = eland_container.get_elements()
+ # just make sure that element tree can serialize the tree
+ xml_str = ElementTree.tostring(xml)
+ e2 = gerald.ELAND(xml=xml)
+
+ for i in range(1,9):
+ l1 = eland_container.results[0][i]
+ l2 = e2.results[0][i]
+ self.failUnlessEqual(l1.reads, l2.reads)
+ self.failUnlessEqual(l1.sample_name, l2.sample_name)
+ self.failUnlessEqual(l1.lane_id, l2.lane_id)
+ if isinstance(l1, eland.ElandLane):
+ self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
+ self.failUnlessEqual(len(l1.mapped_reads), 17)
+ for k in l1.mapped_reads.keys():
+ self.failUnlessEqual(l1.mapped_reads[k],
+ l2.mapped_reads[k])
+
+ self.failUnlessEqual(len(l1.match_codes), 9)
+ self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
+ for k in l1.match_codes.keys():
+ self.failUnlessEqual(l1.match_codes[k],
+ l2.match_codes[k])
+ elif isinstance(l1, eland.SequenceLane):
+ self.failUnlessEqual(l1.sequence_type, l2.sequence_type)
+
+ def test_runfolder(self):
+ return
+ runs = runfolder.get_runs(self.runfolder_dir)
+
+ # do we get the flowcell id from the filename?
+ self.failUnlessEqual(len(runs), 1)
+ name = 'run_4286GAAXX_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
+ self.failUnlessEqual(runs[0].name, name)
+
+ # do we get the flowcell id from the FlowcellId.xml file
+ make_flowcell_id(self.runfolder_dir, '207BTAAXY')
+ runs = runfolder.get_runs(self.runfolder_dir)
+ self.failUnlessEqual(len(runs), 1)
+ name = 'run_207BTAAXY_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
+ self.failUnlessEqual(runs[0].name, name)
+
+ r1 = runs[0]
+ xml = r1.get_elements()
+ xml_str = ElementTree.tostring(xml)
+
+ r2 = runfolder.PipelineRun(xml=xml)
+ self.failUnlessEqual(r1.name, r2.name)
+ self.failIfEqual(r2.image_analysis, None)
+ self.failIfEqual(r2.bustard, None)
+ self.failIfEqual(r2.gerald, None)
+
+
+def suite():
+ return unittest.makeSuite(RunfolderTests,'test')
+
+if __name__ == "__main__":
+ unittest.main(defaultTest="suite")
+
--- /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>0</AutoFlag>\r
+ <AutoLane>0</AutoLane>\r
+ <Cycle>0</Cycle>\r
+ <CycleOffset>0</CycleOffset>\r
+ <FirstCycle>1</FirstCycle>\r
+ <LastCycle>38</LastCycle>\r
+ <Read>1</Read>\r
+ </Matrix>\r
+ <Phasing Path="">\r
+ <AutoFlag>0</AutoFlag>\r
+ <AutoLane>0</AutoLane>\r
+ <Cycle>0</Cycle>\r
+ <CycleOffset>0</CycleOffset>\r
+ <FirstCycle>1</FirstCycle>\r
+ <LastCycle>38</LastCycle>\r
+ <Read>1</Read>\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="38" Number="38" />\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>38</LastCycle>\r
+ <RunFolder>D:\Runs\090608_HWI-EAS229_0117_4286GAAXX</RunFolder>\r
+ </ImagingReads>\r
+ <Instrument>HWI-EAS229</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>38</LastCycle>\r
+ <RunFolder>D:\Runs\090608_HWI-EAS229_0117_4286GAAXX</RunFolder>\r
+ </Reads>\r
+ <RunFolder>D:\Runs\090608_HWI-EAS229_0117_4286GAAXX</RunFolder>\r
+ <RunFolderDate>0</RunFolderDate>\r
+ <RunFolderId>0</RunFolderId>\r
+ </RunParameters>\r
+ <Software Name="RTA" Version="1.4.6.0" />\r
+ <TileSelection>\r
+ <Lane Index="1">\r
+ <Sample>s</Sample>\r
+ <TileRange Max="100" Min="1" />\r
+ </Lane>\r
+ <Lane Index="2">\r
+ <Sample>s</Sample>\r
+ <TileRange Max="100" Min="1" />\r
+ </Lane>\r
+ <Lane Index="3">\r
+ <Sample>s</Sample>\r
+ <TileRange Max="100" Min="1" />\r
+ </Lane>\r
+ <Lane Index="4">\r
+ <Sample>s</Sample>\r
+ <TileRange Max="100" Min="1" />\r
+ </Lane>\r
+ <Lane Index="5">\r
+ <Sample>s</Sample>\r
+ <TileRange Max="100" Min="1" />\r
+ </Lane>\r
+ <Lane Index="6">\r
+ <Sample>s</Sample>\r
+ <TileRange Max="100" Min="1" />\r
+ </Lane>\r
+ <Lane Index="7">\r
+ <Sample>s</Sample>\r
+ <TileRange Max="100" Min="1" />\r
+ </Lane>\r
+ <Lane Index="8">\r
+ <Sample>s</Sample>\r
+ <TileRange Max="100" Min="1" />\r
+ </Lane>\r
+ </TileSelection>\r
+ <Time />\r
+ <User />\r
+ </Run>\r
+</BaseCallAnalysis>
\ No newline at end of file
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>\r
+<ImageAnalysis xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema">\r
+ <Run Name="Intensities">\r
+ <Cycles First="1" Last="38" Number="38" />\r
+ <ImageParameters>\r
+ <AutoOffsetFlag>0</AutoOffsetFlag>\r
+ <AutoSizeFlag>0</AutoSizeFlag>\r
+ <Fwhm>0</Fwhm>\r
+ <RemappingDistance>0</RemappingDistance>\r
+ <Threshold>0</Threshold>\r
+ </ImageParameters>\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>38</LastCycle>\r
+ <RunFolder>D:\Runs\090608_HWI-EAS229_0117_4286GAAXX</RunFolder>\r
+ </ImagingReads>\r
+ <Instrument>HWI-EAS229</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>38</LastCycle>\r
+ <RunFolder>D:\Runs\090608_HWI-EAS229_0117_4286GAAXX</RunFolder>\r
+ </Reads>\r
+ <RunFolderDate>090608</RunFolderDate>\r
+ <RunFolderId>117</RunFolderId>\r
+ </RunParameters>\r
+ <Software Name="RTA" Version="1.4.6.0" />\r
+ <TileSelection>\r
+ <Lane Index="1">\r
+ <Sample>s</Sample>\r
+ <Tile>1</Tile>\r
+ <Tile>2</Tile>\r
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+ </TileSelection>\r
+ <Time />\r
+ <User />\r
+ </Run>\r
+</ImageAnalysis>
\ No newline at end of file
projects / htsworkflow.git / commitdiff