-"""
-Core information needed to inspect a runfolder.
+"""Core information needed to inspect a runfolder.
"""
from glob import glob
import logging
import tarfile
import time
-import lxml.etree as ElementTree
-
LOGGER = logging.getLogger(__name__)
-EUROPEAN_STRPTIME = "%d-%m-%Y"
-EUROPEAN_DATE_RE = "([0-9]{1,2}-[0-9]{1,2}-[0-9]{4,4})"
-VERSION_RE = "([0-9\.]+)"
-USER_RE = "([a-zA-Z0-9]+)"
-LANES_PER_FLOWCELL = 8
-LANE_LIST = range(1, LANES_PER_FLOWCELL + 1)
-
+from htsworkflow.pipelines import firecrest
+from htsworkflow.pipelines import ipar
+from htsworkflow.pipelines import bustard
+from htsworkflow.pipelines import gerald
+from htsworkflow.pipelines import ElementTree, \
+ EUROPEAN_STRPTIME, EUROPEAN_DATE_RE, \
+ VERSION_RE, USER_RE, \
+ LANES_PER_FLOWCELL, LANE_LIST
+from htsworkflow.pipelines.samplekey import LANE_SAMPLE_KEYS
from htsworkflow.util.alphanum import alphanum
from htsworkflow.util.ethelp import indent, flatten
from htsworkflow.util.queuecommands import QueueCommands
from htsworkflow.pipelines import srf
class PipelineRun(object):
- """
- Capture "interesting" information about a pipeline run
+ """Capture "interesting" information about a pipeline run
+
+ :Variables:
+ - `pathname` location of the root of this runfolder
+ - `serialization_filename` read only property containing name of run xml file
+ - `flowcell_id` read-only property containing flowcell id (bar code)
+ - `datadir` location of the runfolder data dir.
+ - `image_analysis` generic name for Firecrest or IPAR image analysis
+ - `bustard` summary base caller
+ - `gerald` summary of sequence alignment and quality control metrics
"""
XML_VERSION = 1
PIPELINE_RUN = 'PipelineRun'
FLOWCELL_ID = 'FlowcellID'
def __init__(self, pathname=None, flowcell_id=None, xml=None):
+ """Initialize a PipelineRun object
+
+ :Parameters:
+ - `pathname` the root directory of this run folder.
+ - `flowcell_id` the flowcell ID in case it can't be determined
+ - `xml` Allows initializing an object from a serialized xml file.
+
+ :Types:
+ - `pathname` str
+ - `flowcell_id` str
+ - `ElementTree` str
+ """
if pathname is not None:
self.pathname = os.path.normpath(pathname)
else:
self._name = None
self._flowcell_id = flowcell_id
self.datadir = None
+ self.suffix = None
self.image_analysis = None
self.bustard = None
self.gerald = None
self.set_elements(xml)
def _get_flowcell_id(self):
+ """Return the flowcell ID
+
+ Attempts to find the flowcell ID through several mechanisms.
+ """
# extract flowcell ID
if self._flowcell_id is None:
self._flowcell_id = self._get_flowcell_id_from_runinfo()
def _get_flowcell_id_from_flowcellid(self):
"""Extract flowcell id from a Config/FlowcellId.xml file
+
+ :return: flowcell_id or None if not found
"""
config_dir = os.path.join(self.pathname, 'Config')
flowcell_id_path = os.path.join(config_dir, 'FlowcellId.xml')
def _get_flowcell_id_from_runinfo(self):
"""Read RunInfo file for flowcell id
+
+ :return: flowcell_id or None if not found
"""
runinfo = os.path.join(self.pathname, 'RunInfo.xml')
if os.path.exists(runinfo):
if len(fc_nodes) == 1:
return fc_nodes[0].text
-
def _get_flowcell_id_from_path(self):
"""Guess a flowcell name from the path
+
+ :return: flowcell_id or None if not found
"""
path_fields = self.pathname.split('_')
if len(path_fields) > 0:
return path_fields[-1]
def _get_runfolder_name(self):
- if self.gerald is None:
- return None
- else:
+ if self.gerald:
return self.gerald.runfolder_name
+ elif hasattr(self.image_analysis, 'runfolder_name'):
+ return self.image_analysis.runfolder_name
+ else:
+ return None
runfolder_name = property(_get_runfolder_name)
- def get_elements(self):
+ def _get_run_dirname(self):
+ """Return name of directory to hold result files from one analysis
+
+ For pre-multiplexing runs this is just the cycle range C1-123
+ For post-multiplexing runs the "suffix" that we add to
+ differentiate runs will be added to the range.
+ E.g. Unaligned_6mm may produce C1-200_6mm
"""
- make one master xml file from all of our sub-components.
+ if self.image_analysis is None:
+ raise ValueError("Not initialized yet")
+ start = self.image_analysis.start
+ stop = self.image_analysis.stop
+ cycle_fragment = "C%d-%d" % (start, stop)
+ if self.suffix:
+ cycle_fragment += self.suffix
+
+ return cycle_fragment
+ run_dirname = property(_get_run_dirname)
+
+ def get_elements(self):
+ """make one master xml file from all of our sub-components.
+
+ :return: an ElementTree containing all available pipeline
+ run xml compoents.
"""
root = ElementTree.Element(PipelineRun.PIPELINE_RUN)
flowcell = ElementTree.SubElement(root, PipelineRun.FLOWCELL_ID)
flowcell.text = self.flowcell_id
root.append(self.image_analysis.get_elements())
root.append(self.bustard.get_elements())
- root.append(self.gerald.get_elements())
+ if self.gerald:
+ root.append(self.gerald.get_elements())
return root
def set_elements(self, tree):
- # this file gets imported by all the others,
- # so we need to hide the imports to avoid a cyclic imports
- from htsworkflow.pipelines import firecrest
- from htsworkflow.pipelines import ipar
- from htsworkflow.pipelines import bustard
- from htsworkflow.pipelines import gerald
+ """Initialize a PipelineRun object from an run.xml ElementTree.
+ :param tree: parsed ElementTree
+ :type tree: ElementTree
+ """
tag = tree.tag.lower()
if tag != PipelineRun.PIPELINE_RUN.lower():
raise ValueError('Pipeline Run Expecting %s got %s' % (
else:
LOGGER.warn('PipelineRun unrecognized tag %s' % (tag,))
- def _get_run_name(self):
- """
- Given a run tuple, find the latest date and use that as our name
+ def _get_serialization_filename(self):
+ """Compute the filename for the run xml file
+
+ Attempts to find the latest date from all of the run
+ components.
+
+ :return: filename run_{flowcell id}_{timestamp}.xml
+ :rtype: str
"""
if self._name is None:
- tmax = max(self.image_analysis.time, self.bustard.time, self.gerald.time)
+ components = [self.image_analysis, self.bustard, self.gerald]
+ tmax = max([ c.time for c in components if c ])
timestamp = time.strftime('%Y-%m-%d', time.localtime(tmax))
self._name = 'run_' + self.flowcell_id + "_" + timestamp + '.xml'
return self._name
- name = property(_get_run_name)
+ serialization_filename = property(_get_serialization_filename)
def save(self, destdir=None):
+ """Save a run xml file.
+
+ :param destdir: Directory name to save too, uses current directory
+ if not specified.
+ :type destdir: str
+ """
if destdir is None:
destdir = ''
- LOGGER.info("Saving run report " + self.name)
+ LOGGER.info("Saving run report " + self.serialization_filename)
xml = self.get_elements()
indent(xml)
- dest_pathname = os.path.join(destdir, self.name)
+ dest_pathname = os.path.join(destdir, self.serialization_filename)
ElementTree.ElementTree(xml).write(dest_pathname)
def load(self, filename):
+ """Load a run xml into this object.
+
+ :Parameters:
+ - `filename` location of a run xml file
+
+ :Types:
+ - `filename` str
+ """
LOGGER.info("Loading run report from " + filename)
tree = ElementTree.parse(filename).getroot()
self.set_elements(tree)
Load and instantiate a Pipeline run from a run xml file
:Parameters:
- - `pathname` : location of an run xml file
+ - `pathname` location of an run xml file
:Returns: initialized PipelineRun object
"""
return run
def get_runs(runfolder, flowcell_id=None):
- """
- Search through a run folder for all the various sub component runs
- and then return a PipelineRun for each different combination.
+ """Find all runs associated with a runfolder.
+
+ We end up with multiple analysis runs as we sometimes
+ need to try with different parameters. This attempts
+ to return a list of all the various runs.
For example if there are two different GERALD runs, this will
generate two different PipelineRun objects, that differ
in there gerald component.
"""
- from htsworkflow.pipelines import firecrest
- from htsworkflow.pipelines import ipar
- from htsworkflow.pipelines import bustard
- from htsworkflow.pipelines import gerald
-
- def scan_post_image_analysis(runs, runfolder, datadir, image_analysis,
- pathname):
- added = build_aligned_runs(image_analysis, runs, datadir, runfolder)
- # If we're a multiplexed run, don't look for older run type.
- if added > 0:
- return
-
- LOGGER.info("Looking for bustard directories in %s" % (pathname,))
- 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:
- LOGGER.info("Found bustard directory %s" % (bustard_pathname,))
- b = bustard.bustard(bustard_pathname)
- build_gerald_runs(runs, b, image_analysis, bustard_pathname, datadir, pathname, runfolder)
-
-
- def build_gerald_runs(runs, b, image_analysis, bustard_pathname, datadir, pathname, runfolder):
- start = len(runs)
- 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))
- return len(runs) - start
-
-
- def build_aligned_runs(image_analysis, runs, datadir, runfolder):
- start = len(runs)
- 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)
- bustard_pathname = os.path.join(runfolder, g.runfolder_name)
-
- p.datadir = datadir
- p.image_analysis = image_analysis
- p.bustard = bustard.bustard(bustard_pathname)
- p.gerald = g
- runs.append(p)
- except IOError, e:
- LOGGER.error("Ignoring " + str(e))
- return len(runs) - start
datadir = os.path.join(runfolder, 'Data')
LOGGER.info('Searching for runs in ' + datadir)
)
else:
scan_post_image_analysis(
- runs, runfolder, datadir, image_analysis, firecrest_pathname
+ runs, runfolder, datadir, image_analysis, firecrest_pathname, flowcell_id
)
# scan for IPAR directories
ipar_dirs = glob(os.path.join(datadir, "IPAR_*"))
)
else:
scan_post_image_analysis(
- runs, runfolder, datadir, image_analysis, ipar_pathname
+ runs, runfolder, datadir, image_analysis, ipar_pathname, flowcell_id
)
return runs
+def scan_post_image_analysis(runs, runfolder, datadir, image_analysis,
+ pathname, flowcell_id):
+ added = build_hiseq_runs(image_analysis, runs, datadir, runfolder, flowcell_id)
+ # If we're a multiplexed run, don't look for older run type.
+ if added > 0:
+ return
+
+ LOGGER.info("Looking for bustard directories in %s" % (pathname,))
+ 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:
+ LOGGER.info("Found bustard directory %s" % (bustard_pathname,))
+ b = bustard.bustard(bustard_pathname)
+ build_gerald_runs(runs, b, image_analysis, bustard_pathname, datadir, pathname,
+ runfolder, flowcell_id)
+
+
+def build_gerald_runs(runs, b, image_analysis, bustard_pathname, datadir, pathname, runfolder,
+ flowcell_id):
+ start = len(runs)
+ 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))
+ return len(runs) - start
+
+
+def build_hiseq_runs(image_analysis, runs, datadir, runfolder, flowcell_id):
+ start = len(runs)
+ aligned_glob = os.path.join(runfolder, 'Aligned*')
+ unaligned_glob = os.path.join(runfolder, 'Unaligned*')
+
+ aligned_paths = glob(aligned_glob)
+ unaligned_paths = glob(unaligned_glob)
+
+ matched_paths = hiseq_match_aligned_unaligned(aligned_paths, unaligned_paths)
+ LOGGER.debug("Matched HiSeq analysis: %s", str(matched_paths))
+
+ for aligned, unaligned, suffix in matched_paths:
+ if unaligned is None:
+ LOGGER.warn("Aligned directory %s without matching unalinged, skipping", aligned)
+ continue
+
+ try:
+ p = PipelineRun(runfolder, flowcell_id)
+ p.datadir = datadir
+ p.suffix = suffix
+ p.image_analysis = image_analysis
+ p.bustard = bustard.bustard(unaligned)
+ assert p.bustard
+ if aligned:
+ p.gerald = gerald.gerald(aligned)
+ runs.append(p)
+ except IOError, e:
+ LOGGER.error("Ignoring " + str(e))
+ return len(runs) - start
+
+def hiseq_match_aligned_unaligned(aligned, unaligned):
+ """Match aligned and unaligned folders from seperate lists
+ """
+ unaligned_suffix_re = re.compile('Unaligned(?P<suffix>[\w]*)')
+
+ aligned_by_suffix = build_dir_dict_by_suffix('Aligned', aligned)
+ unaligned_by_suffix = build_dir_dict_by_suffix('Unaligned', unaligned)
+
+ keys = set(aligned_by_suffix.keys()).union(set(unaligned_by_suffix.keys()))
+
+ matches = []
+ for key in keys:
+ a = aligned_by_suffix.get(key)
+ u = unaligned_by_suffix.get(key)
+ matches.append((a, u, key))
+ return matches
+
+def build_dir_dict_by_suffix(prefix, dirnames):
+ """Build a dictionary indexed by suffix of last directory name.
+
+ It assumes a constant prefix
+ """
+ regex = re.compile('%s(?P<suffix>[\w]*)' % (prefix,))
+
+ by_suffix = {}
+ for absname in dirnames:
+ basename = os.path.basename(absname)
+ match = regex.match(basename)
+ if match:
+ by_suffix[match.group('suffix')] = absname
+ return by_suffix
+
def get_specific_run(gerald_dir):
"""
Given a gerald directory, construct a PipelineRun out of its parents
Summarize cluster numbers and mapped read counts for a runfolder
"""
report = []
+ eland_keys = []
for run in runs:
# print a run name?
- report.append('Summary for %s' % (run.name,))
+ report.append('Summary for %s' % (run.serialization_filename,))
# sort the report
- eland_keys = sorted(run.gerald.eland_results.keys())
+ if run.gerald:
+ eland_keys = sorted(run.gerald.eland_results.keys())
+ else:
+ report.append("Alignment not done, no report possible")
+
for lane_id in eland_keys:
report.extend(summarize_lane(run.gerald, lane_id))
report.append('---')
else:
return False
-def save_flowcell_reports(data_dir, cycle_dir):
+def save_flowcell_reports(data_dir, run_dirname):
"""
Save the flowcell quality reports
"""
data_dir = os.path.abspath(data_dir)
status_file = os.path.join(data_dir, 'Status.xml')
reports_dir = os.path.join(data_dir, 'reports')
- reports_dest = os.path.join(cycle_dir, 'flowcell-reports.tar.bz2')
+ reports_dest = os.path.join(run_dirname, 'flowcell-reports.tar.bz2')
if os.path.exists(reports_dir):
cmd_list = [ 'tar', 'cjvf', reports_dest, 'reports/' ]
if os.path.exists(status_file):
os.chdir(cwd)
-def save_summary_file(pipeline, cycle_dir):
+def save_summary_file(pipeline, run_dirname):
# Copy Summary.htm
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)
+ LOGGER.info('Copying %s to %s' % (gerald_summary, run_dirname))
+ shutil.copy(gerald_summary, run_dirname)
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)
+ LOGGER.info('Copying %s to %s' % (status_files_summary, run_dirname))
+ shutil.copy(status_files_summary, run_dirname)
else:
LOGGER.info('Summary file %s was not found' % (summary_path,))
-def save_ivc_plot(bustard_object, cycle_dir):
+def save_ivc_plot(bustard_object, run_dirname):
"""
Save the IVC page and its supporting images
"""
plot_image_path = os.path.join(bustard_object.pathname, 'Plots')
plot_images = os.path.join(plot_image_path, 's_?_[a-z]*.png')
- plot_target_path = os.path.join(cycle_dir, 'Plots')
+ plot_target_path = os.path.join(run_dirname, 'Plots')
if os.path.exists(plot_html):
LOGGER.debug("Saving %s" % (plot_html,))
LOGGER.debug("Saving %s" % (plot_images,))
- shutil.copy(plot_html, cycle_dir)
+ shutil.copy(plot_html, run_dirname)
if not os.path.exists(plot_target_path):
os.mkdir(plot_target_path)
for plot_file in glob(plot_images):
LOGGER.warning('Missing IVC.html file, not archiving')
-def compress_score_files(bustard_object, cycle_dir):
+def compress_score_files(bustard_object, run_dirname):
"""
Compress score files into our result directory
"""
tar_cmd = ['tar', 'c'] + score_files
bzip_cmd = [ 'bzip2', '-9', '-c' ]
- tar_dest_name = os.path.join(cycle_dir, 'scores.tar.bz2')
+ tar_dest_name = os.path.join(run_dirname, 'scores.tar.bz2')
tar_dest = open(tar_dest_name, 'w')
LOGGER.info("Compressing score files from %s" % (scores_path,))
LOGGER.info("Running tar: " + " ".join(tar_cmd[:10]))
tar.wait()
-def compress_eland_results(gerald_object, cycle_dir, num_jobs=1):
+def compress_eland_results(gerald_object, run_dirname, num_jobs=1):
"""
Compress eland result files into the archive directory
"""
"Lane ID %s does not have a filename." % (eland_lane.lane_id,))
else:
path, name = os.path.split(source_name)
- dest_name = os.path.join(cycle_dir, name)
+ dest_name = os.path.join(run_dirname, name)
LOGGER.info("Saving eland file %s to %s" % \
(source_name, dest_name))
if not os.path.exists(result_dir):
os.mkdir(result_dir)
- # create cycle_dir
- cycle = "C%d-%d" % (r.image_analysis.start, r.image_analysis.stop)
- LOGGER.info("Filling in %s" % (cycle,))
- cycle_dir = os.path.join(result_dir, cycle)
- cycle_dir = os.path.abspath(cycle_dir)
- if os.path.exists(cycle_dir):
- LOGGER.error("%s already exists, not overwriting" % (cycle_dir,))
+ # create directory to add this runs results to
+ LOGGER.info("Filling in %s" % (r.run_dirname,))
+ run_dirname = os.path.join(result_dir, r.run_dirname)
+ run_dirname = os.path.abspath(run_dirname)
+ if os.path.exists(run_dirname):
+ LOGGER.error("%s already exists, not overwriting" % (run_dirname,))
continue
else:
- os.mkdir(cycle_dir)
+ os.mkdir(run_dirname)
# save run file
- r.save(cycle_dir)
+ r.save(run_dirname)
# save illumina flowcell status report
save_flowcell_reports(os.path.join(r.image_analysis.pathname, '..'),
- cycle_dir)
+ run_dirname)
# save stuff from bustard
# grab IVC plot
- save_ivc_plot(r.bustard, cycle_dir)
+ save_ivc_plot(r.bustard, run_dirname)
# build base call saving commands
if site is not None:
- save_raw_data(num_jobs, r, site, raw_format, cycle_dir)
+ save_raw_data(num_jobs, r, site, raw_format, run_dirname)
# save stuff from GERALD
# copy stuff out of the main run
- g = r.gerald
+ if r.gerald:
+ g = r.gerald
- # save summary file
- save_summary_file(r, cycle_dir)
+ # save summary file
+ save_summary_file(r, run_dirname)
- # compress eland result files
- compress_eland_results(g, cycle_dir, num_jobs)
+ # compress eland result files
+ compress_eland_results(g, run_dirname, num_jobs)
# md5 all the compressed files once we're done
- md5_commands = srf.make_md5_commands(cycle_dir)
- srf.run_commands(cycle_dir, md5_commands, num_jobs)
+ md5_commands = srf.make_md5_commands(run_dirname)
+ srf.run_commands(run_dirname, md5_commands, num_jobs)
-def save_raw_data(num_jobs, r, site, raw_format, cycle_dir):
+def save_raw_data(num_jobs, r, site, raw_format, run_dirname):
lanes = []
- for lane in r.gerald.lanes:
- lane_parameters = r.gerald.lanes.get(lane, None)
- if lane_parameters is not None:
- lanes.append(lane)
+ if r.gerald:
+ for lane in r.gerald.lanes:
+ lane_parameters = r.gerald.lanes.get(lane, None)
+ if lane_parameters is not None:
+ lanes.append(lane)
+ else:
+ # assume default list of lanes
+ lanes = LANE_SAMPLE_KEYS
run_name = srf.pathname_to_run_name(r.pathname)
seq_cmds = []
LOGGER.info("Raw Format is: %s" % (raw_format, ))
if raw_format == 'fastq':
- rawpath = os.path.join(r.pathname, r.gerald.runfolder_name)
+ LOGGER.info("Reading fastq files from %s", r.bustard.pathname)
+ rawpath = os.path.join(r.pathname, r.bustard.pathname)
LOGGER.info("raw data = %s" % (rawpath,))
- srf.copy_hiseq_project_fastqs(run_name, rawpath, site, cycle_dir)
+ srf.copy_hiseq_project_fastqs(run_name, rawpath, site, run_dirname)
elif raw_format == 'qseq':
- seq_cmds = srf.make_qseq_commands(run_name, r.bustard.pathname, lanes, site, cycle_dir)
+ seq_cmds = srf.make_qseq_commands(run_name, r.bustard.pathname, lanes, site, run_dirname)
elif raw_format == 'srf':
- seq_cmds = srf.make_srf_commands(run_name, r.bustard.pathname, lanes, site, cycle_dir, 0)
+ seq_cmds = srf.make_srf_commands(run_name, r.bustard.pathname, lanes, site, run_dirname, 0)
else:
raise ValueError('Unknown --raw-format=%s' % (raw_format))
srf.run_commands(r.bustard.pathname, seq_cmds, num_jobs)
projects / htsworkflow.git / blobdiff