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 in matched_paths:
+ if unaligned is None:
+ LOGGER.warn("Aligned directory %s without matching unalinged, skipping", aligned)
+ continue
+
+ g = gerald.gerald(aligned)
+ print "scan for aligned then remove them from unaligned list"
+ try:
+ p = PipelineRun(runfolder, flowcell_id)
+ p.datadir = datadir
+ p.image_analysis = image_analysis
+ p.bustard = bustard.bustard(unaligned)
+ 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))
+ 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
projects / htsworkflow.git / blobdiff