import re
import stat
import sys
+import types
-from htsworkflow.pipelines.runfolder import ElementTree, LANE_LIST
+from htsworkflow.pipelines import ElementTree, LANE_LIST
+from htsworkflow.pipelines.samplekey import SampleKey
+from htsworkflow.pipelines.genomemap import GenomeMap
from htsworkflow.util.ethelp import indent, flatten
from htsworkflow.util.opener import autoopen
XML_VERSION = 2
LANE = 'ResultLane'
- def __init__(self, pathnames=None, lane_id=None, end=None, xml=None):
+ def __init__(self, pathnames=None, sample=None, lane_id=None, end=None,
+ xml=None):
self.pathnames = pathnames
- self._sample_name = None
+ self.sample_name = sample
self.lane_id = lane_id
self.end = end
self._reads = None
"""
pass
- def _update_name(self):
- # extract the sample name
- if self.pathnames is None or len(self.pathnames) == 0:
- return
-
- sample_names = set()
- for pathname in self.pathnames:
- path, name = os.path.split(pathname)
- split_name = name.split('_')
- sample_names.add(split_name[0])
- if len(sample_names) > 1:
- errmsg = "Attempting to update from more than one sample %s"
- raise RuntimeError(errmsg % (",".join(sample_names)))
- self._sample_name = sample_names.pop()
- return self._sample_name
-
- def _get_sample_name(self):
- if self._sample_name is None:
- self._update_name()
- return self._sample_name
- sample_name = property(_get_sample_name)
-
def _get_reads(self):
if self._reads is None:
self._update()
def get_elements(self):
return None
+ def __repr__(self):
+ name = []
+
+ name.append('L%s' % (self.lane_id,))
+ name.append('R%s' % (self.end,))
+ name.append('S%s' % (self.sample_name,))
+
+ return '<ResultLane(' + ",".join(name) + ')>'
+
class ElandLane(ResultLane):
"""
Process an eland result file
SCORE_QC = 1
SCORE_READ = 2
- def __init__(self, pathnames=None, lane_id=None, end=None, genome_map=None, eland_type=None, xml=None):
- super(ElandLane, self).__init__(pathnames, lane_id, end)
+ def __init__(self, pathnames=None, sample=None, lane_id=None, end=None,
+ genome_map=None, eland_type=None, xml=None):
+ super(ElandLane, self).__init__(pathnames, sample, lane_id, end)
self._mapped_reads = None
self._match_codes = None
- if genome_map is None:
- genome_map = {}
- self.genome_map = genome_map
+ self._reads = None
+ self.genome_map = GenomeMap(genome_map)
self.eland_type = None
if xml is not None:
self.set_elements(xml)
+ def __repr__(self):
+ name = []
+
+ name.append('L%s' % (self.lane_id,))
+ name.append('R%s' % (self.end,))
+ name.append('S%s' % (self.sample_name,))
+
+ reads = str(self._reads) if self._reads is not None else 'Uncounted'
+ return '<ElandLane(' + ",".join(name) + ' = '+ reads + ')>'
+
def _guess_eland_type(self, pathname):
if self.eland_type is None:
# attempt autodetect eland file type
for element in tree:
tag = element.tag.lower()
if tag == SAMPLE_NAME.lower():
- self._sample_name = element.text
+ self.sample_name = element.text
elif tag == LANE_ID.lower():
self.lane_id = int(element.text)
elif tag == END.lower():
FASTQ_TYPE = 2
SEQUENCE_DESCRIPTION = { NONE_TYPE: 'None', SCARF_TYPE: 'SCARF', FASTQ_TYPE: 'FASTQ' }
- def __init__(self, pathname=None, lane_id=None, end=None, xml=None):
+ def __init__(self, pathnames=None, sample=None, lane_id=None, end=None,
+ xml=None):
self.sequence_type = None
- super(SequenceLane, self).__init__(pathname, lane_id, end, xml)
+ super(SequenceLane, self).__init__(pathnames, sample, lane_id, end, xml)
def _guess_sequence_type(self, pathname):
"""
for element in tree:
tag = element.tag.lower()
if tag == SAMPLE_NAME.lower():
- self._sample_name = element.text
+ self.sample_name = element.text
elif tag == LANE_ID.lower():
self.lane_id = int(element.text)
elif tag == END.lower():
else:
LOGGER.warn("SequenceLane unrecognized tag %s" % (element.tag,))
-class ELAND(object):
+class ELAND(collections.MutableMapping):
"""
Summarize information from eland files
"""
ELAND = 'ElandCollection'
LANE = 'Lane'
LANE_ID = 'id'
+ SAMPLE = 'sample'
END = 'end'
def __init__(self, xml=None):
# we need information from the gerald config.xml
- self.results = [{},{}]
+ self.results = {}
if xml is not None:
self.set_elements(xml)
- if len(self.results[0]) == 0:
- # Initialize our eland object with meaningless junk
- for l in LANE_LIST:
- self.results[0][l] = ResultLane(lane_id=l, end=0)
+ def __getitem__(self, key):
+ if not isinstance(key, SampleKey):
+ raise ValueError("Key must be a %s" % (str(type(SampleKey))))
+ return self.results[key]
+
+ def __setitem__(self, key, value):
+ if not isinstance(key, SampleKey):
+ raise ValueError("Key must be a %s" % (str(type(SampleKey))))
+ self.results[key] = value
+
+ def __delitem__(self, key):
+ del self.result[key]
+
+ def __iter__(self):
+ keys = self.results.iterkeys()
+ for k in sorted(keys):
+ yield k
+
+ def __len__(self):
+ return len(self.results)
+ def find_keys(self, search):
+ """Return results that match key"""
+ if not isinstance(search, SampleKey):
+ raise ValueError("Key must be a %s" % (str(type(SampleKey))))
+ if not search.iswild:
+ yield self[search]
+ for key in self.keys():
+ if key.matches(search): yield key
def get_elements(self):
root = ElementTree.Element(ELAND.ELAND,
{'version': unicode(ELAND.XML_VERSION)})
- for end in range(len(self.results)):
- end_results = self.results[end]
- for lane_id, lane in end_results.items():
- eland_lane = lane.get_elements()
- if eland_lane is not None:
- eland_lane.attrib[ELAND.END] = unicode (end)
- eland_lane.attrib[ELAND.LANE_ID] = unicode(lane_id)
- root.append(eland_lane)
+
+ for key in self:
+ eland_lane = self[key].get_elements()
+ eland_lane.attrib[ELAND.END] = unicode(self[key].end-1)
+ eland_lane.attrib[ELAND.LANE_ID] = unicode(self[key].lane_id)
+ eland_lane.attrib[ELAND.SAMPLE] = unicode(self[key].sample_name)
+ root.append(eland_lane)
+ return root
return root
def set_elements(self, tree):
for element in list(tree):
lane_id = int(element.attrib[ELAND.LANE_ID])
end = int(element.attrib.get(ELAND.END, 0))
+ sample = element.attrib.get(ELAND.SAMPLE, 's')
if element.tag.lower() == ElandLane.LANE.lower():
lane = ElandLane(xml=element)
elif element.tag.lower() == SequenceLane.LANE.lower():
lane = SequenceLane(xml=element)
- self.results[end][lane_id] = lane
+ key = SampleKey(lane=lane_id, read=end+1, sample=sample)
+ self.results[key] = lane
-def check_for_eland_file(basedir, pattern, lane_id, end):
- #if end is None:
- # full_lane_id = lane_id
- #else:
- # full_lane_id = "%d_%d" % ( lane_id, end )
- eland_files = []
- eland_pattern = pattern % (lane_id, end)
- eland_re = re.compile(eland_pattern)
- LOGGER.debug("Eland pattern: %s" %(eland_pattern,))
- for filename in os.listdir(basedir):
- if eland_re.match(filename):
- LOGGER.info('found eland file %s' % (filename,))
- eland_files.append(os.path.join(basedir, filename))
- return eland_files
+ def update_result_with_eland(self, gerald, key, pathnames,
+ genome_maps):
+ # yes the lane_id is also being computed in ElandLane._update
+ # I didn't want to clutter up my constructor
+ # but I needed to persist the sample_name/lane_id for
+ # runfolder summary_report
+ names = [ os.path.split(p)[1] for p in pathnames]
+ LOGGER.info("Adding eland files %s" %(",".join(names),))
+ basedir = os.path.split(pathnames[0])[0]
+ gs_template = "{0}_*_L{1:03}_genomesize.xml"
+ genomesize = glob(
+ os.path.join(basedir,
+ gs_template.format(key.sample, key.lane)))
-def update_result_with_eland(gerald, results, lane_id, end, pathnames, genome_maps):
- # yes the lane_id is also being computed in ElandLane._update
- # I didn't want to clutter up my constructor
- # but I needed to persist the sample_name/lane_id for
- # runfolder summary_report
- names = [ os.path.split(p)[1] for p in pathnames]
- LOGGER.info("Adding eland files %s" %(",".join(names),))
- genome_map = {}
- if genome_maps is not None:
- genome_map = genome_maps[lane_id]
- elif gerald is not None:
- genome_dir = gerald.lanes[lane_id].eland_genome
- if genome_dir is not None:
- genome_map = build_genome_fasta_map(genome_dir)
+ genome_map = GenomeMap()
+ if genome_maps is not None:
+ genome_map = GenomeMap(genome_maps[key.lane])
+ elif len(genomesize) > 0:
+ LOGGER.info("Found {0}".format(genomesize))
+ genome_map.parse_genomesize(genomesize[0])
+ elif gerald is not None:
+ genome_dir = gerald.lanes[key].eland_genome
+ if genome_dir is not None:
+ genome_map.scan_genome_dir(genome_dir)
- lane = ElandLane(pathnames, lane_id, end, genome_map)
+ lane = ElandLane(pathnames, key.sample, key.lane, key.read, genome_map)
- if end is None:
- effective_end = 0
- else:
- effective_end = end - 1
+ self.results[key] = lane
- results[effective_end][lane_id] = lane
+ def update_result_with_sequence(self, gerald, key, pathnames,
+ genome_maps=None):
+ self.results[key] = SequenceLane(pathnames,
+ key.sample, key.lane, key.read)
-def update_result_with_sequence(gerald, results, lane_id, end, pathname):
- result = SequenceLane(pathname, lane_id, end)
- if end is None:
- effective_end = 0
- else:
- effective_end = end - 1
+def eland(gerald_dir, gerald=None, genome_maps=None):
+ e = ELAND()
+ eland_files = ElandMatches(e)
+ # collect
+ for path, dirnames, filenames in os.walk(gerald_dir):
+ for filename in filenames:
+ pathname = os.path.abspath(os.path.join(path, filename))
+ eland_files.add(pathname)
+ for key in eland_files:
+ eland_files.count(key, gerald, genome_maps)
+ return e
- results[effective_end][lane_id] = result
+class ElandMatches(collections.MutableMapping):
+ def __init__(self, eland_container):
+ # the order in patterns determines the preference for what
+ # will be found.
+ self.eland_container = eland_container
+ MAPPED = eland_container.update_result_with_eland
+ SEQUENCE = eland_container.update_result_with_sequence
+
+ sample = '(?P<sample>[^_]+)'
+ hiIndex = '_(?P<index>(NoIndex|[AGCT])+)'
+ hiLane = '_L(?P<lane>[\d]+)'
+ gaLane = '_(?P<lane>[\d]+)'
+ hiRead = '_R(?P<read>[\d]+)'
+ gaRead = '(_(?P<read>[\d])+)?'
+ part = '_(?P<part>[\d]+)'
+ ext = '(?P<extention>(\.bz2|\.gz)?)'
+
+ hiPrefix = sample + hiIndex + hiLane + hiRead + part
+ gaPrefix = sample + gaLane + gaRead
+ P = collections.namedtuple('Patterns', 'pattern counter priority')
+ self.patterns = [
+ P(hiPrefix +'_export.txt' + ext, MAPPED, 6),
+ P(gaPrefix + '_eland_result.txt' + ext, MAPPED, 5),
+ P(gaPrefix + '_eland_extended.txt' + ext, MAPPED, 4),
+ P(gaPrefix + '_eland_multi.txt' + ext, MAPPED, 3),
+ P(gaPrefix + '_export.txt' + ext, MAPPED, 2),
+ P(gaPrefix + '_sequence.txt' + ext, SEQUENCE, 1),
+ ]
+ self.file_sets = {}
+ self.file_priority = {}
+ self.file_counter = {}
+
+ def add(self, pathname):
+ """Add pathname to our set of files
+ """
+ path, filename = os.path.split(pathname)
+
+ for pattern, counter, priority in self.patterns:
+ rematch = re.match(pattern, filename)
+ if rematch is not None:
+ m = ElandMatch(pathname, counter, **rematch.groupdict())
+ key = m.make_samplekey()
+ old_priority = self.file_priority.get(key, 0)
+ if priority > old_priority:
+ self.file_sets[key] = set((m,))
+ self.file_counter[key] = counter
+ self.file_priority[key] = priority
+ elif priority == old_priority:
+ self.file_sets[key].add(m)
+
+ def count(self, key, gerald=None, genome_maps=None):
+ #previous sig: gerald, e.results, lane_id, end, pathnames, genome_maps
+ counter = self.file_counter[key]
+ file_set = self.file_sets[key]
+ filenames = [ f.filename for f in file_set ]
+ return counter(gerald, key,
+ filenames, genome_maps)
-def eland(gerald_dir, gerald=None, genome_maps=None):
- e = ELAND()
+ def __iter__(self):
+ return iter(self.file_sets)
- lane_ids = range(1,9)
- ends = [None, 1, 2]
-
- basedirs = [gerald_dir]
-
- # if there is a basedir/Temp change basedir to point to the temp
- # directory, as 1.1rc1 moves most of the files we've historically
- # cared about to that subdirectory.
- # we should look into what the official 'result' files are.
- # and 1.3 moves them back
- basedir_temp = os.path.join(gerald_dir, 'Temp')
- if os.path.isdir(basedir_temp):
- basedirs.append(basedir_temp)
-
- # So how about scanning for Project*/Sample* directories as well
- sample_pattern = os.path.join(gerald_dir, 'Project_*', 'Sample_*')
- basedirs.extend(glob(sample_pattern))
-
- # the order in patterns determines the preference for what
- # will be found.
- MAPPED_ELAND = 0
- SEQUENCE = 1
- patterns = [
- ('(?P<sampleId>[^_]+)_(?P<index>(NoIndex|[AGCT])+)_L00%s(_R%s)_(?P<part>[\d]+)_export.txt(?P<ext>(\.bz2|\.gz)?)', MAPPED_ELAND),
- ('s_(?P<lane>%s)(_(?P<end>%s))?_eland_result.txt(?P<ext>(\.bz2|\.gz)?)',
- MAPPED_ELAND),
- ('s_(?P<lane>%s)(_(?P<end>%s))?_eland_extended.txt(?P<ext>(\.bz2|\.gz)?)',
- MAPPED_ELAND),
- ('s_(?P<lane>%s)(_(?P<end>%s))?_eland_multi.txt(?P<ext>(\.bz2|\.gz)?)',
- MAPPED_ELAND),
- ('s_(?P<lane>%s)(_(?P<end>%s))?_export.txt(?P<ext>(\.bz2|\.gz)?)',
- MAPPED_ELAND),
- ('s_(?P<lane>%s)(_(?P<end>%s))?_sequence.txt(?P<ext>(\.bz2|\.gz)?)',
- SEQUENCE),
-
- #('s_%s_eland_result.txt', MAPPED_ELAND),
- #('s_%s_eland_result.txt.bz2', MAPPED_ELAND),
- #('s_%s_eland_result.txt.gz', MAPPED_ELAND),
- #('s_%s_eland_extended.txt', MAPPED_ELAND),
- #('s_%s_eland_extended.txt.bz2', MAPPED_ELAND),
- #('s_%s_eland_extended.txt.gz', MAPPED_ELAND),
- #('s_%s_eland_multi.txt', MAPPED_ELAND),
- #('s_%s_eland_multi.txt.bz2', MAPPED_ELAND),
- #('s_%s_eland_multi.txt.gz', MAPPED_ELAND),
- #('s_%s_export.txt', MAPPED_ELAND),
- #('s_%s_export.txt.bz2', MAPPED_ELAND),
- #('s_%s_export.txt.gz', MAPPED_ELAND),
- #('s_%s_sequence.txt', SEQUENCE),
- ]
-
- for basedir in basedirs:
- for end in ends:
- for lane_id in lane_ids:
- for p in patterns:
- pathnames = check_for_eland_file(basedir, p[0], lane_id, end)
- if len(pathnames) > 0:
- if p[1] == MAPPED_ELAND:
- update_result_with_eland(gerald, e.results, lane_id, end, pathnames, genome_maps)
- elif p[1] == SEQUENCE:
- update_result_with_sequence(gerald, e.results, lane_id, end, pathnames)
- break
- else:
- LOGGER.debug("No eland file found in %s for lane %s and end %s" %(basedir, lane_id, end))
- continue
+ def __len__(self):
+ return len(self.file_sets)
- return e
+ def __getitem__(self, key):
+ return self.file_sets[key]
-def build_genome_fasta_map(genome_dir):
- # build fasta to fasta file map
- LOGGER.info("Building genome map")
- genome = genome_dir.split(os.path.sep)[-1]
- fasta_map = {}
- for vld_file in glob(os.path.join(genome_dir, '*.vld')):
- is_link = False
- if os.path.islink(vld_file):
- is_link = True
- vld_file = os.path.realpath(vld_file)
- path, vld_name = os.path.split(vld_file)
- name, ext = os.path.splitext(vld_name)
- if is_link:
- fasta_map[name] = name
- else:
- fasta_map[name] = os.path.join(genome, name)
- return fasta_map
+ def __setitem__(self, key, value):
+ if not isintance(value, set):
+ raise ValueError("Expected set for value")
+ self.file_sets[key] = value
+
+ def __delitem__(self, key):
+ del self.file_sets[key]
+
+class ElandMatch(object):
+ def __init__(self, pathname, counter,
+ lane=None, read=None, extension=None,
+ sample=None, index=None, part=None, **kwargs):
+ self.filename = pathname
+ self.counter = counter
+ self._lane = lane
+ self._read = read
+ self.extension = extension
+ self.sample = sample
+ self.index = index
+ self._part = part
+ LOGGER.info("Found %s: L%s R%s Samp%s" % (
+ self.filename, self._lane, self._read, self.sample))
+
+ def make_samplekey(self):
+ read = self._read if self._read is not None else 1
+ return SampleKey(lane=self.lane, read=read, sample=self.sample)
+
+ def _get_lane(self):
+ if self._lane is not None:
+ return int(self._lane)
+ return self._lane
+ lane = property(_get_lane)
+
+ def _get_read(self):
+ if self._read is not None:
+ return int(self._read)
+ return self._read
+ read = property(_get_read)
+
+ def _get_part(self):
+ if self._part is not None:
+ return int(self._part)
+ return self._part
+ part = property(_get_part)
+
+ def __repr__(self):
+ name = []
+ if self.sample is not None: name.append(self.sample)
+ if self._lane is not None: name.append('L%s' % (self.lane,))
+ if self._read is not None: name.append('R%s' % (self.read,))
+ if self._part is not None: name.append('P%s' % (self.part,))
+ return '<ElandMatch(' + "_".join(name) + ')>'
def extract_eland_sequence(instream, outstream, start, end):
for a in args:
LOGGER.info("Starting scan of %s" % (a,))
e = eland(a)
- print e.get_elements()
-
+ print ElementTree.tostring(e.get_elements())
return