"""
Process an eland result file
"""
- XML_VERSION = 1
+ XML_VERSION = 2
LANE = 'ElandLane'
SAMPLE_NAME = 'SampleName'
LANE_ID = 'LaneID'
+ END = 'End'
GENOME_MAP = 'GenomeMap'
GENOME_ITEM = 'GenomeItem'
MAPPED_READS = 'MappedReads'
ELAND_EXTENDED = 2
ELAND_EXPORT = 3
- def __init__(self, pathname=None, genome_map=None, eland_type=None, xml=None):
+ def __init__(self, pathname=None, lane_id=None, end=None, genome_map=None, eland_type=None, xml=None):
self.pathname = pathname
self._sample_name = None
- self._lane_id = None
+ self.lane_id = lane_id
+ self.end = end
self._reads = None
self._mapped_reads = None
self._match_codes = None
path, name = os.path.split(self.pathname)
split_name = name.split('_')
self._sample_name = split_name[0]
- self._lane_id = int(split_name[1])
def _get_sample_name(self):
if self._sample_name is None:
return self._sample_name
sample_name = property(_get_sample_name)
- def _get_lane_id(self):
- if self._lane_id is None:
- self._update_name()
- return self._lane_id
- lane_id = property(_get_lane_id)
-
def _get_reads(self):
if self._reads is None:
self._update()
sample_tag.text = self.sample_name
lane_tag = ElementTree.SubElement(lane, ElandLane.LANE_ID)
lane_tag.text = str(self.lane_id)
+ if self.end is not None:
+ end_tag = ElementTree.SubElement(lane, ElandLane.END)
+ end_tag.text = str(self.end)
genome_map = ElementTree.SubElement(lane, ElandLane.GENOME_MAP)
for k, v in self.genome_map.items():
item = ElementTree.SubElement(
if tag == ElandLane.SAMPLE_NAME.lower():
self._sample_name = element.text
elif tag == ElandLane.LANE_ID.lower():
- self._lane_id = int(element.text)
+ self.lane_id = int(element.text)
+ elif tag == ElandLane.END.lower():
+ self.end = int(element.text)
elif tag == ElandLane.GENOME_MAP.lower():
for child in element:
name = child.attrib['name']
"""
Summarize information from eland files
"""
- XML_VERSION = 1
+ XML_VERSION = 2
ELAND = 'ElandCollection'
LANE = 'Lane'
LANE_ID = 'id'
+ 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)
- def __len__(self):
- return len(self.results)
-
- def keys(self):
- return self.results.keys()
-
- def values(self):
- return self.results.values()
-
- def items(self):
- return self.results.items()
-
- def __getitem__(self, key):
- return self.results[key]
-
def get_elements(self):
root = ElementTree.Element(ELAND.ELAND,
{'version': unicode(ELAND.XML_VERSION)})
- for lane_id, lane in self.results.items():
- eland_lane = lane.get_elements()
- eland_lane.attrib[ELAND.LANE_ID] = unicode(lane_id)
- root.append(eland_lane)
+ 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()
+ eland_lane.attrib[ELAND.END] = unicode (end)
+ eland_lane.attrib[ELAND.LANE_ID] = unicode(lane_id)
+ root.append(eland_lane)
return root
def set_elements(self, tree):
raise ValueError('Expecting %s', ELAND.ELAND)
for element in list(tree):
lane_id = int(element.attrib[ELAND.LANE_ID])
+ end = int(element.attrib.get(ELAND.END, 0))
lane = ElandLane(xml=element)
- self.results[lane_id] = lane
+ self.results[end][lane_id] = 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 )
-def check_for_eland_file(basedir, lane_id, pattern):
- basename = pattern % (lane_id,)
+ basename = pattern % (full_lane_id,)
pathname = os.path.join(basedir, basename)
if os.path.exists(pathname):
return pathname
def eland(basedir, gerald=None, genome_maps=None):
e = ELAND()
- file_list = glob(os.path.join(basedir, "*_eland_result.txt"))
- if len(file_list) == 0:
- # lets handle compressed eland files too
- file_list = glob(os.path.join(basedir, "*_eland_result.txt.bz2"))
+ #file_list = glob(os.path.join(basedir, "*_eland_result.txt"))
+ #if len(file_list) == 0:
+ # # lets handle compressed eland files too
+ # file_list = glob(os.path.join(basedir, "*_eland_result.txt.bz2"))
lane_ids = range(1,9)
+ ends = [None, 1, 2]
+
# the order in patterns determines the preference for what
# will be found.
- patterns = ['s_%d_eland_result.txt',
- 's_%d_eland_result.txt.bz2',
- 's_%d_eland_result.txt.gz',
- 's_%d_eland_extended.txt',
- 's_%d_eland_extended.txt.bz2',
- 's_%d_eland_extended.txt.gz',
- 's_%d_eland_multi.txt',
- 's_%d_eland_multi.txt.bz2',
- 's_%d_eland_multi.txt.gz',]
-
- for lane_id in lane_ids:
- for p in patterns:
- pathname = check_for_eland_file(basedir, lane_id, p)
- if pathname is not None:
- break
- else:
- continue
- # 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
- path, name = os.path.split(pathname)
- logging.info("Adding eland file %s" %(name,))
- split_name = name.split('_')
- lane_id = int(split_name[1])
-
- 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
- genome_map = build_genome_fasta_map(genome_dir)
- else:
- genome_map = {}
+ patterns = ['s_%s_eland_result.txt',
+ 's_%s_eland_result.txt.bz2',
+ 's_%s_eland_result.txt.gz',
+ 's_%s_eland_extended.txt',
+ 's_%s_eland_extended.txt.bz2',
+ 's_%s_eland_extended.txt.gz',
+ 's_%s_eland_multi.txt',
+ 's_%s_eland_multi.txt.bz2',
+ 's_%s_eland_multi.txt.gz',]
+
+ for end in ends:
+ for lane_id in lane_ids:
+ for p in patterns:
+ pathname = check_for_eland_file(basedir, p, lane_id, end)
+ if pathname is not None:
+ break
+ else:
+ continue
+ # 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
+ path, name = os.path.split(pathname)
+ logging.info("Adding eland file %s" %(name,))
+ # split_name = name.split('_')
+ # lane_id = int(split_name[1])
+
+ 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
+ genome_map = build_genome_fasta_map(genome_dir)
+ else:
+ genome_map = {}
- eland_result = ElandLane(pathname, genome_map)
- e.results[lane_id] = eland_result
+ eland_result = ElandLane(pathname, lane_id, end, genome_map)
+ if end is None:
+ effective_end = 0
+ else:
+ effective_end = end - 1
+ e.results[effective_end][lane_id] = eland_result
return e
def build_genome_fasta_map(genome_dir):
projects / htsworkflow.git / blobdiff