def split_gtf_file(gtf_file,
split_dir,
ref_gtf_file,
category_stats_file,
bufsize=(1 << 30)):
# split input gtf by library and mark test ids
keyfunc = lambda myid: os.path.join(split_dir, "%s.gtf" % (myid))
bufobj = BufferedFileSplitter(keyfunc, bufsize)
ref_fileh = open(ref_gtf_file, 'w')
stats_dict = collections.defaultdict(lambda: CategoryStats())
logging.info("Splitting transcripts by library")
for line in open(gtf_file):
f = GTFFeature.from_string(line)
is_ref = bool(int(f.attrs[GTFAttr.REF]))
if is_ref:
print >> ref_fileh, str(f)
continue
library_id = f.attrs[GTFAttr.LIBRARY_ID]
# keep statistics
if f.feature_type == 'transcript':
is_test = bool(int(f.attrs[GTFAttr.TEST]))
if is_test:
category = Category.SAME_STRAND
else:
category = int(f.attrs[GTFAttr.CATEGORY])
score = float(f.attrs[GTFAttr.SCORE])
statsobj = stats_dict[library_id]
statsobj.library_id = library_id
statsobj.counts[category] += 1
statsobj.signal[category] += score
# write features from each library to separate files
bufobj.write(library_id, line)
# close open file handles
ref_fileh.close()
bufobj.close()
logging.debug("Buffer flushes: %d" % (bufobj.flushes))
# write library category statistics
logging.info("Writing category statistics")
fh = open(category_stats_file, "w")
print >> fh, '\t'.join(CategoryStats.header_fields())
for statsobj in stats_dict.itervalues():
fields = statsobj.to_fields()
print >> fh, '\t'.join(map(str, fields))
fh.close()
def split_gtf_file(gtf_file, split_dir, ref_gtf_file, category_stats_file, bufsize=(1 << 30)):
# split input gtf by library and mark test ids
keyfunc = lambda myid: os.path.join(split_dir, "%s.gtf" % (myid))
bufobj = BufferedFileSplitter(keyfunc, bufsize)
ref_fileh = open(ref_gtf_file, "w")
stats_dict = collections.defaultdict(lambda: CategoryStats())
logging.info("Splitting transcripts by library")
for line in open(gtf_file):
f = GTFFeature.from_string(line)
is_ref = bool(int(f.attrs[GTFAttr.REF]))
if is_ref:
print >> ref_fileh, str(f)
continue
library_id = f.attrs[GTFAttr.LIBRARY_ID]
# keep statistics
if f.feature_type == "transcript":
is_test = bool(int(f.attrs[GTFAttr.TEST]))
if is_test:
category = Category.SAME_STRAND
else:
category = int(f.attrs[GTFAttr.CATEGORY])
score = float(f.attrs[GTFAttr.SCORE])
statsobj = stats_dict[library_id]
statsobj.library_id = library_id
statsobj.counts[category] += 1
statsobj.signal[category] += score
# write features from each library to separate files
bufobj.write(library_id, line)
# close open file handles
ref_fileh.close()
bufobj.close()
logging.debug("Buffer flushes: %d" % (bufobj.flushes))
# write library category statistics
logging.info("Writing category statistics")
fh = open(category_stats_file, "w")
print >> fh, "\t".join(CategoryStats.header_fields())
for statsobj in stats_dict.itervalues():
fields = statsobj.to_fields()
print >> fh, "\t".join(map(str, fields))
fh.close()
def annotate_gtf(gtf_file, bed_dbs):
# read reference databases
bed_trees = []
for name,filename in bed_dbs:
logging.debug("Loading BED db '%s' file '%s'" % (name,filename))
trees = build_interval_tree_from_bed(filename)
bed_trees.append((name, trees))
# parse gtf file and annotate
logging.debug("Annotating GTF")
for lines in parse_loci(open(gtf_file)):
features = []
transcripts = []
transcript_matches = collections.defaultdict(lambda: collections.defaultdict(lambda: set()))
for line in lines:
f = GTFFeature.from_string(line)
features.append(f)
t_id = f.attrs['transcript_id']
if f.feature_type == 'transcript':
transcripts.append(f)
elif f.feature_type == 'exon':
for dbname,dbtrees in bed_trees:
# intersect this exon with features
hits = dbtrees[f.seqid].find(f.start, f.end)
matches = set(hit.value for hit in hits if hit.strand == f.strand)
f.attrs[dbname] = ','.join(sorted(matches))
# update transcript level matches
transcript_matches[t_id][dbname].update(matches)
# set transcript annotations
for f in transcripts:
t_id = f.attrs['transcript_id']
for dbname,dbtrees in bed_trees:
matches = transcript_matches[t_id][dbname]
f.attrs[dbname] = ','.join(sorted(matches))
# write features
for f in features:
print str(f)
logging.debug("Done")
