def filter_chimeras(input_file, output_file, index_dir, bam_file,
weighted_unique_frags, median_isize, max_isize,
isoform_fraction, false_pos_file):
logging.debug("Filtering Parameters")
logging.debug("\tweighted unique fragments: %f" % (weighted_unique_frags))
logging.debug("\tmedian insert size: %d" % (median_isize))
logging.debug("\tmax insert size allowed: %d" % (max_isize))
logging.debug("\tfraction of wild-type isoform: %f" % (isoform_fraction))
logging.debug("\tfalse positive chimeras file: %s" % (false_pos_file))
# get false positive chimera list
if (false_pos_file is not None) and (false_pos_file is not ""):
logging.debug("Parsing false positive chimeras")
false_pos_pairs = read_false_pos_file(false_pos_file)
else:
false_pos_pairs = set()
# open BAM file for checking wild-type isoform
bamfh = pysam.Samfile(bam_file, "rb")
# filter chimeras
logging.debug("Checking chimeras")
num_chimeras = 0
num_filtered_chimeras = 0
tmp_file = make_temp(os.path.dirname(output_file), suffix=".txt")
f = open(tmp_file, "w")
for c in Chimera.parse(open(input_file)):
num_chimeras += 1
good = filter_weighted_frags(c, weighted_unique_frags)
if not good:
continue
good = good and filter_inner_dist(c, max_isize)
if not good:
continue
false_pos_key = (c.partner5p.tx_name, c.partner5p.end,
c.partner3p.tx_name, c.partner3p.start)
good = good and (false_pos_key not in false_pos_pairs)
if not good:
continue
good = good and filter_chimeric_isoform_fraction(
c, isoform_fraction, median_isize, bamfh)
if good:
print >> f, '\t'.join(map(str, c.to_list()))
num_filtered_chimeras += 1
f.close()
logging.debug("Total chimeras: %d" % num_chimeras)
logging.debug("Filtered chimeras: %d" % num_filtered_chimeras)
# cleanup memory for false positive chimeras
del false_pos_pairs
bamfh.close()
# find highest coverage chimeras among isoforms
gene_file = os.path.join(index_dir, config.GENE_FEATURE_FILE)
kept_chimeras = get_highest_coverage_isoforms(tmp_file, gene_file)
num_filtered_chimeras = 0
f = open(output_file, "w")
for c in Chimera.parse(open(tmp_file)):
if c.name in kept_chimeras:
num_filtered_chimeras += 1
print >> f, '\t'.join(map(str, c.to_list()))
f.close()
logging.debug("\tAfter choosing best isoform: %d" % num_filtered_chimeras)
os.remove(tmp_file)
return config.JOB_SUCCESS
def filter_spanning_chimeras(input_file, output_file, gene_file,
mate_pval, max_isize):
'''
processes chimera isoforms and chooses the one with the
highest coverage and omits the rest
'''
# apply more filters
tmpfile = make_temp(os.path.dirname(output_file), suffix='.bedpe')
fh = open(tmpfile, "w")
for c in SpanningChimera.parse(open(input_file)):
res = filter_insert_size(c, max_isize)
if res:
print >>fh, '\t'.join(['\t'.join(map(str,c.to_list()))])
fh.close()
# choose best isoform from remaining isoforms
logging.debug("Building gene/genome index")
ggmap = build_gene_to_genome_map(open(gene_file))
logging.debug("Choosing highest coverage chimeras")
fh = open(output_file, "w")
for c in choose_highest_coverage_chimeras(tmpfile, ggmap):
print >>fh, '\t'.join(['\t'.join(map(str,c.to_list()))])
fh.close()
# remove temporary file
os.remove(tmpfile)
def filter_spanning_chimeras(input_file, output_file, gene_file, mate_pval,
max_isize):
'''
processes chimera isoforms and chooses the one with the
highest coverage and omits the rest
'''
# apply more filters
tmpfile = make_temp(os.path.dirname(output_file), suffix='.bedpe')
fh = open(tmpfile, "w")
for c in SpanningChimera.parse(open(input_file)):
res = filter_insert_size(c, max_isize)
if res:
print >> fh, '\t'.join(['\t'.join(map(str, c.to_list()))])
fh.close()
# choose best isoform from remaining isoforms
logging.debug("Building gene/genome index")
ggmap = build_gene_to_genome_map(open(gene_file))
logging.debug("Choosing highest coverage chimeras")
fh = open(output_file, "w")
for c in choose_highest_coverage_chimeras(tmpfile, ggmap):
print >> fh, '\t'.join(['\t'.join(map(str, c.to_list()))])
fh.close()
# remove temporary file
os.remove(tmpfile)
def filter_chimeras(input_file, output_file,
index_dir, bam_file,
weighted_unique_frags,
median_isize,
max_isize,
isoform_fraction,
false_pos_file):
logging.debug("Filtering Parameters")
logging.debug("\tweighted unique fragments: %f" % (weighted_unique_frags))
logging.debug("\tmedian insert size: %d" % (median_isize))
logging.debug("\tmax insert size allowed: %d" % (max_isize))
logging.debug("\tfraction of wild-type isoform: %f" % (isoform_fraction))
logging.debug("\tfalse positive chimeras file: %s" % (false_pos_file))
# get false positive chimera list
if (false_pos_file is not None) and (false_pos_file is not ""):
logging.debug("Parsing false positive chimeras")
false_pos_pairs = read_false_pos_file(false_pos_file)
else:
false_pos_pairs = set()
# open BAM file for checking wild-type isoform
bamfh = pysam.Samfile(bam_file, "rb")
# filter chimeras
logging.debug("Checking chimeras")
num_chimeras = 0
num_filtered_chimeras = 0
tmp_file = make_temp(os.path.dirname(output_file), suffix=".txt")
f = open(tmp_file, "w")
for c in Chimera.parse(open(input_file)):
num_chimeras += 1
good = filter_weighted_frags(c, weighted_unique_frags)
if not good:
continue
good = good and filter_inner_dist(c, max_isize)
if not good:
continue
false_pos_key = (c.partner5p.tx_name, c.partner5p.end,
c.partner3p.tx_name, c.partner3p.start)
good = good and (false_pos_key not in false_pos_pairs)
if not good:
continue
good = good and filter_chimeric_isoform_fraction(c, isoform_fraction, median_isize, bamfh)
if good:
print >>f, '\t'.join(map(str, c.to_list()))
num_filtered_chimeras += 1
f.close()
logging.debug("Total chimeras: %d" % num_chimeras)
logging.debug("Filtered chimeras: %d" % num_filtered_chimeras)
# cleanup memory for false positive chimeras
del false_pos_pairs
bamfh.close()
# find highest coverage chimeras among isoforms
gene_file = os.path.join(index_dir, config.GENE_FEATURE_FILE)
kept_chimeras = get_highest_coverage_isoforms(tmp_file, gene_file)
num_filtered_chimeras = 0
f = open(output_file, "w")
for c in Chimera.parse(open(tmp_file)):
if c.name in kept_chimeras:
num_filtered_chimeras += 1
print >>f, '\t'.join(map(str, c.to_list()))
f.close()
logging.debug("\tAfter choosing best isoform: %d" %
num_filtered_chimeras)
os.remove(tmp_file)
return config.JOB_SUCCESS
