def nominate_spanning_reads(discordant_reads_fh, chimeras_fh, fastq_fh):
# build index of chimera candidates
logging.info("Indexing chimera candidates")
tx5p = collections.defaultdict(lambda: [])
tx3p = collections.defaultdict(lambda: [])
for chimera in Chimera.parse(chimeras_fh):
tx5p[chimera.mate5p.tx_name].append(chimera.mate5p.end)
tx3p[chimera.mate3p.tx_name].append(chimera.mate3p.start)
# parse discordant reads
logging.info("Nominating spanning reads")
read1, read2 = None, None
prev_qname = None
for frag in parse_discordant_reads(discordant_reads_fh):
if frag.discordant_type.is_genome:
continue
qname = frag.qname
if prev_qname is not None and (qname != prev_qname):
if read1 is not None:
print >> fastq_fh, read1
if read2 is not None:
print >> fastq_fh, read2
read1, read2 = None, None
# skip if reads already found
if (read1 is not None) and (read2 is not None):
continue
# update read fastq
r1, r2 = check_fragment(frag, tx5p, tx3p)
if read1 is None: read1 = r1
if read2 is None: read2 = r2
prev_qname = qname
if read1 is not None:
print >> fastq_fh, read1
if read2 is not None:
print >> fastq_fh, read2
def filter_encompassing_chimeras(input_file, output_file, gene_file,
max_multimap=1,
multimap_cov_ratio=0.10,
max_isize=1000,
strand_pval=0.01,
keep_overlap=False):
logging.debug("Filtering chimeras")
logging.debug("Must have a read with <= %d multimaps" % (max_multimap))
logging.debug("Coverage to reads ratio >= %f" % (multimap_cov_ratio))
logging.debug("Insert size < %d" % (max_isize))
logging.debug("Strand balance p-value > %f" % (strand_pval))
# first perform basic filtering
tmpfile1 = make_temp(base_dir=os.path.dirname(output_file),
suffix='.bedpe')
fh = open(tmpfile1, "w")
for c in Chimera.parse(open(input_file)):
res = filter_multimapping(c, max_multimap=max_multimap,
multimap_cov_ratio=multimap_cov_ratio)
res = res and filter_insert_size(c, max_isize)
if not keep_overlap:
res = res and filter_overlapping(c)
res = res and filter_strand_balance(c, strand_pval)
if res:
print >>fh, '\t'.join(map(str, c.to_list()))
fh.close()
logging.debug("Building gene/genome index")
ggmap = build_gene_to_genome_map(open(gene_file))
logging.debug("Finding junction permiscuity")
juncmap5p, juncmap3p = collect_permiscuity_stats(tmpfile1, ggmap)
fh = open(output_file, "w")
for c in Chimera.parse(open(tmpfile1)):
frac5p, frac3p = calc_permiscuity(c, juncmap5p, juncmap3p, ggmap)
c.mate5p.frac = frac5p
c.mate3p.frac = frac3p
print >>fh, '\t'.join(map(str, c.to_list()))
fh.close()
# delete tmp files
os.remove(tmpfile1)
def nominate_spanning_reads(discordant_reads_fh,
chimeras_fh,
fastq_fh):
# build index of chimera candidates
logging.info("Indexing chimera candidates")
tx5p = collections.defaultdict(lambda: [])
tx3p = collections.defaultdict(lambda: [])
for chimera in Chimera.parse(chimeras_fh):
tx5p[chimera.mate5p.tx_name].append(chimera.mate5p.end)
tx3p[chimera.mate3p.tx_name].append(chimera.mate3p.start)
# parse discordant reads
logging.info("Nominating spanning reads")
read1, read2 = None, None
prev_qname = None
for frag in parse_discordant_reads(discordant_reads_fh):
if frag.discordant_type.is_genome:
continue
qname = frag.qname
if prev_qname is not None and (qname != prev_qname):
if read1 is not None:
print >>fastq_fh, read1
if read2 is not None:
print >>fastq_fh, read2
read1, read2 = None, None
# skip if reads already found
if (read1 is not None) and (read2 is not None):
continue
# update read fastq
r1, r2 = check_fragment(frag, tx5p, tx3p)
if read1 is None: read1 = r1
if read2 is None: read2 = r2
prev_qname = qname
if read1 is not None:
print >>fastq_fh, read1
if read2 is not None:
print >>fastq_fh, read2
def collect_permiscuity_stats(input_file, ggmap):
# break name into 5'/3' genes linked in a dictionary
logging.debug("Building chimera permiscuity map")
juncmap5p, juncmap3p = \
build_junc_permiscuity_map(Chimera.parse(open(input_file)), ggmap)
return juncmap5p, juncmap3p
