def main(args):
if not os.path.exists(args.input):
print >> sys.stderr, "Input file {0} does not exist. Abort.".format(args.fasta)
sys.exit(-1)
if not os.path.exists(args.sam):
print >> sys.stderr, "SAM file {0} does not exist. Abort.".format(args.sam)
sys.exit(-1)
# check for duplicate IDs
check_ids_unique(args.input, is_fq=args.fq)
ignored_fout = open(args.prefix + '.ignored_ids.txt', 'w')
if args.flnc_coverage > 0:
f_good = open(args.prefix + '.collapsed.good.gff', 'w')
f_bad = open(args.prefix + '.collapsed.bad.gff', 'w')
cov_threshold = args.flnc_coverage
else:
f_good = open(args.prefix + '.collapsed.gff', 'w')
f_bad = f_good
cov_threshold = 1
f_txt = open(args.prefix + '.collapsed.group.txt', 'w')
b = branch_simple2.BranchSimple(args.input, cov_threshold=cov_threshold, min_aln_coverage=args.min_aln_coverage, min_aln_identity=args.min_aln_identity, is_fq=args.fq)
iter = b.iter_gmap_sam(args.sam, ignored_fout)
for recs in iter:
for v in recs.itervalues():
if len(v) > 0: b.process_records(v, args.allow_extra_5exon, False, f_good, f_bad, f_txt)
ignored_fout.close()
f_good.close()
try:
f_bad.close()
except:
pass
f_txt.close()
if args.max_fuzzy_junction > 0: # need to further collapse those that have fuzzy junctions!
collapse_fuzzy_junctions(f_good.name, f_txt.name, args.allow_extra_5exon, internal_fuzzy_max_dist=args.max_fuzzy_junction)
os.rename(f_good.name, f_good.name+'.unfuzzy')
os.rename(f_txt.name, f_txt.name+'.unfuzzy')
os.rename(f_good.name+'.fuzzy', f_good.name)
os.rename(f_txt.name+'.fuzzy', f_txt.name)
if args.fq:
outfile = args.prefix+".collapsed.rep.fq"
else:
outfile = args.prefix+".collapsed.rep.fa"
if args.allow_extra_5exon: # 5merge, pick longest
pick_rep(args.input, f_good.name, f_txt.name, outfile, is_fq=args.fq, pick_least_err_instead=False, bad_gff_filename=f_bad.name)
else:
pick_rep(args.input, f_good.name, f_txt.name, outfile, is_fq=args.fq, pick_least_err_instead=True, bad_gff_filename=f_bad.name)
print >> sys.stderr, "Ignored IDs written to:", ignored_fout.name
print >> sys.stderr, "Output written to:"
print >> sys.stderr, f_good.name
print >> sys.stderr, f_txt.name
print >> sys.stderr, outfile
print >> sys.stderr, args
def main(args):
if not os.path.exists(args.input):
print >> sys.stderr, "Input file {0} does not exist. Abort.".format(
args.fasta)
sys.exit(-1)
if not os.path.exists(args.sam):
print >> sys.stderr, "SAM file {0} does not exist. Abort.".format(
args.sam)
sys.exit(-1)
# check for duplicate IDs
check_ids_unique(args.input, is_fq=args.fq)
ignored_fout = open(args.prefix + '.ignored_ids.txt', 'w')
f_gff = open(args.prefix + '.collapsed.gff', 'w')
f_txt = open(args.prefix + '.collapsed.group.txt', 'w')
b = branch_simple2.BranchSimple(args.input,
cov_threshold=1,
min_aln_coverage=args.min_aln_coverage,
min_aln_identity=args.min_aln_identity,
is_fq=args.fq)
iter = b.iter_gmap_sam(args.sam, ignored_fout)
for recs in iter:
for v in recs.itervalues():
if len(v) > 0:
b.process_records(v, args.allow_extra_5exon, False, f_gff,
f_gff, f_txt)
ignored_fout.close()
f_gff.close()
f_txt.close()
if args.fq:
outfile = args.prefix + ".collapsed.rep.fq"
else:
outfile = args.prefix + ".collapsed.rep.fa"
pick_rep(args.input, f_gff.name, f_txt.name, outfile, is_fq=args.fq)
print >> sys.stderr, "Ignored IDs written to:", ignored_fout.name
print >> sys.stderr, "Output written to:"
print >> sys.stderr, f_gff.name
print >> sys.stderr, f_txt.name
print >> sys.stderr, outfile
print >> sys.stderr, args
def fusion_main(fa_or_fq_filename,
sam_filename,
output_prefix,
is_fq=False,
allow_extra_5_exons=True,
skip_5_exon_alt=True,
prefix_dict_pickle_filename=None,
min_locus_coverage=.05,
min_total_coverage=.99,
min_locus_coverage_bp=1,
min_dist_between_loci=10000):
"""
(1) identify fusion candidates (based on mapping, total coverage, identity, etc)
(2) group/merge the fusion exons, using an index to point to each individual part
(3) use BranchSimple to write out a tmp GFF where
PBfusion.1.1 is the first part of a fusion gene
PBfusion.1.2 is the second part of a fusion gene
(4) read the tmp file from <3> and modify it so that
PBfusion.1 just represents the fusion gene (a single transcript GFF format)
"""
compressed_records_pointer_dict = defaultdict(lambda: [])
merged_exons = []
merged_i = 0
# step (0). check for duplicate IDs
check_ids_unique(fa_or_fq_filename, is_fq=is_fq)
# step (1). identify fusion candidates
bs = branch_simple2.BranchSimple(fa_or_fq_filename, is_fq=is_fq)
fusion_candidates = find_fusion_candidates(
sam_filename, bs.transfrag_len_dict, min_locus_coverage,
min_locus_coverage_bp, min_total_coverage, min_dist_between_loci)
# step (2). merge the fusion exons
for recs in iter_gmap_sam_for_fusion(sam_filename, fusion_candidates,
bs.transfrag_len_dict):
for v in recs.itervalues():
if len(v) > 0:
o = merge_fusion_exons(v,
max_fusion_point_dist=100,
max_exon_end_dist=0,
allow_extra_5_exons=allow_extra_5_exons)
for group in o:
merged_exons.append(group)
for r in group:
compressed_records_pointer_dict[r.qID].append(merged_i)
merged_i += 1
# step (3). use BranchSimple to write a temporary file
# f_good = open(output_prefix + '.gff', 'w')
f_group = open('branch_tmp.group.txt', 'w')
# f_bad = f_good
gene_index = 1
already_seen = set()
for qid, indices in compressed_records_pointer_dict.iteritems():
combo = tuple(indices)
if combo in already_seen:
print "combo seen:", combo
#raw_input("")
continue
already_seen.add(combo)
# if gene_index == 7:
# pdb.set_trace()
for isoform_index, i in enumerate(indices):
bs.cuff_index = gene_index # for set to the same
records = merged_exons[i]
f_group.write("{p}.{i}.{j}\t{ids}\n".format(
p="PBfusion",
i=gene_index,
j=isoform_index,
ids=",".join(r.qID for r in records)))
# bs.process_records(records, allow_extra_5_exons, skip_5_exon_alt, \
# f_good, f_bad, f_group, tolerate_end=100, \
# starting_isoform_index=isoform_index, gene_prefix='PBfusion')
gene_index += 1
# f_good.close()
# f_bad.close()
f_group.close()
# step (4). read the tmp file and modify to display per fusion gene
f_group = open(output_prefix + '.group.txt', 'w')
group_info = {} # ex: PBfusion.1 --> [id1, id2, id3...]
count = 0
with open('branch_tmp.group.txt') as f:
while True:
line = f.readline().strip()
if len(line) == 0: break
pbid1, groups1 = line.strip().split('\t')
pbid2, groups2 = f.readline().strip().split('\t')
assert pbid1.split('.')[1] == pbid2.split('.')[1]
group = set(groups1.split(',')).intersection(groups2.split(','))
f_group.write("{0}\t{1}\n".format(pbid1[:pbid1.rfind('.')],
",".join(group)))
group_info[pbid1[:pbid1.rfind('.')]] = list(group)
count += 1
f_group.close()
#os.remove('branch_tmp.group.txt')
gff_filename = output_prefix + '.gff'
group_filename = output_prefix + '.group.txt'
if is_fq:
output_filename = output_prefix + '.rep.fq'
else:
output_filename = output_prefix + '.rep.fa'
pick_rep(fa_or_fq_filename,
sam_filename,
gff_filename,
group_filename,
output_filename,
is_fq=is_fq,
pick_least_err_instead=False)
print >> sys.stderr, "{0} fusion candidates identified.".format(count)
print >> sys.stderr, "Output written to: {0}.gff, {0}.group.txt, {1}".format(
output_prefix, output_filename)
# (optional) step 5. get count information
if prefix_dict_pickle_filename is not None:
with open(prefix_dict_pickle_filename) as f:
d = load(f)
d1 = d['HQ']
d1.update(d['LQ'])
tofu_wrap.get_abundance(output_prefix, d1, output_prefix)
print >> sys.stderr, "Count information written to: {0}.abundance.txt".format(
output_prefix)
def main(args):
if not os.path.exists(args.input):
print >> sys.stderr, "Input file {0} does not exist. Abort.".format(
args.fasta)
sys.exit(-1)
if not os.path.exists(args.sam):
print >> sys.stderr, "SAM file {0} does not exist. Abort.".format(
args.sam)
sys.exit(-1)
# check for duplicate IDs
check_ids_unique(args.input, is_fq=args.fq)
ignored_fout = open(args.prefix + '.ignored_ids.txt', 'w')
if args.flnc_coverage > 0:
f_good = open(args.prefix + '.collapsed.good.gff', 'w')
f_bad = open(args.prefix + '.collapsed.bad.gff', 'w')
cov_threshold = args.flnc_coverage
else:
f_good = open(args.prefix + '.collapsed.gff', 'w')
f_bad = f_good
cov_threshold = 1
f_txt = open(args.prefix + '.collapsed.group.txt', 'w')
b = branch_simple2.BranchSimple(args.input,
cov_threshold=cov_threshold,
min_aln_coverage=args.min_aln_coverage,
min_aln_identity=args.min_aln_identity,
is_fq=args.fq)
iter = b.iter_gmap_sam(args.sam, ignored_fout)
for recs in iter:
for v in recs.itervalues():
if len(v) > 0:
b.process_records(v, args.allow_extra_5exon, False, f_good,
f_bad, f_txt)
ignored_fout.close()
f_good.close()
try:
f_bad.close()
except:
pass
f_txt.close()
if args.max_fuzzy_junction > 0: # need to further collapse those that have fuzzy junctions!
collapse_fuzzy_junctions(
f_good.name,
f_txt.name,
args.allow_extra_5exon,
internal_fuzzy_max_dist=args.max_fuzzy_junction)
os.rename(f_good.name, f_good.name + '.unfuzzy')
os.rename(f_txt.name, f_txt.name + '.unfuzzy')
os.rename(f_good.name + '.fuzzy', f_good.name)
os.rename(f_txt.name + '.fuzzy', f_txt.name)
if args.fq:
outfile = args.prefix + ".collapsed.rep.fq"
else:
outfile = args.prefix + ".collapsed.rep.fa"
if args.allow_extra_5exon: # 5merge, pick longest
pick_rep(args.input,
f_good.name,
f_txt.name,
outfile,
is_fq=args.fq,
pick_least_err_instead=False,
bad_gff_filename=f_bad.name)
else:
pick_rep(args.input,
f_good.name,
f_txt.name,
outfile,
is_fq=args.fq,
pick_least_err_instead=True,
bad_gff_filename=f_bad.name)
print >> sys.stderr, "Ignored IDs written to:", ignored_fout.name
print >> sys.stderr, "Output written to:"
print >> sys.stderr, f_good.name
print >> sys.stderr, f_txt.name
print >> sys.stderr, outfile
print >> sys.stderr, args
def fusion_main(fa_or_fq_filename, sam_filename, output_prefix, is_fq=False, allow_extra_5_exons=True, skip_5_exon_alt=True, prefix_dict_pickle_filename=None, min_locus_coverage=.05, min_total_coverage=.99, min_locus_coverage_bp=1, min_dist_between_loci=10000):
"""
(1) identify fusion candidates (based on mapping, total coverage, identity, etc)
(2) group/merge the fusion exons, using an index to point to each individual part
(3) use BranchSimple to write out a tmp GFF where
PBfusion.1.1 is the first part of a fusion gene
PBfusion.1.2 is the second part of a fusion gene
(4) read the tmp file from <3> and modify it so that
PBfusion.1 just represents the fusion gene (a single transcript GFF format)
"""
compressed_records_pointer_dict = defaultdict(lambda: [])
merged_exons = []
merged_i = 0
# step (0). check for duplicate IDs
check_ids_unique(fa_or_fq_filename, is_fq=is_fq)
# step (1). identify fusion candidates
bs = branch_simple2.BranchSimple(fa_or_fq_filename, is_fq=is_fq)
fusion_candidates = find_fusion_candidates(sam_filename, bs.transfrag_len_dict, min_locus_coverage, min_locus_coverage_bp, min_total_coverage, min_dist_between_loci)
# step (2). merge the fusion exons
for recs in iter_gmap_sam_for_fusion(sam_filename, fusion_candidates, bs.transfrag_len_dict):
for v in recs.itervalues():
if len(v) > 0:
o = merge_fusion_exons(v, max_fusion_point_dist=100, max_exon_end_dist=0, allow_extra_5_exons=allow_extra_5_exons)
for group in o:
merged_exons.append(group)
for r in group: compressed_records_pointer_dict[r.qID].append(merged_i)
merged_i += 1
# step (3). use BranchSimple to write a temporary file
# f_good = open(output_prefix + '.gff', 'w')
f_group = open('branch_tmp.group.txt', 'w')
# f_bad = f_good
gene_index = 1
already_seen = set()
for qid,indices in compressed_records_pointer_dict.iteritems():
combo = tuple(indices)
if combo in already_seen:
print "combo seen:", combo
#raw_input("")
continue
already_seen.add(combo)
# if gene_index == 7:
# pdb.set_trace()
for isoform_index,i in enumerate(indices):
bs.cuff_index = gene_index # for set to the same
records = merged_exons[i]
f_group.write("{p}.{i}.{j}\t{ids}\n".format(p="PBfusion", i=gene_index, j=isoform_index, ids=",".join(r.qID for r in records)))
# bs.process_records(records, allow_extra_5_exons, skip_5_exon_alt, \
# f_good, f_bad, f_group, tolerate_end=100, \
# starting_isoform_index=isoform_index, gene_prefix='PBfusion')
gene_index += 1
# f_good.close()
# f_bad.close()
f_group.close()
# step (4). read the tmp file and modify to display per fusion gene
f_group = open(output_prefix + '.group.txt', 'w')
group_info = {} # ex: PBfusion.1 --> [id1, id2, id3...]
count = 0
with open('branch_tmp.group.txt') as f:
while True:
line = f.readline().strip()
if len(line) == 0: break
pbid1, groups1 = line.strip().split('\t')
pbid2, groups2 = f.readline().strip().split('\t')
assert pbid1.split('.')[1] == pbid2.split('.')[1]
group = set(groups1.split(',')).intersection(groups2.split(','))
f_group.write("{0}\t{1}\n".format(pbid1[:pbid1.rfind('.')], ",".join(group)))
group_info[pbid1[:pbid1.rfind('.')]] = list(group)
count += 1
f_group.close()
#os.remove('branch_tmp.group.txt')
gff_filename = output_prefix + '.gff'
group_filename = output_prefix + '.group.txt'
if is_fq:
output_filename = output_prefix + '.rep.fq'
else:
output_filename = output_prefix + '.rep.fa'
pick_rep(fa_or_fq_filename, sam_filename, gff_filename, group_filename, output_filename, is_fq=is_fq, pick_least_err_instead=False)
print >> sys.stderr, "{0} fusion candidates identified.".format(count)
print >> sys.stderr, "Output written to: {0}.gff, {0}.group.txt, {1}".format(output_prefix, output_filename)
# (optional) step 5. get count information
if prefix_dict_pickle_filename is not None:
with open(prefix_dict_pickle_filename) as f:
d = load(f)
d1 = d['HQ']
d1.update(d['LQ'])
tofu_wrap.get_abundance(output_prefix, d1, output_prefix)
print >> sys.stderr, "Count information written to: {0}.abundance.txt".format(output_prefix)
