def annotate_fusion(ref_f, junc_bed, secondary_flag=0, denovo_flag=0):
"""
Align fusion juncrions to gene annotations
"""
print('Start to annotate fusion junctions...')
# gene annotations
genes, novel_genes, gene_info, chrom_info = parse_ref(ref_f, 1)
fusion_bed = junc_bed
fusions, fusion_index = parse_bed(fusion_bed) # fusion junctions
total = set()
annotated_fusion_f = 'annotated_fusion.txt.tmp'
with open(annotated_fusion_f, 'w') as outf:
for chrom in chrom_info:
# overlap gene annotations with fusion juncrions
result = []
# overlap genes
if chrom in genes:
result += Interval.overlapwith(genes[chrom].interval,
fusions[chrom])
# overlap novel genes in denovo mode
if denovo_flag and chrom in novel_genes:
result += Interval.overlapwith(novel_genes[chrom].interval,
fusions[chrom])
for itl in result:
# extract gene annotations
iso = list([x for x in itl[2:] if x.startswith('iso')])
# for each overlapped fusion junction
for fus in itl[(2 + len(iso)):]:
reads = fus.split()[1]
fus_start, fus_end = fusion_index[fus]
fus_loc = '%s\t%d\t%d\tFUSIONJUNC/%s' % (chrom, fus_start,
fus_end, reads)
edge_annotations = [] # first or last exon flag
secondary_exon = defaultdict(dict) # secondary exons
annotate_flag = 0
for iso_id in iso:
g, i, c, s = iso_id.split()[1:]
start = gene_info[iso_id][0][0]
end = gene_info[iso_id][-1][-1]
# fusion junction excesses boundaries of gene
# annotation
if fus_start < start - 10 or fus_end > end + 10:
if not secondary_flag:
continue
(fusion_info,
index,
edge,
secondary) = map_fusion_to_iso(fus_start,
fus_end, s,
gene_info[iso_id])
if fusion_info:
annotate_flag += 1
bed_info = '\t'.join([fus_loc, '0', s,
str(fus_start),
str(fus_start), '0,0,0'])
bed = '\t'.join([bed_info, fusion_info, g, i,
index])
if not edge: # not first or last exon
outf.write(bed + '\n')
total.add(fus)
else: # first or last exon
edge_annotations.append(bed)
elif secondary_flag and secondary is not None:
li, ri = secondary
gene = ':'.join([g, s])
if li is not None:
li = str(li)
secondary_exon['left'][gene] = ':'.join([i,
li])
if ri is not None:
ri = str(ri)
secondary_exon['right'][gene] = ':'.join([i,
ri])
if edge_annotations:
for bed in edge_annotations:
outf.write(bed + '\n')
total.add(fus)
if secondary_flag and not annotate_flag:
for gene in secondary_exon['left']:
if gene in secondary_exon['right']:
left = secondary_exon['left'][gene]
right = secondary_exon['right'][gene]
g, s = gene.split(':')
# for avoid dup, use fus_loc_new
fus_loc_new = fus_loc + '\t0\t%s' % s
outf.write('%s\t%s:%s\t%s:%s\n' % (fus_loc_new,
g, left, g,
right))
print('Annotated %d fusion junctions!' % len(total))
def fix_fusion(ref_f, genome_fa, out_file, no_fix, secondary_flag=0,
denovo_flag=0):
"""
Realign fusion juncrions
"""
print('Start to fix fusion junctions...')
fa = check_fasta(genome_fa)
ref = parse_ref(ref_f, 2)
annotated_fusion_f = 'annotated_fusion.txt.tmp'
fusions, fusion_names, fixed_flag = fix_bed(annotated_fusion_f, ref, fa,
no_fix, denovo_flag)
total = 0
annotations = set()
fixed_fusion_f = out_file
if secondary_flag:
secondary_f = open('low_conf_%s' % out_file, 'w')
with open(fixed_fusion_f, 'w') as outf:
for fus in fusion_names:
reads = str(fusions[fus])
fixed = fixed_flag[fus]
if fixed > 0:
total += 1
fixed = str(fixed)
name = 'circular_RNA/' + reads
if fus.startswith('secondary'):
_, loc, strand, left_info, right_info = fus.split('|')
secondary_f.write('\t'.join([loc, name, fixed, strand,
left_info, right_info]))
secondary_f.write('\n')
continue
gene, iso, chrom, strand, index = fus.split()
starts, ends = ref['\t'.join([gene, iso, chrom, strand])]
exon_num = len(starts)
intron_num = exon_num - 1
if ',' in index: # back spliced exons
s, e = [int(x) for x in index.split(',')]
if strand == '+':
index_info = ','.join(str(x + 1) for x in range(s, e + 1))
else:
index_info = ','.join(str(exon_num - x)
for x in range(s, e + 1))
start = str(starts[s])
end = str(ends[e])
length = str(e - s + 1)
sizes, offsets = generate_bed(int(start), starts[s:(e + 1)],
ends[s:(e + 1)])
annotation_info = '\t'.join([chrom, start, end, sizes,
offsets])
# remove circular RNA info duplications in denovo mode
if denovo_flag and annotation_info in annotations:
continue
if s == 0:
left_intron = 'None'
else:
left_intron = '%s:%d-%d' % (chrom, ends[s - 1], starts[s])
if e == len(ends) - 1:
right_intron = 'None'
else:
right_intron = '%s:%d-%d' % (chrom, ends[e], starts[e + 1])
intron = '|'.join([left_intron, right_intron])
bed = '\t'.join([chrom, start, end, name, fixed, strand, start,
start, '0,0,0', length, sizes, offsets,
reads, 'circRNA', gene, iso, index_info,
intron])
else: # ciRNAs
index, start, end = index.split('|')
size = str(int(end) - int(start))
annotation_info = '\t'.join([chrom, start, end, size, '0'])
# remove circular RNA info duplications in denovo mode
if denovo_flag and annotation_info in annotations:
continue
index = int(index)
if strand == '+':
index_info = str(index + 1)
else:
index_info = str(intron_num - index)
intron = '%s:%d-%d' % (chrom, ends[index], starts[index + 1])
bed = '\t'.join([chrom, start, end, name, fixed, strand, start,
start, '0,0,0', '1', size, '0',
reads, 'ciRNA', gene, iso, index_info,
intron])
if denovo_flag: # in denovo mode
annotations.add(annotation_info)
outf.write(bed + '\n')
if secondary_flag:
secondary_f.close()
os.remove('annotated_fusion.txt.tmp')
print('Fixed %d fusion junctions!' % total)
def annotate_fusion(ref_f, out_dir, denovo_flag=0):
"""
Align fusion juncrions to gene annotations
"""
print('Start to annotate fusion junctions...')
# gene annotations
genes, novel_genes, gene_info, chrom_info = parse_ref(ref_f, 1)
fusion_bed = '%s/../fusion_junction.bed' % out_dir
fusions, fusion_index = parse_bed(fusion_bed) # fusion junctions
total = set()
annotated_fusion_f = '%s/annotated_fusion.txt' % out_dir
with open(annotated_fusion_f, 'w') as outf:
for chrom in chrom_info:
# overlap gene annotations with fusion juncrions
result = []
# overlap genes
if chrom in genes:
result += Interval.overlapwith(genes[chrom].interval,
fusions[chrom])
# overlap novel genes in denovo mode
if denovo_flag and chrom in novel_genes:
result += Interval.overlapwith(novel_genes[chrom].interval,
fusions[chrom])
for itl in result:
# extract gene annotations
iso = list(filter(lambda x: x.startswith('iso'), itl[2:]))
# for each overlapped fusion junction
for fus in itl[(2 + len(iso)):]:
reads = fus.split()[1]
fus_start, fus_end = fusion_index[fus]
edge_annotations = [] # first or last exon flag
for iso_id in iso:
g, i, c, s = iso_id.split()[1:]
start = gene_info[iso_id][0][0]
end = gene_info[iso_id][-1][-1]
# fusion junction excesses boundaries of gene
# annotation
if fus_start < start - 10 or fus_end > end + 10:
continue
(fusion_info,
index,
edge) = map_fusion_to_iso(fus_start,
fus_end, s,
gene_info[iso_id])
if fusion_info:
fus_start_str = str(fus_start)
fus_end_str = str(fus_end)
bed_info = '\t'.join([chrom, fus_start_str,
fus_end_str,
'FUSIONJUNC/%s' % reads,
'0', s, fus_start_str,
fus_start_str, '0,0,0'])
bed = '\t'.join([bed_info, fusion_info, g, i,
index])
if not edge: # not first or last exon
outf.write(bed + '\n')
total.add(fus)
else: # first or last exon
edge_annotations.append(bed)
if edge_annotations:
for bed in edge_annotations:
outf.write(bed + '\n')
total.add(fus)
print('Annotated %d fusion junctions!' % len(total))
def annotate_fusion(ref_f, out_dir, denovo_flag=0):
"""
Align fusion juncrions to gene annotations
"""
print('Start to annotate fusion junctions...')
# gene annotations
genes, novel_genes, gene_info, chrom_info = parse_ref(ref_f, 1)
fusion_bed = '%s/../fusion_junction.bed' % out_dir
fusions, fusion_index = parse_bed(fusion_bed) # fusion junctions
total = set()
annotated_fusion_f = '%s/annotated_fusion.txt' % out_dir
with open(annotated_fusion_f, 'w') as outf:
for chrom in chrom_info:
# overlap gene annotations with fusion juncrions
result = []
# overlap genes
if chrom in genes:
result += Interval.overlapwith(genes[chrom].interval,
fusions[chrom])
# overlap novel genes in denovo mode
if denovo_flag and chrom in novel_genes:
result += Interval.overlapwith(novel_genes[chrom].interval,
fusions[chrom])
for itl in result:
# extract gene annotations
iso = list(filter(lambda x: x.startswith('iso'), itl[2:]))
# for each overlapped fusion junction
for fus in itl[(2 + len(iso)):]:
reads = fus.split()[1]
fus_start, fus_end = fusion_index[fus]
edge_annotations = [] # first or last exon flag
for iso_id in iso:
g, i, c, s = iso_id.split()[1:]
start = gene_info[iso_id][0][0]
end = gene_info[iso_id][-1][-1]
# fusion junction excesses boundaries of gene
# annotation
if fus_start < start - 10 or fus_end > end + 10:
continue
(fusion_info, index,
edge) = map_fusion_to_iso(fus_start, fus_end, s,
gene_info[iso_id])
if fusion_info:
fus_start_str = str(fus_start)
fus_end_str = str(fus_end)
bed_info = '\t'.join([
chrom, fus_start_str, fus_end_str,
'FUSIONJUNC/%s' % reads, '0', s, fus_start_str,
fus_start_str, '0,0,0'
])
bed = '\t'.join(
[bed_info, fusion_info, g, i, index])
if not edge: # not first or last exon
outf.write(bed + '\n')
total.add(fus)
else: # first or last exon
edge_annotations.append(bed)
if edge_annotations:
for bed in edge_annotations:
outf.write(bed + '\n')
total.add(fus)
print('Annotated %d fusion junctions!' % len(total))
def fix_fusion(ref_f, genome_fa, out_dir, no_fix, denovo_flag=0):
"""
Realign fusion juncrions
"""
print('Start to fix fusion junctions...')
fa = check_fasta(genome_fa)
ref = parse_ref(ref_f, 2)
annotated_fusion_f = '%s/annotated_fusion.txt' % out_dir
fusions, fusion_names, fixed_flag = fix_bed(annotated_fusion_f, ref, fa,
no_fix, denovo_flag)
total = 0
annotations = set()
fixed_fusion_f = '%s/circ_fusion.txt' % out_dir
with open(fixed_fusion_f, 'w') as outf:
for fus in fusion_names:
reads = str(fusions[fus])
fixed = fixed_flag[fus]
if fixed > 0:
total += 1
fixed = str(fixed)
name = 'circular_RNA/' + reads
gene, iso, chrom, strand, index = fus.split()
starts, ends = ref['\t'.join([gene, iso, chrom, strand])]
exon_num = len(starts)
intron_num = exon_num - 1
if ',' in index: # back spliced exons
s, e = [int(x) for x in index.split(',')]
if strand == '+':
index_info = ','.join(str(x + 1) for x in xrange(s, e + 1))
else:
index_info = ','.join(str(exon_num - x)
for x in xrange(s, e + 1))
start = str(starts[s])
end = str(ends[e])
length = str(e - s + 1)
sizes, offsets = generate_bed(int(start), starts[s:(e + 1)],
ends[s:(e + 1)])
annotation_info = '\t'.join([chrom, start, end, sizes,
offsets])
# remove circular RNA info duplications in denovo mode
if denovo_flag and annotation_info in annotations:
continue
if s == 0:
left_intron = 'None'
else:
left_intron = '%s:%d-%d' % (chrom, ends[s - 1], starts[s])
if e == len(ends) - 1:
right_intron = 'None'
else:
right_intron = '%s:%d-%d' % (chrom, ends[e], starts[e + 1])
intron = '|'.join([left_intron, right_intron])
bed = '\t'.join([chrom, start, end, name, fixed, strand, start,
start, '0,0,0', length, sizes, offsets,
reads, 'circRNA', gene, iso, index_info,
intron])
else: # ciRNAs
index, start, end = index.split('|')
size = str(int(end) - int(start))
annotation_info = '\t'.join([chrom, start, end, size, '0'])
# remove circular RNA info duplications in denovo mode
if denovo_flag and annotation_info in annotations:
continue
index = int(index)
if strand == '+':
index_info = str(index + 1)
else:
index_info = str(intron_num - index)
intron = '%s:%d-%d' % (chrom, ends[index], starts[index + 1])
bed = '\t'.join([chrom, start, end, name, fixed, strand, start,
start, '0,0,0', '1', size, '0',
reads, 'ciRNA', gene, iso, index_info,
intron])
if denovo_flag: # in denovo mode
annotations.add(annotation_info)
outf.write(bed + '\n')
print('Fixed %d fusion junctions!' % total)