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fix issue #26 
1 parent de3102d commit 0aa723f

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Lines changed: 182 additions & 172 deletions

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‎CHANGELOG.md‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,8 @@
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## 2.3.5 (2018-12-30)
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Improvements:
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Using the temporary file to allow to run CIRCexplorer2 in the same directory simultaneously (issue #26). Thanks @egaffo. Happy New Year!
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## 2.3.4 (2018-10-26)
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38
Bugfixes:

‎circ2/annotate.py‎

Lines changed: 86 additions & 83 deletions
Original file line numberDiff line numberDiff line change
@@ -19,6 +19,7 @@
1919
from .parser import parse_ref, parse_bed, check_fasta
2020
from .helper import logger, map_fusion_to_iso, fix_bed, generate_bed
2121
from collections import defaultdict
22+
import tempfile
2223

2324
__author__ = [
2425
'Xiao-Ou Zhang (zhangxiaoou@picb.ac.cn)',
@@ -30,15 +31,17 @@
3031

3132
@logger
3233
def annotate(options):
34+
# create temporary annotated fusion file
35+
fusion_tmp = tempfile.TemporaryFile(mode='w+')
3336
# annotate fusion junctions
34-
annotate_fusion(options['--ref'], options['--bed'],
37+
annotate_fusion(options['--ref'], options['--bed'], fusion_tmp,
3538
secondary_flag=options['--low-confidence'])
3639
# fix fusion juncrions
37-
fix_fusion(options['--ref'], options['--genome'], options['--output'],
40+
fix_fusion(options['--ref'], options['--genome'], fusion_tmp, options['--output'],
3841
options['--no-fix'], secondary_flag=options['--low-confidence'])
3942

4043

41-
def annotate_fusion(ref_f, junc_bed, secondary_flag=0, denovo_flag=0):
44+
def annotate_fusion(ref_f, junc_bed, fusion_tmp, secondary_flag=0, denovo_flag=0):
4245
"""
4346
Align fusion juncrions to gene annotations
4447
"""
@@ -48,96 +51,96 @@ def annotate_fusion(ref_f, junc_bed, secondary_flag=0, denovo_flag=0):
4851
fusion_bed = junc_bed
4952
fusions, fusion_index = parse_bed(fusion_bed) # fusion junctions
5053
total = set()
51-
annotated_fusion_f = 'annotated_fusion.txt.tmp'
52-
with open(annotated_fusion_f, 'w') as outf:
53-
for chrom in chrom_info:
54-
# overlap gene annotations with fusion juncrions
55-
result = []
56-
# overlap genes
57-
if chrom in genes:
58-
result += Interval.overlapwith(genes[chrom].interval,
59-
fusions[chrom])
60-
# overlap novel genes in denovo mode
61-
if denovo_flag and chrom in novel_genes:
62-
result += Interval.overlapwith(novel_genes[chrom].interval,
63-
fusions[chrom])
64-
for itl in result:
65-
# extract gene annotations
66-
iso = list([x for x in itl[2:] if x.startswith('iso')])
67-
# for each overlapped fusion junction
68-
for fus in itl[(2 + len(iso)):]:
69-
reads = fus.split()[1]
70-
fus_start, fus_end = fusion_index[fus]
71-
fus_loc = '%s\t%d\t%d\tFUSIONJUNC/%s' % (chrom, fus_start,
72-
fus_end, reads)
73-
edge_annotations = [] # first or last exon flag
74-
secondary_exon = defaultdict(dict) # secondary exons
75-
annotate_flag = 0
76-
for iso_id in iso:
77-
g, i, c, s = iso_id.split()[1:]
78-
start = gene_info[iso_id][0][0]
79-
end = gene_info[iso_id][-1][-1]
80-
# fusion junction excesses boundaries of gene
81-
# annotation
82-
if fus_start < start - 10 or fus_end > end + 10:
83-
if not secondary_flag:
84-
continue
85-
(fusion_info,
86-
index,
87-
edge,
88-
secondary) = map_fusion_to_iso(fus_start,
89-
fus_end, s,
90-
gene_info[iso_id])
91-
if fusion_info:
92-
annotate_flag += 1
93-
bed_info = '\t'.join([fus_loc, '0', s,
94-
str(fus_start),
95-
str(fus_start), '0,0,0'])
96-
bed = '\t'.join([bed_info, fusion_info, g, i,
97-
index])
98-
if not edge: # not first or last exon
99-
outf.write(bed + '\n')
100-
total.add(fus)
101-
else: # first or last exon
102-
edge_annotations.append(bed)
103-
elif secondary_flag and secondary is not None:
104-
li, ri = secondary
105-
gene = ':'.join([g, s])
106-
if li is not None:
107-
li = str(li)
108-
secondary_exon['left'][gene] = ':'.join([i,
109-
li])
110-
if ri is not None:
111-
ri = str(ri)
112-
secondary_exon['right'][gene] = ':'.join([i,
113-
ri])
114-
if edge_annotations:
115-
for bed in edge_annotations:
54+
outf = fusion_tmp
55+
for chrom in chrom_info:
56+
# overlap gene annotations with fusion juncrions
57+
result = []
58+
# overlap genes
59+
if chrom in genes:
60+
result += Interval.overlapwith(genes[chrom].interval,
61+
fusions[chrom])
62+
# overlap novel genes in denovo mode
63+
if denovo_flag and chrom in novel_genes:
64+
result += Interval.overlapwith(novel_genes[chrom].interval,
65+
fusions[chrom])
66+
for itl in result:
67+
# extract gene annotations
68+
iso = list([x for x in itl[2:] if x.startswith('iso')])
69+
# for each overlapped fusion junction
70+
for fus in itl[(2 + len(iso)):]:
71+
reads = fus.split()[1]
72+
fus_start, fus_end = fusion_index[fus]
73+
fus_loc = '%s\t%d\t%d\tFUSIONJUNC/%s' % (chrom, fus_start,
74+
fus_end, reads)
75+
edge_annotations = [] # first or last exon flag
76+
secondary_exon = defaultdict(dict) # secondary exons
77+
annotate_flag = 0
78+
for iso_id in iso:
79+
g, i, c, s = iso_id.split()[1:]
80+
start = gene_info[iso_id][0][0]
81+
end = gene_info[iso_id][-1][-1]
82+
# fusion junction excesses boundaries of gene
83+
# annotation
84+
if fus_start < start - 10 or fus_end > end + 10:
85+
if not secondary_flag:
86+
continue
87+
(fusion_info,
88+
index,
89+
edge,
90+
secondary) = map_fusion_to_iso(fus_start,
91+
fus_end, s,
92+
gene_info[iso_id])
93+
if fusion_info:
94+
annotate_flag += 1
95+
bed_info = '\t'.join([fus_loc, '0', s,
96+
str(fus_start),
97+
str(fus_start), '0,0,0'])
98+
bed = '\t'.join([bed_info, fusion_info, g, i,
99+
index])
100+
if not edge: # not first or last exon
116101
outf.write(bed + '\n')
117-
total.add(fus)
118-
if secondary_flag and not annotate_flag:
119-
for gene in secondary_exon['left']:
120-
if gene in secondary_exon['right']:
121-
left = secondary_exon['left'][gene]
122-
right = secondary_exon['right'][gene]
123-
g, s = gene.split(':')
124-
# for avoid dup, use fus_loc_new
125-
fus_loc_new = fus_loc + '\t0\t%s' % s
126-
outf.write('%s\t%s:%s\t%s:%s\n' % (fus_loc_new,
127-
g, left, g,
128-
right))
102+
total.add(fus)
103+
else: # first or last exon
104+
edge_annotations.append(bed)
105+
elif secondary_flag and secondary is not None:
106+
li, ri = secondary
107+
gene = ':'.join([g, s])
108+
if li is not None:
109+
li = str(li)
110+
secondary_exon['left'][gene] = ':'.join([i,
111+
li])
112+
if ri is not None:
113+
ri = str(ri)
114+
secondary_exon['right'][gene] = ':'.join([i,
115+
ri])
116+
if edge_annotations:
117+
for bed in edge_annotations:
118+
outf.write(bed + '\n')
119+
total.add(fus)
120+
if secondary_flag and not annotate_flag:
121+
for gene in secondary_exon['left']:
122+
if gene in secondary_exon['right']:
123+
left = secondary_exon['left'][gene]
124+
right = secondary_exon['right'][gene]
125+
g, s = gene.split(':')
126+
# for avoid dup, use fus_loc_new
127+
fus_loc_new = fus_loc + '\t0\t%s' % s
128+
outf.write('%s\t%s:%s\t%s:%s\n' % (fus_loc_new,
129+
g, left, g,
130+
right))
129131
print('Annotated %d fusion junctions!' % len(total))
130132

131133

132-
def fix_fusion(ref_f, genome_fa, out_file, no_fix, secondary_flag=0,
134+
def fix_fusion(ref_f, genome_fa, fusion_tmp, out_file, no_fix, secondary_flag=0,
133135
denovo_flag=0):
134136
"""
135137
Realign fusion juncrions
136138
"""
137139
print('Start to fix fusion junctions...')
138140
fa = check_fasta(genome_fa)
139141
ref = parse_ref(ref_f, 2)
140-
annotated_fusion_f = 'annotated_fusion.txt.tmp'
142+
annotated_fusion_f = fusion_tmp
143+
annotated_fusion_f.seek(0) ## from the start
141144
fusions, fusion_names, fixed_flag = fix_bed(annotated_fusion_f, ref, fa,
142145
no_fix, denovo_flag)
143146
total = 0
@@ -216,6 +219,6 @@ def fix_fusion(ref_f, genome_fa, out_file, no_fix, secondary_flag=0,
216219
if secondary_flag:
217220
secondary_f.close()
218221

219-
os.remove('annotated_fusion.txt.tmp')
222+
fusion_tmp.close()
220223

221224
print('Fixed %d fusion junctions!' % total)

‎circ2/denovo.py‎

Lines changed: 5 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -32,6 +32,7 @@
3232
import pysam
3333
from scipy.stats import fisher_exact, binom
3434
from .genomic_interval import Interval
35+
import tempfile
3536

3637
__author__ = [
3738
'Xiao-Ou Zhang (zhangxiaoou@picb.ac.cn)',
@@ -66,11 +67,13 @@ def denovo(options):
6667
print('Warning: no cufflinks directory %s!' % options['--cuff'])
6768
print('Please run CIRCexplorer2 assembly before this step!')
6869
ref_path = options['--ref']
70+
# create temporary annotated fusion file
71+
fusion_tmp = tempfile.TemporaryFile(mode='w+')
6972
# annotate fusion junctions
70-
annotate_fusion(ref_path, options['--bed'], denovo_flag=1)
73+
annotate_fusion(ref_path, options['--bed'], fusion_tmp, denovo_flag=1)
7174
# fix fusion juncrions
7275
out_f = '%s/circularRNA_full.txt' % denovo_dir
73-
fix_fusion(ref_path, options['--genome'], out_f,
76+
fix_fusion(ref_path, options['--genome'], fusion_tmp, out_f,
7477
options['--no-fix'], denovo_flag=1)
7578
# extract novel circRNAs
7679
extract_novel_circ(denovo_dir, options['--ref'])

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