-
Notifications
You must be signed in to change notification settings - Fork 6
/
generateMAPfile.py
173 lines (152 loc) · 5.76 KB
/
generateMAPfile.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
import sys
import vcf
import numpy as np
import copy
from bedtools import IntervalFile
from getopt import getopt
def show_help():
print >>sys.stderr,"generateMAPfile.py: generation of MAP(chain) file for conversion between cancer and ref genome"
print >>sys.stderr,"Version:"+Version+"\n"
print >>sys.stderr,"Library dependency: vcf, numpy, copy, bedtools"
print >>sys.stderr,"Usage: generateMAPfile.py -l [chromLength_file] -i [cancer_vcf_file(indel_dup_inv)] > output_chain_file"
print >>sys.stderr,"Example: generateMAPfile.py -l chromInfo_hg18.txt -i cancer_indel_dup_inv.vcf > map_chain.txt"
print >>sys.stderr,"Option:"
print >>sys.stderr," -h,--help"
print >>sys.stderr," -l,--chromLen file containing information of chromosome length for specific genome"
print >>sys.stderr," format:"
print >>sys.stderr," chr1 1 247249719"
print >>sys.stderr," chr10 1 135374737"
print >>sys.stderr," ......"
print >>sys.stderr," -i,--inputVcf standard vcf file containing information of indels, duplications and inversions for cancer"
Version="1.0"
if len(sys.argv)<2:
show_help()
exit(0)
opts,restlist=getopt(sys.argv[1:],"hl:i:",["help","chromLen","inputVcf="])
for o,a in opts:
if o in ("-h","--help"):
show_help()
exit(0)
elif o in ("-l","chromLen"):
chro_length=open(a)
elif o in ("-i","inputVcf"):
vcf_name=a
#chro_length=open(sys.argv[1])
#vcf_name=sys.argv[2]
vcf_data=vcf.VCFReader(open(vcf_name))
open(vcf_name).close()
#collect and store indels and tandom duplications information
chro_length=chro_length.read().split('\n')
indicator=[]
for i in vcf_data:
if len(i.CHROM)>2:
sv_chro=i.CHROM
else:
sv_chro="chr"+i.CHROM
sv_pos=i.POS
sv_ref=i.REF
alt=i.ALT[0]
if alt.startswith('<'):
svtype=i.INFO['SVTYPE']
length=i.INFO['SVLEN']
end=i.INFO['END']
else:
svtype='none'
length=len(i.ALT)-len(sv_ref)
if (svtype!='none')&(svtype!='INV'):
indicator.append((sv_chro,sv_pos,length,svtype))
elif svtype=='INV':
indicator.append((sv_chro,end,end-sv_pos+1,svtype))
elif (svtype=='none')&(length>0):
indicator.append((sv_chro,sv_pos,length,"INS"))
elif (svtype=='none')&(length<0):
indicator.append((sv_chro,sv_pos,length,"DEL"))
for j in chro_length:
if j!='':
k=j.split('\t')
indicator.append((k[0],int(k[1]),0,'STA'))
indicator.append((k[0],int(k[2]),0,'END'))
dtype=[('chro','S8'),('start','i4'),('length','i4'),('type','S3')]
indi_array=np.array(indicator,dtype=dtype)
indi_array=np.sort(indi_array,order=['chro','start'])
'''
for i in indi_array:
print "\t".join(str(f) for f in i)
'''
#function for inversion covers previous segments
def changeUponInversion(window_num,pos,length,pos2,start,start2,map_file,map_window):
k=len(map_file)-1
while map_file[k][1]>pos-length:
k=k-1
start_inv=pos-length+1
if map_file[k][7]=='-':
window_num=window_num+1
map_window.append([chro,start_inv-99,start_inv-1,"+","chrW"+str(window_num),1,99,"+"])
map_window.append([chro,pos-98,pos,"+","chrW"+str(window_num),100,198,"-"])
map_window.append([chro,start_inv,start_inv+98,"+","chrW"+str(window_num+1),1,99,"-"])
map_window.append([chro,pos+1,pos+99,"+","chrW"+str(window_num+1),100,198,"+"])
window_num=window_num+1
else:
start2_inv=start_inv-map_file[k][2]+map_file[k][6]
insert=copy.deepcopy(map_file[k])
insert[1]=start_inv
insert[5]=start2_inv
map_file.insert(k+1,insert)
map_file[k][2]=start_inv-1
map_file[k][6]=start2_inv-1
map_file.append([chro,start,pos,"+",chro,start2,pos2,"+"])
for i in range(k+1,len(map_file)):
temp=map_file[i][5]
map_file[i][5]=start2_inv+pos2-map_file[i][6]
map_file[i][6]=start2_inv+pos2-temp
temp=map_file[i][7]
if temp=='+':
map_file[i][7]='-'
else:
map_file[i][7]='+'
start=pos+1
start2=pos2+1
return (window_num,start,start2,map_file,map_window)
map_file=[]
start=start2=1
map_window=[]
window_num=0
for i in range(1,len(indi_array)):
info=indi_array[i]
chro=info[0]
pos=info[1]
length=info[2]
typ=info[3]
pos2=pos-start+start2
if typ=='STA':
start=start2=1
continue
elif typ=='INS':
map_file.append([chro,start,pos,'+',chro,start2,pos2,'+'])
map_file.append([chro,pos+1,pos+1,'+',chro,pos2+1,pos2+1+length,'+'])
start=pos+2
start2=pos2+2+length
elif typ=='DEL':
map_file.append([chro,start,pos,'+',chro,start2,pos2,'+'])
map_file.append([chro,pos+1,pos+1-length,'+',chro,pos2+1,pos2+1,'+'])
start=pos+2-length
start2=pos2+2
elif typ=='DUP':
map_file.append([chro,start,pos+length,'+',chro,start2,pos2+length,'+'])
map_file.append([chro,pos+1,pos+length,'+',chro,pos2+length+1,pos2+2*length,'+'])
start=pos+length+1
start2=pos2+2*length+1
elif typ=='END':
map_file.append([chro,start,pos,'+',chro,start2,pos2,'+'])
elif typ=='INV':
if start<=pos-length:
map_file.append([chro,start,pos-length,'+',chro,start2,pos2-length,'+'])
map_file.append([chro,pos-length+1,pos,'+',chro,pos-length+1,pos2,'-'])
start=pos+1
start2=pos2+1
else:
window_num,start,start2,map_file,map_window=changeUponInversion(window_num,pos,length,pos2,start,start2,map_file,map_window)
for i in map_file:
print "\t".join(str(f) for f in i)
for i in map_window:
print "\t".join(str(f) for f in i)