forked from misko/minichr
-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathresolve_bp.py
165 lines (136 loc) · 3.58 KB
/
resolve_bp.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
#!/usr/bin/python
import sys
if len(sys.argv)!=4:
print "%s assembled.fa ref1.fa ref2.fa" % sys.argv[0]
sys.exit(1)
def reverse_complement(s):
s2=""
for x in s:
if x=="c":
s2="g"+s2
elif x=="C":
s2="G"+s2
elif x=="a":
s2="t"+s2
elif x=="A":
s2="T"+s2
elif x=="g":
s2="c"+s2
elif x=="G":
s2="C"+s2
elif x=="t":
s2="a"+s2
elif x=="T":
s2="A"+s2
elif x=="N":
s2="N"+s2
else:
print "ERROR"
sys.exit(1)
return s2
def read_fa(f):
h=open(f,'r')
lines=h.readlines()
h.close()
return (lines[0][1:].strip(),"".join(map(lambda x : x.strip(),lines[1:])))
afa=read_fa(sys.argv[1])
r1fa=read_fa(sys.argv[2])
r2fa=read_fa(sys.argv[3])
r1_algn=()
r2_algn=()
mxa=0
mxb=0
for alignment in sys.stdin.readlines():
alignment=alignment.strip().split()
sc=int(alignment[0])
if sc<150:# or int(alignment[0])<=mx:
#print >> sys.stderr, "#SKIPPING"
continue
#it blat
#956 1 0 0 0 0 0 0 + Genome_LEN_2324 2324 1306 2263 chr7:54413327-54414627 1301 344 1301 1 957, 1306, 344,
#987 0 0 0 0 0 0 0 + Genome_LEN_2324 2324 320 1307 chr12:60845840-60847140 1301 0 987 1 987, 320, 0,
a=[alignment[9],int(alignment[11])+1,int(alignment[12])+1]
b=[alignment[13],int(alignment[15])+1,int(alignment[16])+1]
b_reverse=False
if alignment[8]=='-':
b_reverse=True
t=b[1]
b[1]=b[2]
b[2]=t
if b[0]==r1fa[0]:
if sc>mxa:
mxa=sc
r1_algn=(a,b,b_reverse)
elif b[0]==r2fa[0]:
if sc>mxb:
mxb=sc
r2_algn=(a,b,b_reverse)
else:
print >> sys.stderr, "ERROR!"
#print b
if len(r1_algn)==0 or len(r2_algn)==0:
print "#-1\t#no bp"
sys.exit(1)
#print r1_algn, r2_algn
if r2_algn[0][1]<r1_algn[0][1]:
t=r2_algn
r2_algn=r1_algn
r1_algn=t
t=r1fa
r1fa=r2fa
r2fa=t
insert=[]
micro_homology=[]
if r1_algn[0][2]>r2_algn[0][1]:
sz=r1_algn[0][2]-r2_algn[0][1]
if not r1_algn[2]:
micro_homology.append(r1fa[1][r1_algn[1][1]-1:r1_algn[1][2]-1][-sz:])
else:
micro_homology.append(reverse_complement(r1fa[1][r1_algn[1][2]-1:r1_algn[1][1]-1])[-sz:])
if not r2_algn[2]:
micro_homology.append(r2fa[1][r2_algn[1][1]-1:r2_algn[1][2]-1][:sz])
else:
micro_homology.append(reverse_complement(r2fa[1][r2_algn[1][2]-1:r2_algn[1][1]-1])[:sz])
elif r1_algn[0][2]<r2_algn[0][1]:
insert.append(afa[r1_algn[0][2]-1:r2_algn[0][1]-1])
def to_pos(s):
chr=s.split(':')[0]
f,t=map(lambda x : int(x) ,s.split(':')[1].split('-'))
return [chr,f,t+1]
r1p=to_pos(r1fa[0])
r2p=to_pos(r2fa[0])
#r1 is first, followed by r2
if not r1_algn[2] and not r2_algn[2]:
# both forward
#type 0
ty=0
#print r1p,r1_algn[1]
r1p.append(r1p[1]+r1_algn[1][2]-1)
r2p.append(r2p[1]+r2_algn[1][1]-1)
elif r1_algn[2] and not r2_algn[2]:
#goes from back to forward
# type 3
r1p.append(r1p[1]+r1_algn[1][2]-1)
r2p.append(r2p[1]+r2_algn[1][1]-1)
ty=3
elif not r1_algn[2] and r2_algn[2]:
#goes from forward to back
r1p.append(r1p[1]+r1_algn[1][2]-1)
r2p.append(r2p[1]+r2_algn[1][1]-1)
# type 2
ty=2
elif r1_algn[2] and r2_algn[2]:
#goes from back to back
#type 1
r1p.append(r1p[1]+r1_algn[1][2]-1)
r2p.append(r2p[1]+r2_algn[1][1]-1)
ty=1
print r1p[0],r1p[3],r2p[0],r2p[3],ty,insert,micro_homology
# print a[1],a[2],afa[1][a[1]-1:a[2]]
# if b_reverse:
# print b[1],b[2],reverse_complement(ref[1][b[2]-1:b[1]])
# else:
# print b[1],b[2],ref[1][b[1]-1:b[2]]
# print a,b
#Genome_LEN_1793 1277 1563; chr12:60845840-60847140 987 701; score = 27001.000000 (-)
#Genome_LEN_1793 321 1280; chr7:54413327-54414627 1301 342; score = 90161.000000 (-)