-
Notifications
You must be signed in to change notification settings - Fork 0
/
benchmark.py
194 lines (182 loc) · 6.22 KB
/
benchmark.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
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
from benchlib import *
import sys
Percentage=0.8
near=-1
Contigs=None
Contigs=None#["22"]
Samples=None
Samples=None#["HG00403"]
SamplesFile=None#one sample name per line
PrintResult=False
PrintOuts=False
PrintSample=None
MinLength=0#Minimum Variant Length
MinScore=0
MaxAF=1#Max allele frequency, only apply for gold standard
#GSF='/mnt/c/Users/CRE/Productive/Programming/data/HG00514.BIP-unified.vcf.gz'
#GSF='/mnt/c/Users/CRE/Productive/Programming/data/ALL_Illumina_Integrate_20170206.vcf.gz'
#GSF='/mnt/c/Users/CRE/Productive/Programming/data/delly.bcf'
#GSF='/mnt/c/Users/CRE/Productive/Programming/data/nstd152.GRCh38.variant_call.vcf.gz'
#GSF='/mnt/c/Users/CRE/Productive/Programming/data/chr22_indels_HG00403.recode.vcf'
GSF='/home/cre/data/chr22_indels_CHS.recode.vcf'
#GSF='/mnt/c/Users/CRE/Productive/Programming/Workspace/jc/results/CHS_chr22_hs37d5_nc.vcf'
#GSF='/mnt/c/Users/CRE/Productive/Programming/data/delly_hs37d5_HG004xx.bcf'
MyF=[]#"test/512-4_chr22_testcall.txt"
Merge=False
MG=""
Format="VCF"
if len(sys.argv)>1:
i=1
while i<len(sys.argv):
a=sys.argv[i]
if a=="-G":
GSF=sys.argv[i+1]
i+=1
elif a=='-F':
Format=sys.argv[i+1]
i+=1
elif a=='-C':
if Contigs==None:
Contigs=[sys.argv[i+1]]
else:
Contigs.append(sys.argv[i+1])
i+=1
elif a=='-S':
Samples=[sys.argv[i+1]]
i+=1
elif a=='-SF':
SamplesFile=sys.argv[i+1]
i+=1
elif a=='-ML':
MinLength=int(sys.argv[i+1])
i+=1
elif a=='-MAF':
MaxAF=float(sys.argv[i+1])
i+=1
elif a=="-PO":
PrintOuts=True
elif a=="-PS":
PrintSample=sys.argv[i+1]
i+=1
elif a=="-PD":
PrintResult=True
elif a=="-MSC":
MinScore=float(sys.argv[i+1])
i+=1
elif a=="-P":
Percentage=float(sys.argv[i+1])
i+=1
elif a=="-M":
Merge=True
elif a=="-MG":#merge groups, 10,1,3 to indicate number of vcfs of each group
MG=sys.argv[i+1]
i+=1
else:
MyF.append(a)
i+=1
if SamplesFile!=None:
Samples=[]
SF=open(SamplesFile,"r")
for line in SF:
if line.strip()!="":
Samples.append(line.strip())
SF.close()
Gold=VariantRecords("Gold")
Gold.parseVcfCNV(GSF,Contigs,Samples,MinLength,MaxAF)
if PrintSample!=None:
Gold.printSample(PrintSample)
exit(0)
if (not Merge) or len(MyF)==1:
Test=VariantRecords("Test")
for i in range(len(MyF)):
try:
Test.parseVcfCNV(MyF[i],Contigs,Samples,MinLength,1,MinScore)
except Exception as e:
print(e,file=sys.stderr)
print(Test.interpret(Test.matchAll(Gold,Percentage),PrintResult))
else:
#Merge rule: same type overlap>=MergeThreshold or match to same gs
MergeThreshold=0.95
if MG!="":
MG=MG.split(",")
for i in range(len(MG)):
MG[i]=int(MG[i])
else:
for i in range(len(MyF)):
MG.append(1)
Tests=[]
TResults=[]
Matched=[]
MyFL=0
for i in range(len(MG)):
Tests.append(VariantRecords("Test%s"%i))
Test=Tests[-1]
for j in range(MyFL, MyFL+MG[i]):
try:
Test.parseVcfCNV(MyF[j],Contigs,Samples,MinLength,1,MinScore)
except Exception as e:
print(e,file=sys.stderr)
MyFL+=MG[i]
TResults.append(Test.matchAll(Gold,Percentage))
Matched.append([])
for ss in TResults[-1]["Samples"]:
if TResults[-1]["Samples"][ss]==None:
continue
for m in TResults[-1]["Samples"][ss]:
Matched[-1].append(m[1])
Tests[i].Variants.sort()
MergedN=[0,0,0,0]#Merged Del, Merged Dup, Merged Matched DEL, merged Matched DUP
SameMergeN=0
for i in range(len(MG)):
Test=Tests[i]
j=0
while j< len(Test.Variants):
v=Test.Variants[j]
Merged=False
for k in range(len(MG)):
if k==i:
continue
m=0
while m < len(Tests[k].Variants):
x=Tests[k].Variants[m]
if x.Start>v.End:
break
if x.Type!=v.Type or x.Sample!=v.Sample:
m+=1
continue
Over=calcOverlap(v.Start,v.End,x.Start,x.End)
if (Over/(v.End-v.Start)>=MergeThreshold and Over/(x.End-x.Start)>=MergeThreshold) or (v.MatchTo!=None and v.MatchTo==x.MatchTo):
if x.MatchTo!=None:
MergedN[2+(0 if v.Type=="DEL" else 1)]+=1
if x.MatchTo==v.MatchTo:
SameMergeN+=1
if v.MatchTo!=None and v.MatchTo==x.MatchTo:
try:
Matched[i].remove(v.MatchTo)
Matched[k].remove(x.MatchTo)
except ValueError:
pass
del Tests[k].Variants[m]
Merged=True
MergedN[0 if v.Type=="DEL" else 1]+=1
continue
m+=1
if False and (not Merged) and v.MatchTo!=None:
for k in range(len(MG)):
if k==i:
continue
if v.MatchTo in Matched[k]:
Matched[k].remove(v.MatchTo)
del Test.Variants[j]
MergedN[0 if v.Type=="DEL" else 1]+=1
MergedN[2+(0 if v.Type=="DEL" else 1)]+=1
break
j+=1
print(MergedN,SameMergeN,file=sys.stderr)
Test=VariantRecords("Test")
for i in range(len(MyF)):
try:
Test.parseVcfCNV(MyF[i],Contigs,Samples,MinLength,1,MinScore)
except Exception as e:
print(e,file=sys.stderr)
print(Test.interpret(Test.matchAll(Gold,Percentage),PrintResult,MergedN))