-
Notifications
You must be signed in to change notification settings - Fork 1
/
hapCall_ABABA_for_input.py
executable file
·202 lines (114 loc) · 5.56 KB
/
hapCall_ABABA_for_input.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
195
196
197
198
199
200
201
202
from __future__ import division
import sys
#input the sample numbers as in the bamlist
#expect "yes" or "no" for "transversions only"
#last input is the hapCall file
#unadmixed
H1_index = int(sys.argv[1]) + 2
#admixed?
H2_index = int(sys.argv[2]) + 2
#H3 will be the admixer
H3_index = int(sys.argv[3]) + 2
#confounder
H4_index = int(sys.argv[4]) + 2
outgroup_index = int(sys.argv[5]) + 2
transversions_only = sys.argv[6]
nABABA = 0
nBAABA = 0
nABBBA = 0
nBABBA = 0
nABBAA = 0
nBABAA = 0
nBBBAA = 0
nAAABA = 0
nBBABA = 0
nAABAA = 0
nABAAA = 0
nBAAAA = 0
nAAAAA = 0
nBBBBA = 0
with open(sys.argv[7]) as file:
for line in file:
if line.startswith("chr"):
continue
line = line.rstrip("\n")
split_line = line.split("\t")
observed_bases = [split_line[H1_index], split_line[H2_index], split_line[H3_index], split_line[H4_index], split_line[outgroup_index]]
if "N" in observed_bases:
continue
observed_bases_unique = list( dict.fromkeys(observed_bases) )
if (len(observed_bases_unique) != 2):
continue
if ( ("C" in observed_bases_unique) and ("T" in observed_bases_unique) ) or ( ("G" in observed_bases_unique) and ("A" in observed_bases_unique) ) and (transversions_only == "yes"):
continue
#extract and count ABABA sites
if ( observed_bases[4] == observed_bases[0]) and ( observed_bases[4] == observed_bases[2]) and ( observed_bases[1] == observed_bases[3]) and (observed_bases[3] != observed_bases[4]):
#print str(observed_bases) + " ABABA"
nABABA += 1
continue
#BAABA sites
if ( observed_bases[4] == observed_bases[1]) and ( observed_bases[4] == observed_bases[2]) and ( observed_bases[0] == observed_bases[3]) and (observed_bases[0] != observed_bases[4]):
#print str(observed_bases) + " BAABA"
nBAABA += 1
continue
#ABBBA sites
if ( observed_bases[4] == observed_bases[0]) and ( observed_bases[1] == observed_bases[2]) and ( observed_bases[1] == observed_bases[3]) and (observed_bases[3] != observed_bases[4]):
#print str(observed_bases) + " ABBBA"
nABBBA += 1
continue
#BABBA sites
if ( observed_bases[4] == observed_bases[1]) and ( observed_bases[0] == observed_bases[2]) and ( observed_bases[0] == observed_bases[3]) and (observed_bases[4] != observed_bases[0]):
#print str(observed_bases) + " BABBA"
nBABBA += 1
continue
#ABBAA sites
if ( observed_bases[4] == observed_bases[0]) and ( observed_bases[1] == observed_bases[2]) and (observed_bases[3] == observed_bases[4]):
#print str(observed_bases) + " ABBAA"
nABBAA += 1
continue
#BABAA sites
if ( observed_bases[4] == observed_bases[1]) and ( observed_bases[0] == observed_bases[2]) and ( observed_bases[1] == observed_bases[3]) and (observed_bases[0] != observed_bases[4]):
#print str(observed_bases) + " BABAA"
nBABAA += 1
continue
#BBBAA sites
if ( observed_bases[4] == observed_bases[3]) and ( observed_bases[0] == observed_bases[2]) and ( observed_bases[1] == observed_bases[0]) and (observed_bases[0] != observed_bases[4]):
nBBBAA += 1
continue
#nAAABA sites
if ( observed_bases[4] == observed_bases[0]) and ( observed_bases[0] == observed_bases[1]) and ( observed_bases[1] == observed_bases[2]) and (observed_bases[3] != observed_bases[4]):
nAAABA += 1
continue
#BBABA sites
if ( observed_bases[4] == observed_bases[2]) and ( observed_bases[0] == observed_bases[1]) and ( observed_bases[1] == observed_bases[3]) and (observed_bases[0] != observed_bases[4]):
nBBABA += 1
continue
#AABAA sites
if ( observed_bases[4] == observed_bases[0]) and ( observed_bases[0] == observed_bases[1]) and ( observed_bases[1] == observed_bases[3]) and (observed_bases[2] != observed_bases[4]):
nAABAA += 1
continue
#ABAAA sites
if ( observed_bases[4] == observed_bases[0]) and ( observed_bases[0] == observed_bases[2]) and ( observed_bases[2] == observed_bases[3]) and (observed_bases[1] != observed_bases[4]):
nABAAA += 1
continue
#BAAAA sites
if ( observed_bases[4] == observed_bases[1]) and ( observed_bases[1] == observed_bases[2]) and ( observed_bases[2] == observed_bases[3]) and (observed_bases[0] != observed_bases[4]):
nBAAAA += 1
continue
if ( observed_bases[4] == observed_bases[1]) and ( observed_bases[1] == observed_bases[2]) and ( observed_bases[2] == observed_bases[3]) and (observed_bases[0] == observed_bases[4]):
nAAAAA += 1
if ( observed_bases[4] != observed_bases[0]) and ( observed_bases[1] == observed_bases[2]) and ( observed_bases[2] == observed_bases[3]) and (observed_bases[0] == observed_bases[1]):
nBBBBA += 1
print "dummy\tdummy\t" + str(nAAAAA) + "\t" + str(nAAABA) + "\t"+ str(nAABAA) + "\t" + str(nAABBA) + "\t" + str(nABAAA) + "\t" + str(nABABA) + "\t" + str(nABBAA) + "\t" + str(nABBBA) + "\t" + str(nBAAAA) + "\t" + str(nBAABA) + "\t" + str(nBABAA) + "\t" + str(nBABBA) + "\t" + str(nBBAAA) + "\t" + str(nBBABA) + "\t" + str(nBBBAA) + "\t" + str(nBBBBA)
print "nABABA: " + str(nABABA)
print "nBAABA: " + str(nBAABA)
print "nABBBA: " + str(nABBBA)
print "nBABBA: " + str(nBABBA)
print "nABBAA: " + str(nABBAA)
print "nBABAA: " + str(nBABAA)
print "nBBBAA: " + str(nBBBAA)
print "nAAABA: " + str(nAAABA)
print "nBBABA: " + str(nBBABA)
print "nAABAA: " + str(nAABAA)
print "nABAAA: " + str(nABAAA)
print "nBAAAA: " + str(nBAAAA)