Mercurial > repos > xuebing > sharplabtool

comparison tools/regVariation/getIndels.py @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 #!/usr/bin/env python
2
3 """
4 Estimate INDELs for pair-wise alignments.
5
6 usage: %prog maf_input out_file1 out_file2
7 """
8
9 from __future__ import division
10 from galaxy import eggs
11 import pkg_resources
12 pkg_resources.require( "bx-python" )
13 try:
14 pkg_resources.require("numpy")
15 except:
16 pass
17 import psyco_full
18 import sys
19 from bx.cookbook import doc_optparse
20 from galaxy.tools.exception_handling import *
21 import bx.align.maf
22
23 assert sys.version_info[:2] >= ( 2, 4 )
24
25 def main():
26 # Parsing Command Line here
27 options, args = doc_optparse.parse( __doc__ )
28
29 try:
30 inp_file, out_file1 = args
31 except:
32 print >> sys.stderr, "Tool initialization error."
33 sys.exit()
34
35 try:
36 fin = open(inp_file,'r')
37 except:
38 print >> sys.stderr, "Unable to open input file"
39 sys.exit()
40 try:
41 fout1 = open(out_file1,'w')
42 #fout2 = open(out_file2,'w')
43 except:
44 print >> sys.stderr, "Unable to open output file"
45 sys.exit()
46
47 try:
48 maf_reader = bx.align.maf.Reader( open(inp_file, 'r') )
49 except:
50 print >>sys.stderr, "Your MAF file appears to be malformed."
51 sys.exit()
52 maf_count = 0
53
54 print >>fout1, "#Block\tSource\tSeq1_Start\tSeq1_End\tSeq2_Start\tSeq2_End\tIndel_length"
55 for block_ind, block in enumerate(maf_reader):
56 if len(block.components) < 2:
57 continue
58 seq1 = block.components[0].text
59 src1 = block.components[0].src
60 start1 = block.components[0].start
61 if len(block.components) == 2:
62 seq2 = block.components[1].text
63 src2 = block.components[1].src
64 start2 = block.components[1].start
65 #for pos in range(len(seq1)):
66 nt_pos1 = start1-1 #position of the nucleotide (without counting gaps)
67 nt_pos2 = start2-1
68 pos = 0 #character column position
69 gaplen1 = 0
70 gaplen2 = 0
71 prev_pos_gap1 = 0
72 prev_pos_gap2 = 0
73 while pos < len(seq1):
74 if prev_pos_gap1 == 0:
75 gaplen1 = 0
76 if prev_pos_gap2 == 0:
77 gaplen2 = 0
78
79 if seq1[pos] == '-':
80 if seq2[pos] != '-':
81 nt_pos2 += 1
82 gaplen1 += 1
83 prev_pos_gap1 = 1
84 #write 2
85 if prev_pos_gap2 == 1:
86 prev_pos_gap2 = 0
87 print >>fout1,"%d\t%s\t%s\t%s\t%s\t%s\t%s" %(block_ind+1,src2,nt_pos1,nt_pos1+1,nt_pos2-1,nt_pos2-1+gaplen2,gaplen2)
88 if pos == len(seq1)-1:
89 print >>fout1,"%d\t%s\t%s\t%s\t%s\t%s\t%s" %(block_ind+1,src1,nt_pos1,nt_pos1+1,nt_pos2+1-gaplen1,nt_pos2+1,gaplen1)
90 else:
91 prev_pos_gap1 = 0
92 prev_pos_gap2 = 0
93 """
94 if prev_pos_gap1 == 1:
95 prev_pos_gap1 = 0
96 print >>fout1,"%d\t%s\t%s\t%s\t%s" %(block_ind+1,src1,nt_pos1-1,nt_pos1,gaplen1)
97 elif prev_pos_gap2 == 1:
98 prev_pos_gap2 = 0
99 print >>fout1,"%d\t%s\t%s\t%s\t%s" %(block_ind+1,src2,nt_pos2-1,nt_pos2,gaplen2)
100 """
101 else:
102 nt_pos1 += 1
103 if seq2[pos] != '-':
104 nt_pos2 += 1
105 #write both
106 if prev_pos_gap1 == 1:
107 prev_pos_gap1 = 0
108 print >>fout1,"%d\t%s\t%s\t%s\t%s\t%s\t%s" %(block_ind+1,src1,nt_pos1-1,nt_pos1,nt_pos2-gaplen1,nt_pos2,gaplen1)
109 elif prev_pos_gap2 == 1:
110 prev_pos_gap2 = 0
111 print >>fout1,"%d\t%s\t%s\t%s\t%s\t%s\t%s" %(block_ind+1,src2,nt_pos1-gaplen2,nt_pos1,nt_pos2-1,nt_pos2,gaplen2)
112 else:
113 gaplen2 += 1
114 prev_pos_gap2 = 1
115 #write 1
116 if prev_pos_gap1 == 1:
117 prev_pos_gap1 = 0
118 print >>fout1,"%d\t%s\t%s\t%s\t%s\t%s\t%s" %(block_ind+1,src1,nt_pos1-1,nt_pos1,nt_pos2,nt_pos2+gaplen1,gaplen1)
119 if pos == len(seq1)-1:
120 print >>fout1,"%d\t%s\t%s\t%s\t%s\t%s\t%s" %(block_ind+1,src2,nt_pos1+1-gaplen2,nt_pos1+1,nt_pos2,nt_pos2+1,gaplen2)
121 pos += 1
122 if __name__ == "__main__":
123 main()