Mercurial > repos > arkarachai-fungtammasan > microsatellite_ngs

comparison PEsortedSAM2readprofile.py @ 0:20ab85af9505

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author arkarachai-fungtammasan
date Fri, 03 Oct 2014 20:54:30 -0400
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-1:000000000000 0:20ab85af9505
1 #!/usr/bin/env python
2
3 import sys
4 from galaxy import eggs
5 import pkg_resources
6 pkg_resources.require( "bx-python" )
7 import bx.seq.twobit
8
9 ##output columns: read_name chr prefix_start prefix_end TR_start TR_end suffix_start suffix_end TR_length TR_sequence
10
11 samf = open(sys.argv[1],'r') #assumes sam file is sorted by readname
12 seq_path = sys.argv[2] #Path to the reference genome in 2bit format
13
14 ##maxTRlength=int(sys.argv[4])
15 ##maxoriginalreadlength=int(sys.argv[5])
16 maxTRlength=int(sys.argv[3])
17 maxoriginalreadlength=int(sys.argv[4])
18 outfile=sys.argv[5]
19 fout = open(outfile,'w')
20
21 twobitfile = bx.seq.twobit.TwoBitFile( file( seq_path ) )
22
23 skipped=0
24 while True:
25 read = samf.readline().strip()
26 if not(read): #EOF reached
27 break
28 if read[0] == "@":
29 #print read
30 continue
31 mate = samf.readline().strip()
32 if not(mate): #EOF reached
33 break
34 read_elems = read.split()
35 mate_elems = mate.split()
36 read_name = read_elems[0].strip()
37 mate_name = mate_elems[0].strip()
38 while True:
39 if read_name == mate_name:
40 break
41 elif read_name != mate_name:
42 #print >>sys.stderr, "Input SAM file doesn't seem to be sorted by readname. Please sort and retry."
43 #break
44 skipped += 1
45 read = mate
46 read_elems = mate_elems
47 mate = samf.readline().strip()
48 read_name = read_elems[0].strip()
49 mate_name = mate_elems[0].strip()
50 if not(mate): #EOF reached
51 break
52 mate_elems = mate.split()
53 #extract XT:A tag
54 #for e in read_elems:
55 # if e.startswith('XT:A'):
56 # read_xt = e
57 #for e in mate_elems:
58 # if e.startswith('XT:A'):
59 # mate_xt = e
60 #if 'XT:A:U' not in read_elems or 'XT:A:U' not in mate_elems: #both read and it's mate need to be mapped uniquely
61 # continue
62 read_chr = read_elems[2]
63 read_start = int(read_elems[3])
64 read_cigar = read_elems[5]
65 if len(read_cigar.split('M')) != 2: #we want perfect matches only..cigar= <someInt>M
66 continue
67 read_len = int(read_cigar.split('M')[0])
68 mate_chr = mate_elems[2]
69 mate_start = int(mate_elems[3])
70 mate_cigar = mate_elems[5]
71 if len(mate_cigar.split('M')) != 2: #we want perfect matches only..cigar= <someInt>M
72 continue
73 mate_len = int(mate_cigar.split('M')[0])
74 if read_chr != mate_chr: # check that they were mapped to the same chromosome
75 continue
76 if abs(read_start - mate_start) > (maxoriginalreadlength+maxTRlength):
77 continue
78 if read_start < mate_start:
79 pre_s = read_start-1
80 pre_e = read_start-1+read_len
81 tr_s = read_start-1+read_len
82 tr_e = mate_start-1
83 suf_s = mate_start-1
84 suf_e = mate_start-1+mate_len
85 else:
86 pre_s = mate_start-1
87 pre_e = mate_start-1+mate_len
88 tr_s = mate_start-1+mate_len
89 tr_e = read_start-1
90 suf_s = read_start-1
91 suf_e = read_start-1+read_len
92 tr_len = abs(tr_e - tr_s)
93 if tr_len > maxTRlength:
94 continue
95 if pre_e >= suf_s: #overlapping prefix and suffix
96 continue
97 tr_ref_seq = twobitfile[read_chr][tr_s:tr_e]
98 ##print >>fout, "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" %(read_name,read_chr,pre_s,pre_e,tr_s,tr_e,suf_s,suf_e,tr_len,tr_ref_seq)
99 fout.writelines('\t'.join(map(str,[read_name,read_chr,pre_s,pre_e,tr_s,tr_e,suf_s,suf_e,tr_len,tr_ref_seq]))+'\n')
100
101 print "Skipped %d unpaired reads" %(skipped)