Mercurial > repos > xuebing > sharplabtool

comparison tools/samtools/pileup_interval.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 Condenses pileup format into ranges of bases.
5
6 usage: %prog [options]
7 -i, --input=i: Input pileup file
8 -o, --output=o: Output pileup
9 -c, --coverage=c: Coverage
10 -f, --format=f: Pileup format
11 -b, --base=b: Base to select
12 -s, --seq_column=s: Sequence column
13 -l, --loc_column=l: Base location column
14 -r, --base_column=r: Reference base column
15 -C, --cvrg_column=C: Coverage column
16 """
17
18 from galaxy import eggs
19 import pkg_resources; pkg_resources.require( "bx-python" )
20 from bx.cookbook import doc_optparse
21 import sys
22
23 def stop_err( msg ):
24 sys.stderr.write( msg )
25 sys.exit()
26
27 def __main__():
28 strout = ''
29 #Parse Command Line
30 options, args = doc_optparse.parse( __doc__ )
31 coverage = int(options.coverage)
32 fin = file(options.input, 'r')
33 fout = file(options.output, 'w')
34 inLine = fin.readline()
35 if options.format == 'six':
36 seqIndex = 0
37 locIndex = 1
38 baseIndex = 2
39 covIndex = 3
40 elif options.format == 'ten':
41 seqIndex = 0
42 locIndex = 1
43 if options.base == 'first':
44 baseIndex = 2
45 else:
46 baseIndex = 3
47 covIndex = 7
48 else:
49 seqIndex = int(options.seq_column) - 1
50 locIndex = int(options.loc_column) - 1
51 baseIndex = int(options.base_column) - 1
52 covIndex = int(options.cvrg_column) - 1
53 lastSeq = ''
54 lastLoc = -1
55 locs = []
56 startLoc = -1
57 bases = []
58 while inLine.strip() != '':
59 lineParts = inLine.split('\t')
60 try:
61 seq, loc, base, cov = lineParts[seqIndex], int(lineParts[locIndex]), lineParts[baseIndex], int(lineParts[covIndex])
62 except IndexError, ei:
63 if options.format == 'ten':
64 stop_err( 'It appears that you have selected 10 columns while your file has 6. Make sure that the number of columns you specify matches the number in your file.\n' + str( ei ) )
65 else:
66 stop_err( 'There appears to be something wrong with your column index values.\n' + str( ei ) )
67 except ValueError, ev:
68 if options.format == 'six':
69 stop_err( 'It appears that you have selected 6 columns while your file has 10. Make sure that the number of columns you specify matches the number in your file.\n' + str( ev ) )
70 else:
71 stop_err( 'There appears to be something wrong with your column index values.\n' + str( ev ) )
72 # strout += str(startLoc) + '\n'
73 # strout += str(bases) + '\n'
74 # strout += '%s\t%s\t%s\t%s\n' % (seq, loc, base, cov)
75 if loc == lastLoc+1 or lastLoc == -1:
76 if cov >= coverage:
77 if seq == lastSeq or lastSeq == '':
78 if startLoc == -1:
79 startLoc = loc
80 locs.append(loc)
81 bases.append(base)
82 else:
83 if len(bases) > 0:
84 fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases)))
85 startLoc = loc
86 locs = [loc]
87 bases = [base]
88 else:
89 if len(bases) > 0:
90 fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases)))
91 startLoc = -1
92 locs = []
93 bases = []
94 else:
95 if len(bases) > 0:
96 fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases)))
97 if cov >= coverage:
98 startLoc = loc
99 locs = [loc]
100 bases = [base]
101 else:
102 startLoc = -1
103 locs = []
104 bases = []
105 lastSeq = seq
106 lastLoc = loc
107 inLine = fin.readline()
108 if len(bases) > 0:
109 fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases)))
110 fout.close()
111 fin.close()
112
113 # import sys
114 # strout += file(fout.name,'r').read()
115 # sys.stderr.write(strout)
116
117 if __name__ == "__main__" : __main__()