Mercurial > repos > xuebing > sharplabtool

comparison tools/new_operations/subtract_query.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 # Greg Von Kuster
3
4 """
5 Subtract an entire query from another query
6 usage: %prog in_file_1 in_file_2 begin_col end_col output
7 """
8 import sys, re
9 from galaxy import eggs
10 import pkg_resources; pkg_resources.require( "bx-python" )
11 from bx.cookbook import doc_optparse
12
13 # Older py compatibility
14 try:
15 set()
16 except:
17 from sets import Set as set
18
19 assert sys.version_info[:2] >= ( 2, 4 )
20
21 def get_lines(fname, begin_col='', end_col=''):
22 lines = set([])
23 i = 0
24 for i, line in enumerate(file(fname)):
25 line = line.rstrip('\r\n')
26 if line and not line.startswith('#'):
27 if begin_col and end_col:
28 """Both begin_col and end_col must be integers at this point."""
29 try:
30 line = line.split('\t')
31 line = '\t'.join([line[j] for j in range(begin_col-1, end_col)])
32 lines.add( line )
33 except: pass
34 else:
35 lines.add( line )
36 if i: return (i+1, lines)
37 else: return (i, lines)
38
39 def main():
40
41 # Parsing Command Line here
42 options, args = doc_optparse.parse( __doc__ )
43
44 try:
45 inp1_file, inp2_file, begin_col, end_col, out_file = args
46 except:
47 doc_optparse.exception()
48
49 begin_col = begin_col.strip()
50 end_col = end_col.strip()
51
52 if begin_col != 'None' or end_col != 'None':
53 """
54 The user selected columns for restriction. We'll allow default
55 values for both begin_col and end_col as long as the user selected
56 at least one of them for restriction.
57 """
58 if begin_col == 'None':
59 begin_col = end_col
60 elif end_col == 'None':
61 end_col = begin_col
62 begin_col = int(begin_col)
63 end_col = int(end_col)
64 """Make sure that begin_col <= end_col (switch if not)"""
65 if begin_col > end_col:
66 tmp_col = end_col
67 end_col = begin_col
68 begin_col = tmp_col
69 else:
70 begin_col = end_col = ''
71
72 try:
73 fo = open(out_file,'w')
74 except:
75 print >> sys.stderr, "Unable to open output file"
76 sys.exit()
77
78 """
79 len1 is the number of lines in inp1_file
80 lines1 is the set of unique lines in inp1_file
81 diff1 is the number of duplicate lines removed from inp1_file
82 """
83 len1, lines1 = get_lines(inp1_file, begin_col, end_col)
84 diff1 = len1 - len(lines1)
85 len2, lines2 = get_lines(inp2_file, begin_col, end_col)
86
87 lines1.difference_update(lines2)
88 """lines1 is now the set of unique lines in inp1_file - the set of unique lines in inp2_file"""
89
90 for line in lines1:
91 print >> fo, line
92
93 fo.close()
94
95 info_msg = 'Subtracted %d lines. ' %((len1 - diff1) - len(lines1))
96
97 if begin_col and end_col:
98 info_msg += 'Restricted to columns c' + str(begin_col) + ' thru c' + str(end_col) + '. '
99
100 if diff1 > 0:
101 info_msg += 'Eliminated %d duplicate/blank/comment/invalid lines from first query.' %diff1
102
103 print info_msg
104
105 if __name__ == "__main__":
106 main()