root/galaxy-central/tools/indels/indel_table.py

リビジョン 2, 4.3 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1#!/usr/bin/env python
2
3"""
4Combines several interval files containing indels with counts. All input files need to have the same number of columns.
5
6usage: %prog [options] [input3 sum3[ input4 sum4[ input5 sum5[...]]]]
7   -1, --input1=1: The first input file
8   -s, --sum1=s: Whether or not to include the totals from first file in overall total
9   -2, --input2=2: The second input file
10   -S, --sum2=S: Whether or not to include the totals from second file in overall total
11   -o, --output=o: The interval output file for the combined files
12"""
13
14import re, sys
15from galaxy import eggs
16import pkg_resources; pkg_resources.require( "bx-python" )
17from bx.cookbook import doc_optparse
18
19
20def stop_err( msg ):
21    sys.stderr.write( '%s\n' % msg )
22    sys.exit()
23
24def numeric_sort( text1, text2 ):
25    """
26    For two items containing space-separated text, compares equivalent pieces
27    numerically if both numeric or as text otherwise
28    """
29    pieces1 = text1.split()
30    pieces2 = text2.split()
31    if len( pieces1 ) == 0:
32        return 1
33    if len( pieces2 ) == 0:
34        return -1
35    for i, pc1 in enumerate( pieces1 ):
36        if i == len( pieces2 ):
37            return 1
38        if not pieces2[i].isdigit():
39            if pc1.isdigit():
40                return -1
41            else:
42                if pc1 > pieces2[i]:
43                    return 1
44                elif pc1 < pieces2[i]:
45                    return -1
46        else:
47            if not pc1.isdigit():
48                return 1
49            else:
50                if int( pc1 ) > int( pieces2[i] ):
51                    return 1
52                elif int( pc1 ) < int( pieces2[i] ):
53                    return -1
54    if i < len( pieces2 ) - 1:
55        return -1
56    return 0
57
58def __main__():
59    # Parse Command Line
60    options, args = doc_optparse.parse( __doc__ )
61    inputs = [ options.input1, options.input2 ]
62    includes = [ options.sum1, options.sum2 ]
63    inputs.extend( [ a for i, a in enumerate( args ) if i % 2 == 0 ] )
64    includes.extend( [ a for i, a in enumerate( args ) if i % 2 == 1 ] )
65    num_cols = 0
66    counts = {}
67    # read in data from all files and get total counts
68    try:
69        for i, input in enumerate( inputs ):
70            for line in open( input, 'rb' ):
71                sp_line = line.strip().split( '\t' )
72                # set num_cols on first pass
73                if num_cols == 0:
74                    if len( sp_line ) < 4:
75                        raise Exception, 'There need to be at least 4 columns in the file: Chrom, Start, End, and Count'
76                    num_cols = len( sp_line )
77                # deal with differing number of columns
78                elif len( sp_line ) != num_cols:
79                    raise Exception, 'All of the files need to have the same number of columns (current %s != %s of first line)' % ( len( sp_line ), num_cols )
80                # get actual counts for each indel
81                indel = '\t'.join( sp_line[:-1] )
82                try:
83                    count = int( sp_line[-1] )
84                except ValueError, e:
85                    raise Exception, 'The last column of each file must be numeric, with the count of the number of instances of that indel: %s' % str( e )
86                # total across all included files
87                if includes[i] == "true":
88                    try:
89                        counts[ indel ]['tot'] += count
90                    except ( IndexError, KeyError ):
91                        counts[ indel ] = { 'tot': count }
92                # counts for ith file
93                counts[ indel ][i] = count
94    except Exception, e:
95        stop_err( 'Failed to read all input files:\n%s' % str( e ) )
96    # output combined results to table file
97    try:
98        output = open( options.output, 'wb' )
99        count_keys = counts.keys()
100        count_keys.sort( numeric_sort )
101        for indel in count_keys:
102            count_out = [ str( counts[ indel ][ 'tot' ] ) ]
103            for i in range( len( inputs ) ):
104                try:
105                    count_out.append( str( counts[ indel ][i] ) )
106                except KeyError:
107                    count_out.append( '0' )
108            output.write( '%s\t%s\n' % ( indel, '\t'.join( count_out ) ) )
109        output.close()
110    except Exception, e:
111        stop_err( 'Failed to output data: %s' % str( e ) )
112
113if __name__=="__main__": __main__()
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