/tools/indels/indel_table.py

  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__()