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