/tools/indels/indel_table.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 113 lines · 83 code · 7 blank · 23 comment · 38 complexity · f5fec1086a2be335914db99eba98fffa MD5 · raw file
- #!/usr/bin/env python
- """
- Combines several interval files containing indels with counts. All input files need to have the same number of columns.
- usage: %prog [options] [input3 sum3[ input4 sum4[ input5 sum5[...]]]]
- -1, --input1=1: The first input file
- -s, --sum1=s: Whether or not to include the totals from first file in overall total
- -2, --input2=2: The second input file
- -S, --sum2=S: Whether or not to include the totals from second file in overall total
- -o, --output=o: The interval output file for the combined files
- """
- import re, sys
- from galaxy import eggs
- import pkg_resources; pkg_resources.require( "bx-python" )
- from bx.cookbook import doc_optparse
- def stop_err( msg ):
- sys.stderr.write( '%s\n' % msg )
- sys.exit()
- def numeric_sort( text1, text2 ):
- """
- For two items containing space-separated text, compares equivalent pieces
- numerically if both numeric or as text otherwise
- """
- pieces1 = text1.split()
- pieces2 = text2.split()
- if len( pieces1 ) == 0:
- return 1
- if len( pieces2 ) == 0:
- return -1
- for i, pc1 in enumerate( pieces1 ):
- if i == len( pieces2 ):
- return 1
- if not pieces2[i].isdigit():
- if pc1.isdigit():
- return -1
- else:
- if pc1 > pieces2[i]:
- return 1
- elif pc1 < pieces2[i]:
- return -1
- else:
- if not pc1.isdigit():
- return 1
- else:
- if int( pc1 ) > int( pieces2[i] ):
- return 1
- elif int( pc1 ) < int( pieces2[i] ):
- return -1
- if i < len( pieces2 ) - 1:
- return -1
- return 0
- def __main__():
- # Parse Command Line
- options, args = doc_optparse.parse( __doc__ )
- inputs = [ options.input1, options.input2 ]
- includes = [ options.sum1, options.sum2 ]
- inputs.extend( [ a for i, a in enumerate( args ) if i % 2 == 0 ] )
- includes.extend( [ a for i, a in enumerate( args ) if i % 2 == 1 ] )
- num_cols = 0
- counts = {}
- # read in data from all files and get total counts
- try:
- for i, input in enumerate( inputs ):
- for line in open( input, 'rb' ):
- sp_line = line.strip().split( '\t' )
- # set num_cols on first pass
- if num_cols == 0:
- if len( sp_line ) < 4:
- raise Exception, 'There need to be at least 4 columns in the file: Chrom, Start, End, and Count'
- num_cols = len( sp_line )
- # deal with differing number of columns
- elif len( sp_line ) != num_cols:
- 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 )
- # get actual counts for each indel
- indel = '\t'.join( sp_line[:-1] )
- try:
- count = int( sp_line[-1] )
- except ValueError, e:
- 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 )
- # total across all included files
- if includes[i] == "true":
- try:
- counts[ indel ]['tot'] += count
- except ( IndexError, KeyError ):
- counts[ indel ] = { 'tot': count }
- # counts for ith file
- counts[ indel ][i] = count
- except Exception, e:
- stop_err( 'Failed to read all input files:\n%s' % str( e ) )
- # output combined results to table file
- try:
- output = open( options.output, 'wb' )
- count_keys = counts.keys()
- count_keys.sort( numeric_sort )
- for indel in count_keys:
- count_out = [ str( counts[ indel ][ 'tot' ] ) ]
- for i in range( len( inputs ) ):
- try:
- count_out.append( str( counts[ indel ][i] ) )
- except KeyError:
- count_out.append( '0' )
- output.write( '%s\t%s\n' % ( indel, '\t'.join( count_out ) ) )
- output.close()
- except Exception, e:
- stop_err( 'Failed to output data: %s' % str( e ) )
- if __name__=="__main__": __main__()