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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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