diff tools/indels/indel_table.py @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/indels/indel_table.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,113 @@
+#!/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__()