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125 lines
4.4 KiB
Python
Executable File
125 lines
4.4 KiB
Python
Executable File
#!/usr/bin/env python
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#Original script from /home/james/work/encode/feature_partitions/split_by_partitions.py
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#Usage: python(2.4) split_by_partitions.py partition_index in_file out_file chrCol startCol endCol strandCol
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from __future__ import division
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import sys
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from galaxy import eggs
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import pkg_resources; pkg_resources.require( "bx-python" )
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from bx.bitset import *
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from bx.bitset_builders import *
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assert sys.version_info[:2] >= ( 2, 4 )
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def stop_err( msg ):
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sys.stderr.write( msg )
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sys.exit()
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def main():
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partition_index = sys.argv[1]
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partition_offset = "/home/universe/encode_feature_partitions/" #should parse perhaps from index filepath
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warnings = []
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# Load up the partitions
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partitions = list()
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try:
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for line in open( partition_index ):
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name, score, filename = line.split()
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partitions.append( ( name, score, binned_bitsets_from_file( open( partition_offset+filename ) ) ) )
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except:
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stop_err( "Error loading partitioning dataset." )
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try:
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in_file = open( sys.argv[2] )
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except:
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stop_err( "Bad input data." )
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try:
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out_file = open( sys.argv[3], "w" )
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except:
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stop_err( "Bad output file." )
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try:
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chrCol = int( sys.argv[4] ) - 1
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except:
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stop_err( "Bad chr column: %s" % ( str( sys.argv[4] ) ) )
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try:
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startCol = int( sys.argv[5] ) - 1
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except:
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stop_err( "Bad start column: %s" % ( str( sys.argv[5] ) ) )
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try:
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endCol = int( sys.argv[6] ) - 1
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except:
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stop_err( "Bad end column: %s" % ( str( sys.argv[6] ) ) )
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try:
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strandCol = int( sys.argv[7] )-1
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except:
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strandCol = -1
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line_count = 0
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skipped_lines = 0
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first_invalid_line = None
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invalid_line = ''
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try:
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for line in in_file:
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line_count += 1
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line = line.rstrip( '\r\n' )
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if line and not line.startswith( '#' ):
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fields = line.split( '\t' )
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try:
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chr, start, end = fields[chrCol], int( fields[startCol] ), int( fields[endCol] )
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except:
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skipped_lines += 1
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if first_invalid_line is None:
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first_invalid_line = line_count
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invalid_line = line
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continue
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label = "input_line_" + str( line_count ) #if input file type was known to be bed, then could guess at label column
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if strandCol < 0:
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strand = "+"
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else:
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try:
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strand = fields[strandCol]
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except:
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strand = "+"
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# Find which partition it overlaps
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overlap = 0
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for name, score, bb in partitions:
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# Is there at least 1bp overlap?
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if chr in bb:
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overlap = bb[chr].count_range( start, end-start )
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if overlap > 0:
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break
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else:
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# No overlap with any partition? For now throw this since the
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# partitions tile the encode regions completely, indicate an interval
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# that does not even overlap an encode region
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warning = "warning: Interval (%s, %d, %d) does not overlap any partition" % ( chr, start, end ) + ", line[" + str( line_count ) + "]. "
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warnings.append( warning )
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name = "no_overlap"
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score = 0
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# Annotate with the name of the partition
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frac_overlap = overlap / ( end-start )
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# BED6 plus?
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print >>out_file, "%s\t%d\t%d\t%s\t%s\t%s\t%s\t%0.4f" % ( chr, start, end, label, score, strand, name, frac_overlap )
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except:
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out_file.close()
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in_file.close()
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stop_err( "Unknown error while processing line # %d: %s" % ( line_count, line ) )
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out_file.close()
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in_file.close()
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if warnings:
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warn_msg = "This tool is useful on ENCODE regions only, %d warnings, 1st is: " % len( warnings )
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warn_msg += warnings[0]
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print warn_msg
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if skipped_lines:
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print "Skipped %d invalid lines starting at line # %d: %s" % ( skipped_lines, first_invalid_line, invalid_line )
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if __name__ == "__main__": main()
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