mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
Nate Coraor
7560751dc8
Whether running locally or via PBS, $PATH should now be handled in your user's environment. This also fixes problems like PYTHONPATH on the new blast nodes being wrong (because they are x86_64 and the frontends are i686). Note that you can actually start Galaxy without having an eggs dir now.
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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stop_err( "Bad strand column: %s" % ( str( sys.argv[7] ) ) )
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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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