root/galaxy-central/tools/filters/gff_to_bed_converter.py @ 2

#!/usr/bin/env python
import sys
from galaxy import eggs
from galaxy.tools.util.gff_util import parse_gff_attributes

assert sys.version_info[:2] >= ( 2, 4 )

def get_bed_line( chrom, name, strand, blocks ):
    """ Returns a BED line for given data. """

    
    if len( blocks ) == 1:
        # Use simple BED format if there is only a single block:
        #   chrom, chromStart, chromEnd, name, score, strand
        #
        start, end = blocks[0]
        return "%s\t%i\t%i\t%s\t0\t%s\n" % ( chrom, start, end, name, strand )

    #
    # Build lists for transcript blocks' starts, sizes.
    #
    
    # Get transcript start, end.
    t_start = sys.maxint
    t_end = -1
    for block_start, block_end in blocks:
        if block_start < t_start:
            t_start = block_start
        if block_end > t_end:
            t_end = block_end
            
    # Get block starts, sizes.
    block_starts = []
    block_sizes = []
    for block_start, block_end in blocks:
        block_starts.append( str( block_start - t_start ) )
        block_sizes.append( str( block_end - block_start ) )
    
    #
    # Create BED entry.
    # Bed format: chrom, chromStart, chromEnd, name, score, strand, \
    #               thickStart, thickEnd, itemRgb, blockCount, blockSizes, blockStarts
    #
    return "%s\t%i\t%i\t%s\t0\t%s\t%i\t%i\t0\t%i\t%s\t%s\n" % \
            ( chrom, t_start, t_end, name, strand, t_start, t_start, len( block_starts ), 
                ",".join( block_sizes ), ",".join( block_starts ) )

def __main__():
    input_name = sys.argv[1]
    output_name = sys.argv[2]
    skipped_lines = 0
    first_skipped_line = 0
    out = open( output_name, 'w' )
    i = 0
    cur_transcript_chrom = None
    cur_transcript_id = None
    cur_transcript_strand = None
    cur_transcripts_blocks = [] # (start, end) for each block.
    for i, line in enumerate( file( input_name ) ):
        line = line.rstrip( '\r\n' )
        if line and not line.startswith( '#' ):
            try:
                # GFF format: chrom source, name, chromStart, chromEnd, score, strand, attributes
                elems = line.split( '\t' )
                start = str( long( elems[3] ) - 1 )
                coords = [ long( start ), long( elems[4] ) ]
                strand = elems[6]
                if strand not in ['+', '-']:
                    strand = '+'
                attributes = parse_gff_attributes( elems[8] )
                t_id = attributes.get( "transcript_id", None )
                    
                if not t_id:
                    #
                    # No transcript ID, so write last transcript and write current line as its own line.
                    #
                    
                    # Write previous transcript.
                    if cur_transcript_id:
                        # Write BED entry.
                        out.write( get_bed_line( cur_transcript_chrome, cur_transcript_id, cur_transcript_strand, cur_transcripts_blocks ) )
                    
                    # Replace any spaces in the name with underscores so UCSC will not complain.
                    name = elems[2].replace(" ", "_")
                    out.write( get_bed_line( elems[0], name, strand, [ coords ] ) )
                    continue
                
                # There is a transcript ID, so process line at transcript level.
                if t_id == cur_transcript_id:
                    # Line is element of transcript and will be a block in the BED entry.
                    cur_transcripts_blocks.append( coords )
                    continue
                    
                #
                # Line is part of new transcript; write previous transcript and start
                # new transcript.
                #
                
                # Write previous transcript.
                if cur_transcript_id:
                    # Write BED entry.
                    out.write( get_bed_line( cur_transcript_chrome, cur_transcript_id, cur_transcript_strand, cur_transcripts_blocks ) )

                # Start new transcript.
                cur_transcript_chrome = elems[0]
                cur_transcript_id = t_id
                cur_transcript_strand = strand
                cur_transcripts_blocks = []
                cur_transcripts_blocks.append( coords )    
            except:
                skipped_lines += 1
                if not first_skipped_line:
                    first_skipped_line = i + 1
        else:
            skipped_lines += 1
            if not first_skipped_line:
                first_skipped_line = i + 1
    
    # Write last transcript.
    if cur_transcript_id:
        # Write BED entry.
        out.write( get_bed_line( cur_transcript_chrome, cur_transcript_id, cur_transcript_strand, cur_transcripts_blocks ) )
    out.close()
    info_msg = "%i lines converted to BED.  " % ( i + 1 - skipped_lines )
    if skipped_lines > 0:
        info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." %( skipped_lines, first_skipped_line )
    print info_msg

if __name__ == "__main__": __main__()