Enhance GFF-to-BED converter to output block data. Added test for new functionality.

lib/galaxy/tools/util/gff_util.py

@@ -39,4 +39,22 @@ def convert_gff_coords_to_bed( interval ):
     elif type ( interval ) is list:
         interval[ 0 ] -= 1
     return interval
-    
+    
+def parse_gff_attributes( attr_str ):
+    """
+    Parses a GFF attribute string and returns a dictionary of name-value pairs. 
+    The general format for a GFF attribute string is name1 "value1" ; name2 "value2"
+    """
+    attributes_list = attr_str.split(";")
+    attributes = {}
+    for name_value_pair in attributes_list:
+        pair = name_value_pair.strip().split(" ")
+        if pair == '':
+            continue
+        name = pair[0].strip()
+        if name == '':
+            continue
+        # Need to strip double quote from values
+        value = pair[1].strip(" \"")
+        attributes[ name ] = value
+    return attributes

tools/filters/gff2bed.xml

@@ -1,4 +1,4 @@
-<tool id="gff2bed1" name="GFF-to-BED">
+<tool id="gff2bed1" name="GFF-to-BED" version="1.0.1">
   <description>converter</description>
   <command interpreter="python">gff_to_bed_converter.py $input $out_file1</command>
   <inputs>
@@ -12,6 +12,10 @@
       <param name="input" value="5.gff" ftype="gff"/>
       <output name="out_file1" file="gff2bed_out.bed"/>
     </test>
+    <test>
+      <param name="input" value="gff2bed_in2.gff" ftype="gff"/>
+      <output name="out_file1" file="gff2bed_out2.bed"/>
+    </test>
   </tests>
   <help>
 

tools/filters/gff_to_bed_converter.py

@@ -1,8 +1,50 @@
 #!/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]
@@ -10,18 +52,61 @@ def __main__():
     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( int( elems[3] ) - 1 )
+                start = str( long( elems[3] ) - 1 )
+                coords = [ long( start ), long( elems[4] ) ]
                 strand = elems[6]
                 if strand not in ['+', '-']:
                     strand = '+'
-                # GFF format: chrom source, name, chromStart, chromEnd, score, strand
-                # Bed format: chrom, chromStart, chromEnd, name, score, strand
-                out.write( "%s\t%s\t%s\t%s\t0\t%s\n" %( elems[0], start, elems[4], elems[2], 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:
@@ -30,6 +115,11 @@ def __main__():
             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: