def build_index(self, filename, indexfile):
        """
        Recipe from Brad Chapman's blog
        <http://bcbio.wordpress.com/2009/07/26/sorting-genomic-alignments-using-python/>
        """
        indexes = interval_index_file.Indexes()
        in_handle = open(filename)

        reader = maf.Reader(in_handle)
        while True:
            pos = reader.file.tell()
            rec = next(reader)
            if rec is None:
                break
            for c in rec.components:
                indexes.add(c.src, c.forward_strand_start,
                        c.forward_strand_end, pos, max=c.src_size )

        index_handle = open(indexfile, "w")
        indexes.write(index_handle)
        index_handle.close()
def build_index ( self , filename , indexfile ) : indexes = interval_index_file . Indexes ( ) in_handle = open ( filename ) reader = maf . Reader ( in_handle ) while True : pos = reader . file . tell ( ) rec = next ( reader ) if rec is None : break for c in rec . components : indexes . add ( c . src , c . forward_strand_start , c . forward_strand_end , pos , max = c . src_size ) index_handle = open ( indexfile , "w" ) indexes . write ( index_handle ) index_handle . close ( )
Recipe from Brad Chapman's blog
        <http://bcbio.wordpress.com/2009/07/26/sorting-genomic-alignments-using-python/>