/tools/filters/ucsc_gene_table_to_intervals.py

#!/usr/bin/env python

"""
Read a table dump in the UCSC gene table format and print a tab separated
list of intervals corresponding to requested features of each gene.

usage: ucsc_gene_table_to_intervals.py [options]

options:
  -h, --help                  show this help message and exit
  -rREGION, --region=REGION
                              Limit to region: one of coding, utr3, utr5, transcribed [default]
  -e, --exons                 Only print intervals overlapping an exon
  -i, --input=inputfile       input file
  -o, --output=outputfile     output file
"""

import optparse, string, sys

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

def main():

    # Parse command line    
    parser = optparse.OptionParser( usage="%prog [options] " )
    parser.add_option( "-r", "--region", dest="region", default="transcribed",
                       help="Limit to region: one of coding, utr3, utr5, transcribed [default]" )
    parser.add_option( "-e", "--exons",  action="store_true", dest="exons",
                       help="Only print intervals overlapping an exon" )
    parser.add_option( "-s", "--strand",  action="store_true", dest="strand",
                       help="Print strand after interval" )
    parser.add_option( "-i", "--input",  dest="input",  default=None,
                       help="Input file" )
    parser.add_option( "-o", "--output", dest="output", default=None,
                       help="Output file" )
    options, args = parser.parse_args()
    assert options.region in ( 'coding', 'utr3', 'utr5', 'transcribed' ), "Invalid region argument"
    
    try:
        out_file = open (options.output,"w")
    except:
        print >> sys.stderr, "Bad output file."
        sys.exit(0)
    
    try:
        in_file = open (options.input)
    except:
        print >> sys.stderr, "Bad input file."
        sys.exit(0)
    
    print "Region:", options.region+";"
    print "Only overlap with Exons:",
    if options.exons:
        print "Yes"
    else:
        print "No"
    
    # Read table and handle each gene
    for line in in_file:
        try:
            if line[0:1] == "#":
                continue
            # Parse fields from gene tabls
            fields = line.split( '\t' )
            name = fields[0]
            chrom = fields[1]
            strand = fields[2].replace(" ","_")
            tx_start = int( fields[3] )
            tx_end = int( fields[4] )
            cds_start = int( fields[5] )
            cds_end = int( fields[6] )

            # Determine the subset of the transcribed region we are interested in
            if options.region == 'utr3':
                if strand == '-': region_start, region_end = tx_start, cds_start
                else: region_start, region_end = cds_end, tx_end 
            elif options.region == 'utr5':
                if strand == '-': region_start, region_end = cds_end, tx_end
                else: region_start, region_end = tx_start, cds_start
            elif options.region == 'coding':
                region_start, region_end = cds_start, cds_end
            else:
                region_start, region_end = tx_start, tx_end

            # If only interested in exons, print the portion of each exon overlapping
            # the region of interest, otherwise print the span of the region
            if options.exons:
                exon_starts = map( int, fields[8].rstrip( ',\n' ).split( ',' ) )
                exon_ends = map( int, fields[9].rstrip( ',\n' ).split( ',' ) )
                for start, end in zip( exon_starts, exon_ends ):
                    start = max( start, region_start )
                    end = min( end, region_end )
                    if start < end:
                        if strand: print_tab_sep(out_file, chrom, start, end, name, "0", strand )
                        else: print_tab_sep(out_file, chrom, start, end )
            else:
                if strand: print_tab_sep(out_file, chrom, region_start, region_end, name, "0", strand )
                else: print_tab_sep(out_file, chrom, region_start, region_end )
        except:
            continue

def print_tab_sep(out_file, *args ):
    """Print items in `l` to stdout separated by tabs"""
    print >>out_file, string.join( [ str( f ) for f in args ], '\t' )

if __name__ == "__main__": main()