bx-python / scripts / 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] < gene_table.txt

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
"""

import optparse, string, sys

def main():
    # Parse command line    
    parser = optparse.OptionParser( usage="%prog [options] < gene_table.txt" )
    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( "-b", "--nobin",  action="store_false", dest="discard_first_column", default=True,
                       help="file doesn't contain a 'bin' column (use this for pre-hg18 files)" )
    options, args = parser.parse_args()
    assert options.region in ( 'coding', 'utr3', 'utr5', 'transcribed' ), "Invalid region argument"

    # Read table from stdin and handle each gene
    for line in sys.stdin:

        # Parse fields from gene tabls
        fields = line.split( '\t' )
        if (options.discard_first_column): fields.pop(0)
        chrom = fields[1]
        strand = fields[2]
        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( chrom, start, end, strand )
                    else: print_tab_sep( chrom, start, end )
        else:
            if strand: print_tab_sep( chrom, region_start, region_end, strand )
            else: print_tab_sep( chrom, region_start, region_end )

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

if __name__ == "__main__": main()
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