19/map2exons.pl

#!/usr/bin/perl -w

use strict;

my %genome;

my $infile = 'chr7.txt';    # based on NCBI36 assembly

open(EXONS, $infile) or die "Could not open $infile\n";

while (<EXONS>) {
    unless (/^\#/) {
        chomp;
        my @columns = split("\t");

        if ( $columns[8] ) {    # if there is a protein identifier

            my $exonStarts = $columns[6];
            $exonStarts =~ s/\,$//;    # remove the trailing ','
            my @exonStarts = split( ',', $exonStarts );

            my $exonEnds = $columns[7];
            $exonEnds =~ s/\,$//;      # remove the trailing ','
            my @exonEnds = split( ',', $exonEnds );

            for ( my $i = 0 ; $i <= $#exonStarts ; $i++ ) {

                my $start = $exonStarts[$i];
                my $stop  = $exonEnds[$i];

                for ( my $j = $start ; $j <= $stop ; $j++ ) {

                    #  save name, strand and proteinID
                    $genome{$j} = "$columns[0] ";
                    $genome{$j} .= "$columns[2] $columns[8]";
                }
            }
        }
    }
}
close EXONS;

$infile = 'bushmen.out';

open(BUSHMEN, $infile) or die "Could not open $infile\n";

while (<BUSHMEN>) {
    my @columns = split("\t");
    my $pos     = $columns[1];
    if ( $genome{$pos} ) { print "$pos $genome{$pos}\n"; }
}
close BUSHMEN;