eda-tools/old-boom/gen2chr

#!/usr/bin/perl

require "parser.pl";
require "match.pl";


sub translate
{
    local ($r) = @_;

    undef %field;
    $field{"REF"} = $r;
    &match_set_error($r);
    if (!&apply_rules()) {
	print "$id{$r}\n" if $negate;
	return;
    }
    return if $negate;
    print $id{$r};
    for (sort keys %field) {
	next if $_ =~ /^_/;
	next if $_ eq "REF";
	print " $_=$field{$_}";
    }
    print "\n";
}


sub usage
{
    print STDERR "usage: $0 [-d|-n] key file ...\n";
    print STDERR "       $0 -q query file ...\n";
    exit(1);
}

while ($ARGV[0] =~ /^-/) {
    if ($ARGV[0] eq "-d") {
	$debug = 1;
    } elsif ($ARGV[0] eq "-n") {
	$negate = 1;
    } elsif ($ARGV[0] eq "-q") {
	$query = 1;
    } else {
	&usage;
    }
    shift @ARGV;
}

$key = shift @ARGV;
&usage unless defined $key;

&parse;

if ($query) {
    $debug = 1;
    &translate($key);
    exit(0);
}

print "#CHR\n";
for (keys %id) {
    next unless $id{$_} eq "$key $_";
    &translate($_);
}