#!/usr/bin/perl -w
#
# separador.pl
#
#   separa per cromosomes
#
# bmorancho & jplanas - UPF - 2002/02/28
# 

use strict;

my $PROG = "$0";
my $s;

if (scalar(@ARGV < 1)) {
    print "USAGE: $PROG <cromosoma>\n";
    exit (1);
    return;
};

my $crom_name_file = "seqs".$ARGV[0].".txt";

open(SEQS, "< refseq.gff");
open(CROM, "> $crom_name_file");

while (<SEQS>) {
    if ($. % 500 == 0) {print STDERR "."}
    next if /^\d+\s*\t*$/o;
    next if /random\t/o;
    next if /^\s*$/o; # skip empty lines
    my @f = split/\t/,$_;	
    $f[0] =  substr($f[0],3);
    if ($f[0] eq "X") {$f[0] = 23;};
    if ($f[0] eq "Y") {$f[0] = 24;};
    next if $f[0] != $ARGV[0];
    print CROM $_;
    $s = $.;
    next;
};
print "[$s]\n";

close(SEQS);
close(CROM);


my $snp_name_file = "snp".$ARGV[0].".txt";

open(SNPS, "< snpNih.txt");
open(CROM, "> $snp_name_file");

while (<SNPS>) {
    if ($. % 5000 == 0) {print STDERR "."}
    next if /^\d+\s*\t*$/o;
    next if /random\t/o;
    next if /^\s*$/o; # skip empty lines
    my @f = split/\t/,$_;
    $f[1] = substr($f[1],3);
    if ($f[1] eq "X") {$f[1] = 23;};
    if ($f[1] eq "Y") {$f[1] = 24;};
    next if $f[1] != $ARGV[0];
    print CROM $_;
    $s = $.;
    next;
};
print "[$s]\n";

close(SNPS);
close(CROM);

#
# END