#!/usr/bin/perl

use strict;
use warnings;
# ^-- Just do it.

my $Gene     = 'ds_chY.xml';
my $filename = 'ID.txt';

open my $fh_i, '<', $Gene
  or die "Cannot open the file '$Gene': $!";
open my $fh_o, '>', $filename
  or die "Could not open file '$filename' $!";
# ^-- use the same style of open() and error message
#     for both file operations
# (I like to put chained and/or conditionals on the next line.)

print {$fh_o} "RS_SNPs\tsubSnpClass\n";
#       ^- use braced filehandles in order to make it explicit we're
#          writing to a file handle

# either use explicit variable for looping:
while (my $line = <$fh_i>) {
	$line =~ s/^\s+//;  # this is probably irrelevant

	# don't write to file immediately - wait a bit

	my ($ssId, $subSnpClass);
	if ( $line =~ /ssId=["](\S*)["]\s/ ) {  # regexp optimization
		$ssId = $1;     # -> no need to s/// and chop
	}
	if ( $line =~ /subSnpClass=["](\S*)["]/ ) {
		$subSnpClass = $1;
	}

	# ...in order to perform a small sanity check
	if (defined $ssId and defined $subSnpClass) {
		print {$fh_o} "$ssId\t$subSnpClass\n";
	}
	elsif (not defined $ssId and not defined $subSnpClass) {
		# nothing
	}
	else {
		print "Data inconsistency detected in line $line\n";
	}
}

# ... or use implicit variable $_:
while (<$fh_i>) {
	s/^\s+//;

	my ($ssId, $subSnpClass);

	if ( /ssId=["](\S*)["]\s/ ) {
		$ssId = $1;
	}
	if ( /subSnpClass=["](\S*)["]/ ) {
		$subSnpClass = $1;
	}

	if (defined $ssId and defined $subSnpClass) {
		print {$fh_o} "$ssId\t$subSnpClass\n";
	}
	elsif (not defined $ssId and not defined $subSnpClass) {
		# nothing
	}
	else {
		print "Data inconsistency detected in line ", $_, "\n";
	}
}