annotate rapsodyn/listfiltering.pl @ 9:ad321ff1b67d draft

Uploaded

#!/usr/bin/perl
use strict;
use Getopt::Long;

my $inputfile;
my $headerfile;
my $nb_col=1;
my %header;

if ($#ARGV<0){
	print "\n";
	print "perl 021_ListFiltering.pl -input_file <file> -header_file <file> -nb_col <integer>[1]\n";
	exit(0);
}

GetOptions (
"input_file=s" => \$inputfile,
"header_file=s" => \$headerfile,
"nb_col=i" => \$nb_col
) or die("Error in command line arguments\n");

open(HF, $headerfile)  or die("Can't open $headerfile\n");
while (my $line=<HF>){
	chomp($line);
	my @fields = split(/\s+/,$line);
	my $ref="";
	my $compt=0;
	while ($compt<$nb_col){
		if ($ref){$ref.="\t";}
		$ref.=$fields[$compt];
		$compt++;
	}
	# my $ref = "$fields[0]\t$fields[1]";
	$header{$ref}=$line;
}
close (HF);


open(IF, $inputfile)  or die("Can't open $inputfile\n");
while (my $line=<IF>){
	my @fields = split(/\s+/,$line);
	my $ref="";
	my $compt=0;
	while ($compt<$nb_col){
		if ($ref){$ref.="\t";}
		$ref.=$fields[$compt];
		$compt++;
	}
	# my $ref = "$fields[0]\t$fields[1]";

	if ($header{$ref}){
		# print $line;
		# print $header{$ref},"\n";
	}
	else {
		print $line;
	}
	
}
close(IF);