view non_miRNA_reads.pl @ 52:8b8c356e6db5 draft

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#!/usr/bin/perl -w
#Filename:
#Author: Tian Dongmei
#Email: [e-mail]
#Date: 2013/7/19
#Modified:
#Description: 
my $version=1.00;

use strict;
use Getopt::Long;

my %opts;
GetOptions(\%opts,"i=s","fa=s","o=s","h");
if (!(defined $opts{i} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments
&usage;
}

my $filein=$opts{'fa'};
my $fileout=$opts{'o'};

open IN,"<$filein"; #input file  
my (%fa,%seq);
while (my $aline=<IN>){
	chomp $aline;
	$aline=~s/^>//;
	my $seq=<IN>;
	chomp $seq;
	#$seq{$seq}=$aline;
	$fa{$aline}=$seq;
}
close IN;

open IN,"<$opts{i}";
while(my $aline=<IN>){
	chomp $aline;
	if($aline=~/^\S+_x\d+/){
		$aline=~/^(\S+_x\d+)/;
		my $name=$1;
		delete($fa{$name});
	}
}
close IN;

open OUT,">$fileout"; #output file  
foreach my $key (keys %fa) {
	print OUT ">$key\n$fa{$key}\n";
}
close OUT;
sub usage{
print <<"USAGE";
Version $version
Usage:
$0 -i -o
options:
-i input file
-o output file
-h help
USAGE
exit(1);
}