Perl script to extract fasta sequence by matching name/ids !!

Surabhi Chaudhary — Tue, 21 Jun 2016 09:28:19 -0500

#!/usr/bin/perl

use strict;
use warnings;
use Text::Trim qw(trim);

#Usage perl extractSeqbyID.pl ids.txt seq.fasta Result.fasta

$ARGV[2] or die "use extractSeqbyID.pl LIST FASTA OUT\n";

my $list = shift @ARGV;
my $fasta = shift @ARGV;
my $out = shift @ARGV;
my %select;

open LINE, "$list" or die;
while () {
    chomp;
    next if /^\s*$/;
    s/>//g; 
    my @ids=split (/\t/, $_);
    $select{$ids[0]} = 1;
}
my $size = keys %select;
print "Total Ids $size\n";
close LINE;

$/ = "\n>";
open OUT, ">$out" or die;
open FILE, "$fasta" or die;
while () {
    trim($_);
    s/>//g;
    my ($id) = split (/\n/, $_);
    #my @i=split (/\s/, $id); # To avoid >flattened_line_10751 circular cases
    print OUT ">$_" if (defined $select{$id});
}
close FILE;
close OUT;

BOL: Perl script to extract fasta sequence by matching name/ids !!

Perl script to extract fasta sequence by matching name/ids !!