BOL: Extracting FASTA sequences based on position with perl script !!

BioScripts
Shruti Paniwala
Extracting FASTA sequences based on position with perl script !!

Extracting FASTA sequences based on position with perl script !!

By Shruti Paniwala 2823 days ago

#!/usr/bin/env perl
 
#Uses: perl sub-seq.pl input.txt range
 
use strict;
use warnings;
 
my $end   = pop;
my $start = pop;
local $/ = '>';
 
while (<>) {
    chomp;
    next unless /(.+)/;
    my ($header) = "$/$1_$start-$end\n";
    my $seq = ${^POSTMATCH};
    $seq =~ s/\s//g;
    print $header;
    print +( substr $seq, $start - 1, $end ) . "\n";
}