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

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

Extracting FASTA sequences based on position with perl script !!

By Shruti Paniwala 2856 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";
}