in reply to Extracting field information from a GenBank file.

Hi all.

Thank you both for the help. In an effort to help others who might find this node, I have included my working code below (assuming of course the format of GenBank files does not change although given the sheer power of perl, modifications should be easy to make): 

#!/usr/bin/perl -w
use strict;
use autodie;

my $dna;
open FH, '<', 'fluseq.txt';
my $data = do {local $/; <FH>};

if ($data =~ /ORIGIN(.*)/s)
{
    $dna = $1;
    $dna =~ s/\s+//g;
    $dna =~ s/\d+//g;
    $dna =~ s/\/\///;
}

print $dna;

close FH;

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Re^2: Extracting field information from a GenBank file.
by hdb (Monsignor) on Jul 15, 2013 at 08:43 UTC

    A couple of comments on your code:

    • If the word 'ORIGIN' appears anywhere else in the test, your code would break.
    • If you use $/='ORIGIN' your file would automatically be split at all occurences of this word and you could just use the last bit.
    • Instead of removing all kinds of unwanted characters you could tell Perl to remove everything but a, c, g, and t.
    Most of it is clearly a matter of taste but it feels more direct to me this way: 

    use strict;
use autodie;

open my $fh, '<', 'fluseq.txt';
my @tmp = do {local $/='ORIGIN'; <$fh>};
my $dna = pop @tmp;
$dna =~ s/[^acgt]//gi; # delete all but a, c, g, and t
print $dna;

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