perl - Parsing a GenBank file

Question

I trying to parse a GenBank file so I could get the accession number, the definition, the size of the file and the DNA sequence

Is there a way to modify my code and make it shorter and just declare all the variables at once like they do in the book and parse the file in one or two blocks of code?

Answer 1

If you have access to Bio Perl, you might find a solution such as the following.

#!/usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;

my $in  = Bio::SeqIO->new( -file   => "input.txt",
                           -format => 'GenBank');

while ( my $seq = $in->next_seq ) {
    my $acc = $seq->accession;
    my $length = $seq->length;
    my $definition = $seq->desc;
    my $type = $seq->molecule;
    my $organism = $seq->species->binomial;

    if ($type eq 'mRNA'              &&
        $organism =~ /homo sapiens/i &&
        $acc =~ /[A-Za-z]{2}_[0-9]{6,}/ )
    {
        print "$acc | $definition | $length
";
        print $seq->seq, "
";
        print "
";
    }
}

I was able to capture the 5 variables from a sample GenBank file I have (input.txt). It should simplify your code.