bioperl genbank into a hash

rolandomantilla has asked for the wisdom of the Perl Monks concerning the following question:

by the way I hate this Bioperl stuff but I'm having problem making a Genbank file into a hash using bioperl, this is what I have


use Bio::SeqIO;
use strict;

my $seqio= '';
my $seqobj= '';
my $seq_stats= '';
my %hash=();
my $seq='';

my $seqio = Bio::SeqIO ->new(-file=> "GenBank_Records.txt",
                            -format => 'genbank');
print "Enter Acc number";
$acc=<STDIN>;
chomp $acc;

$hash{$seq->accession_number}= $seq->seq;
print $hash{$acc};
        exit;
[download]

Comment on bioperl genbank into a hash Download Code

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Re: bioperl genbank into a hash by NetWallah (Canon) on Aug 15, 2011 at 02:05 UTC
$seq is a scalar that has been assigned the value of an empty string. Your code is attempting to access $seq as an object. I think what you need to do is to use the object $seqio instead, so your code should read: `$hash{ $seqio->accession_number() }= $seqio->seq();` [download] Also - it would be helpful to indicate what error you are getting. "I'm having a problem" is rather imprecise. "XML is like violence: if it doesn't solve your problem, use more."	[reply] [d/l]
Re: bioperl genbank into a hash by Cristoforo (Curate) on Aug 15, 2011 at 00:07 UTC
I am not famailiar with Bio modules, but found some here that may get the accession number you want to find.	[reply]
Re: bioperl genbank into a hash by pvaldes (Chaplain) on Aug 15, 2011 at 10:41 UTC
...and Global symbol "$acc" requires explicit package name: `my $acc=<STDIN>;` What's the problem exactly?	[reply] [d/l]