BioPerl: extract CDS error

Question

I am trying to extract CDS and corresponding amino acid sequences from GenBank file using BioPerl. The script is shown below:

while (my $seq_object = $in->next_seq){
for my $feat_object ($seq_object->get_SeqFeatures) {
    if ($feat_object ->primary_tag eq "CDS") {
    #   warn("all tags are ", join ("," , $feat_object->get_all_tags),"\n");        
        if ($feat_object->has_tag ("protein_id")){
            my ($protein_id) = $feat_object->get_tag_values('protein_id');
            my ($pseq) = $feat_object->get_tag_values('translation') ;
            my ($pepseq) = Bio::Seq->new(-id => $protein_id , -description => $seq_object -> accession_number,
                -seq => $pseq);
            $out->write_seq($pepseq);   
        }
    }
}

}

I am getting error message as: Filehandle GEN1 opened only for input at /Library/Perl/5.12/Bio/Root/IO.pm line 533, line 148.

Kindly help me to solve this issue.

Thanks in advance

You didn't show us the whole script. How did you create `$out`? Is that a `Bio::SeqIO` object? — SES, Oct 23 '14 at 18:51
Yes, the $out file is a Bio::SeqIO object, which is created by: my $out = Bio::SeqIO->new( -file => "Oct_test.fasta", -format => 'fasta'); — RonnB, Oct 24 '14 at 06:03

score 0 · Accepted Answer · answered Oct 24 '14 at 17:56

I'll add this as an answer since it is likely the source of the error. When creating a Bio::SeqIO object for output, you must follow the normal Perl rules for open and specify the file is for output. So, try the following:

my $out = Bio::SeqIO->new( -file => ">Oct_test.fasta", -format => 'fasta');

This is a really easy thing to forget and the error message could be a bit more descriptive.

BioPerl: extract CDS error

1 Answers1