[Bioperl-l] Wanting to inject date into a SeqIO object

Hilmar Lapp hlapp at gmx.net
Mon Feb 9 12:45:23 EST 2009

Hi Dave,

$seq->add_date() is the right call, but not all output formats support  
dates. I don't remember exactly about the gcg format, but I do know  
that UniProt can have multiple dates, if that's what you want.

To clarify, did you actually try your second version below and found  
it not to work in the sense that the date did not show up in the  
output file?


On Feb 9, 2009, at 11:54 AM, Dave Jacoby wrote:

> I'm working with a database full of transposable elements. We input  
> things in FASTA format, and save the date of the upload into the  
> database separately. When we want to display in GCG format,  
> specifically, Bio::SeqIO::gcg can't find a date in the object and  
> uses the current date. Using a line out of the x2y.pl example from  
> the wiki,
> we would like to go from this:
>         while (my $inseq = $seq_in->next_seq) {
>            $seq_out->write_seq($inseq);
>         }
> to
>         while (my $inseq = $seq_in->next_seq) {
>            $inseq->add_date($DATE_FROM_DB) ;
>            $seq_out->write_seq($inseq);
>         }
> I have looked through the modules in Bio::SeqIO and I fail to  
> understand how to do such a thing. Can anyone help me?
> -- 
> Dave Jacoby                         Address: WSLR S049
> Purdue Genomics Core                Mail:    jacoby at purdue.edu
>                                    Jabber:  jacoby at jabber.org
>                                    Phone:   hah!
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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