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

[Dave Jacoby]

Hilmar Lapp wrote:
> 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?

No, I tried that second version and found it not to work in the sense 
that it made no sense of add_date().

     Can't locate method "add_date" via package "Bio::Seq">     -hilmar

> 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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>> Bioperl-l mailing list
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> 


-- 
Dave Jacoby                         Address: WSLR S049
Purdue Genomics Core                Mail:    jacoby at purdue.edu
                                     Jabber:  jacoby at jabber.org
                                     Phone:   hah!