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

[Chris Fields]

add_date() is Bio::Seq::RichSeqI (not in Bio::Seq).  You could bless a  
Bio::Seq instance into a Bio::Seq::RichSeq:

bless $seq, 'Bio::Seq::RichSeq';

Though the best way to do this would be to have a Builder object  
create the proper class in the first place.

chris

On Feb 9, 2009, at 11:59 AM, Dave Jacoby wrote:

> 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!
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> -- 
> Dave Jacoby                         Address: WSLR S049
> Purdue Genomics Core                Mail:    jacoby at purdue.edu
>                                    Jabber:  jacoby at jabber.org
>                                    Phone:   hah!
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