[Bioperl-l] seq object usage

Fields, Christopher J cjfields at illinois.edu
Tue Jun 12 11:26:49 EDT 2012


Bio::LiveSeq is supposed to handle cases like this:

http://www.bioperl.org/wiki/HOWTO:Bioperl_Objects#LiveSeq

...but it is severely undocumented.  This is one we're planning on pulling out of core and releasing on its own.  The code hasn't been updated in quite a while, but it's better than starting from scratch if anyone wants to take it.

chris

On Jun 12, 2012, at 8:54 AM, Roy Chaudhuri wrote:

> Bio::Seq's seq method just delegates to Bio::PrimarySeq:
> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Seq.html#CODE2
> 
> So this should work:
> $bio_seq_obj->seq($bio_seq_obj->seq.$some_addition_seq)
> 
> You're right about the memory thing though. Math, couldn't you just print out a Fasta file directly rather than using BioPerl?
> 
> Cheers,
> Roy.
> 
> 
> On 12/06/2012 14:28, Frank Schwach wrote:
>> the Bio::Seq's "seq" method doesn't take an argument to set a new
>> sequence, so I think you would have to do it like this:
>> 
>> $bio_seq_obj->primary_seq(
>> Bio:PrimarySeq->new(
>> -seq => $bio_seq_obj->seq .$some_addition_seq
>> )
>> );
>> 
>> but it wouldn't save you any memory because you still have the whole
>> sequence in memory.
>> 
>> 
>> 
>> 
>> On 12/06/12 11:27, math math wrote:
>>> Hi,
>>> 
>>> consider the following case:
>>> 
>>> A seq object's string field (ie the sequence part) needs to be filled
>>> gradually in a PERL loop. The seq object(s) can be hundreds of millions
>>> bases long at the end of this loop. The final goal is to write this seq
>>> object(s) to an output file (in multi-fasta format).
>>> 
>>> My question is, how can one append progressively more sequence to a seq
>>> object (i.e. instead of all at once, to minimize memory), and make sure
>>> that these get written to a file.
>>> 
>>> Thanks.
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
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