[Bioperl-l] Write a fasta file with custom title line.

Siddhartha Basu basu at pharm.sunysb.edu
Fri Sep 1 11:42:55 EDT 2006


Amir Karger wrote:
>>From: Siddhartha Basu [mailto:basu at pharm.sunysb.edu] 
>>
>>Staffa, Nick (NIH/NIEHS) [C] wrote:
>>
>>>I would like to construct  title lines for the fasta 
>>>sequences I want to right to a file. 
>>>I don't see in the documentation on-line for SeqIO or 
>>>write_seq how to specify this. 
>>>Please point the way.  
>>
>>Hi Nick,
>>
>>You could use Bio::Seq::BaseSeqProcessor to customize the title line. 
>>Write your own title processing class which should inherit from 
>>Bio::Seq::BaseSeqProcessor overriding its "process_seq" 
>>method. 
> 
> 
> I think requiring someone to write a whole class just to get their
> favorite FASTA output is a bit much, don't you?
I beleive it will also depend on the nature of application. If there is 
a potential of reuse, class based inheritance could be advantageous.

>They might as well just
> explicitly print out '>', the ID, a space, the description, a newline,
> and the sequence (while Bioperlers are adding a description setter in
> the FASTA writer, if there isn't one).
That's true, however based on the original poster's intention, i tried 
to adhere closely to the bioperl SeqIO system.

-siddhartha





> 
> -Amir
> 
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