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

Amir Karger akarger at CGR.Harvard.edu
Fri Sep 1 10:54:39 EDT 2006


> 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? 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).

-Amir



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