[Bioperl-l] Write a fasta file with custom title line.
akarger at CGR.Harvard.edu
Fri Sep 1 14:54:39 UTC 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"
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).
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