[Biopython-dev] Bio.Wise

[Michiel De Hoon]

Sebastian Bassi wrote:
> On 8/7/07, Michiel De Hoon <mdehoon at c2b2.columbia.edu> wrote:
> > I was wondering why we go through the Fasta reader/writer instead of
> > reading/writing the file contents directly, as in
> >         for filename, input_file in zip(pair, input_files):
> >             input_file.close()
> >             file(input_file.name, "w").write(file(filename).read())
> 
> The old Fasta writer used to write a 70 column formated fasta file.
> Your method (and I think also the new seq.io) write the fasta data as
> a one big line.

Peter, can we change the behavior of SeqIO.write so that it writes the fasta
data in some fixed column format? For comparison, Bioperl appears to use a
column width of 60 characters:

http://www.bioperl.org/wiki/FASTA_sequence_format

--Michiel.



Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032