[Biopython] Write FASTA sequence on a single line

[Wibowo Arindrarto]

Hi Martin,

A quick glance at Bio.SeqIO.FastaIO.FastaWriter shows that there is indeed
an option to set the line wrapping length. However, the regular writing
function that calls FastaWriter (SeqIO.write) only accepts three parameters
(sequence, handle, and format), so if you really want to use Biopython's
fasta writer, you should call FastaWriter directly.

For example, as shown in the docs:

from Bio.SeqIO.FastaIO import FastaWriter
writer = FastaWriter(open(outfile, 'w'), wrap=0)
writer.write_file(records)

Alternatively, you can iterate over the records manually and write them to
the output file like so:

with open(outfile, 'w') as target:
for rec in records: # records is the list containing your SeqRecord objects
  target.write('>%s\n' % rec.id)
  target.write('%s\n' % rec.seq.tostring())


Hope that helps!
Bow


On Sun, Mar 4, 2012 at 19:09, Martin Mokrejs <mmokrejs at fold.natur.cuni.cz>wrote:

> Hi,
>  is there an option to tell FASTA writer to write output with a
> sequence on a single line (so that a FASTA entry would span just
> two lines altogether)? I see it should be faster to eventually
> parse using SeqIO because one would avoid calls for each line in
> the FASTAinput file.
>
> In my code I have
> for _record in SeqIO.parse(fastah, 'fasta'):
>
> which boils down to biopython's:
> append(line.rstrip().replace(" ","").replace("\r",""))
>
> per every line with _sequence_.
>
> Thank you for comments,
> Martin
>
>
>
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