[Biopython] Write FASTA sequence on a single line

[Willis, Jordan R]

I don't think there is an option, but you could possibly write it in the SeqIO class.

I have to do this all the time and i just write it to a file manually

for _record in SeqIO.parse(fastah,'fasta)
	open(outputfile,'a').write(">"+_record.id+record.seq)

You can of course format these to output to a file anyway you want.

Jordan

On Mar 4, 2012, at 12:09 PM, Martin Mokrejs 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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