[Biopython] need help ,parse fasta format
Peter
biopython at maubp.freeserve.co.uk
Wed May 5 09:55:30 UTC 2010
On Wed, May 5, 2010 at 9:50 AM, ning luwen <bioinformaticsing at gmail.com> wrote:
> Hi,
>
> the code like bellow:
> x=SeqRecord(Seq(temp),id=rec.id,description=rec.description)
> y=x.format('fasta')
> print type(y)
> z=SeqIO.parse(y,'fasta')
>
> I generator a fasta sequence y, but y is str type, then can not be
> parse by SeqIO.
>
> Is there anyway not save y into a file, then parse it by open the saved file?
Yes, using the Python StringIO or cStringIO module to turn the string
into a handle.
http://docs.python.org/library/stringio.html
e.g.:
from Bio import SeqIO
from StringIO import StringIO
handle = StringIO(">Example\nACGT\n")
record = SeqIO.read(handle, "fasta")
Peter
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