[Biopython] SeqIO.write and user-specified wrapping

[Lenna Peterson]

For me, this works as expected. I will paste my exact code below.

I am creating the SeqRecord from your string, so perhaps it's some
difference there.

Cheers,

Lenna

from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.SeqIO.FastaIO import FastaWriter

mystr = """SVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVG
YPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRV
RAGNTDV"""

myseq = Seq(mystr.replace("\n", ""))
myrec = SeqRecord(myseq)

with open("nowrap.fa", "wb") as fh:
    FastaWriter(fh, wrap=0).write_file([myrec])

with open("wrap10.fa", "wb") as fh:
    FastaWriter(fh, wrap=10).write_file([myrec])



On Mon, Mar 4, 2013 at 1:28 PM, Ivan Gregoretti <ivangreg at gmail.com> wrote:

> Sorry to pester the list's subscribers but there seems to be bug in
> FastaWriter
>
> It appears that FastaWriter does not respect the wrap argument:
>
> # No wrapping
> SeqIO.FastaIO.FastaWriter( handle, wrap=0 ).write_file( [record] )
>
> or
>
> # wrap after 10 characters
> SeqIO.FastaIO.FastaWriter( handle, wrap=10 ).write_file( [record] )
>
> both produce the same output:
>
> >M01483:6:000000000-A2WVJ:1:1101:12685:1873
> SVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVG
> YPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRV
> RAGNTDV
> >M01483:6:000000000-A2WVJ:1:1101:19629:2231
> LTLADDRLEAFYDNPNALRDYFRDIGRMVLAAEGRKANDSHADCYQYFCVPEYGTANGRL
> HFHAVHFMRTLPTGSVDPNFGRRVRNRRQLNSLQNTWPYGYSMP
> >M01483:6:000000000-A2WVJ:1:1101:12952:2294
> GFENQKELTKMQLDNQKEIAEMQNETQKEIAGIQSATSRQNTKDQVYAQNEMLAYQQKES
> TARVASIMENTNLSKQQQVSEIMRQMLTQAQTAGQYFTNDQIKEMTRKVS
>
> FastaWriter does produce an error when I pass wrap="hello world", so,
> the argument is interpreted initially. Also, as expected, when I
> comment out the SeqIO.FastaIO.FastaWriter line, there is no output.
>
> I checked and double checked.
>
> I am using Python 2.7.3 on a linux 64bit (Fedora 18) and my Biopython is
> 1.6.1.
>
> Thank you,
>
> Ivan
>
>
>
>
> Ivan Gregoretti, PhD
> Bioinformatics
>
>
>
> On Mon, Mar 4, 2013 at 12:26 PM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
> > On Mon, Mar 4, 2013 at 5:20 PM, Ivan Gregoretti <ivangreg at gmail.com>
> wrote:
> >> I am trying this
> >>
> >> from Bio import SeqIO
> >> SeqIO.FastaIO.FastaWriter( handle, wrap=0 ).write_file( record )
> >>
> >
> > That should be a list of SeqRecord objects, not just one SeqRecord.
> > If you have just one, try [record] instead.
> >
> > Peter
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