[Biopython] NCBIXML.parse
Peter Cock
p.j.a.cock at googlemail.com
Fri May 17 08:55:05 UTC 2013
On Fri, May 17, 2013 at 5:26 AM, Mic <mictadlo at gmail.com> wrote:
> Please find attached the x.blastp.xml file. Do you need more information?
>
>
>>> from Bio.Blast import NCBIXML
>>> with open("x.blastp.xml") as bf:
... for r in NCBIXML.parse(bf):
... for a in r.alignments:
... print r.query, a.hit_id
...
X-snap.4 UniRef90_Q9FX16
(etc)
This matches the first hit in the XML,
<Hit_num>1</Hit_num>
<Hit_id>UniRef90_Q9FX16</Hit_id>
<Hit_def>F12G12.10 protein n=1 Tax=Arabidopsis thaliana
RepID=Q9FX16_ARATH</Hit_def>
<Hit_accession>UniRef90_Q9FX16</Hit_accession>
<Hit_len>308</Hit_len>
If you are getting UR090:UniRef90_Q9FX16 then perhaps some other
part of your code is adding the prefix? What else did your code do
(it was incomplete - there were no print statements for example)?
Regards,
Peter
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