[Biopython] NCBIXML.parse

[Mic]

I am sorry, the XML file which I sent was created with one year old Blast
library. When I run Blast with the following command and a new UniRef90
library

blastp -query X.aa.snap -db /db/uniprot/uniref90 -evalue 0.00001
-max_target_seqs 15 -out x.blastp.xml -num_threads 6 -outfmt 5

Please find attached the new XML file and it looks like that a new schema
has been created
http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/dbfetch.databases?style=xml .

Michal

On Fri, May 17, 2013 at 6:55 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

>
> 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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