[Biopython] NCBIXML.parse

[Peter Cock]

On Thu, May 16, 2013 at 5:57 AM, Mic <mictadlo at gmail.com> wrote:
> Hi,
> Why does NCBIXML.parse attach UR090 to the UniRef90 ids and as results I
> get is UR090:UniRef90_Q9FX16 with the following code:
>
>     with open("x.blastp.xml") as bf:
>         blast_records = NCBIXML.parse(bf)
>
>         for blast_record in blast_records:
>             query_name = blast_record.query
>             for alignment in blast_record.alignments:
>                 hit_id = alignment.hit_id
>
> Is it possible to remove UR090 or maybe it should be UR090:Q9FX16?
>
> Is UR090:UniRef90_Q9FX16 compatible Gbrowse2?
>
> Thank you in advance.
>
> Mic

Can you post your x.blastp.xml online somewhere for us to look at?
If not perhaps you can at least include the relevant snippet of the
XML file in your email, and tell us about the database you are using.

Thanks,

Peter