[Biopython] editing xml blast report

[Peter]

On Wed, Nov 10, 2010 at 12:21 PM, Yvan <yvan.strahm at uni.no> wrote:
> Hello All,
>
> I am wondering if it is possible with biopython to correctly edit a xml
> blast report?
>
> Here my problem;
> I need to filter/exclude some hits according to their length but the xml
> consistency should be conserved.

Biopython has a BLAST XML parser, but nothing to help you write
out BLAST XML.

> Should I parse with it with NCBIXML and recreate a xml file with hard
> coded tags?

That might be the best option.

> I try to use the tabular output of blast+ and reformat it with
> blast_formatter but with no success.

I'm pretty sure the blast_formatter tools in BLAST+ will only convert
from ASN.1 to other BLAST output formats. So that won't work,
unless you can edit the ASN.1 file (but that would probably be
harder than editing XML).

Peter