[BioPython] plain txt blast output - xml instead

Rohini Damle rohini.damle at gmail.com
Wed Jun 14 14:21:18 EDT 2006


Thank you very much for your help.
I have 55-56 proteins & I am using Blast to find out short, nearly exact
matches. The xml parser works fine for first record but even if I used the
iterator, I


On 6/14/06, Peter <biopython at maubp.freeserve.co.uk> wrote:
>
> Rohini Damle wrote:
> > Hi,
> > I am new to bipyton trying to use ncbistandalone parser to parse my
> blast
> > out put which is in txt format.
> > the parser works well for older blast uptputs but breaks down for newer
> > blast outputs.
>
> The NCBI standalone blast and web blast plain text output keeps changing
> slightly, and as a result, the parser isn't always up to date.
>
> > Can someone suggest me a way to overcome this blast parser's
> > problem?
>
> We recommend you use the XML output instead (this is possible with both
> online blast and the standalone tools).
>
> For the stand alone tools, repeat your searches with the command line
> option -m 7 to get XML output.
>
> If you are using the Bio.NCBIStandalone.blastall() command, use argument
> align_view to set this.
>
> You still use NCBIStandalone.Iterator (if you have multiple queries) but
> now use NCBIXML.BlastParser instead of NCBIStandalone.BlastParser
>
> e.g.
> http://bugzilla.open-bio.org/attachment.cgi?id=293&action=view
>
> Peter
>
>


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