[Biopython] Help modify this code so it can do what I want it to do

[Radhouane Aniba]

You can try use coderscrowd.com as well you will have all modifications
separately on your code and you can validate the one it works better for you

Rad



On Mon, Feb 3, 2014 at 1:45 PM, Edson Ishengoma <ishengomae at nm-aist.ac.tz>wrote:

> Thanks Peter.
>
> Here is a link to my script at
> https://gist.github.com/EBIshengoma/efc4ad3e32427891931d
>
> Also, please find attached the sample xml output.
>
>
>
> On Mon, Feb 3, 2014 at 11:14 PM, Peter Cock <p.j.a.cock at googlemail.com
> >wrote:
>
> >
> > On Monday, February 3, 2014, Edson Ishengoma <ishengomae at nm-aist.ac.tz>
> > wrote:
> >
> >> Hi Peter,
> >>
> >> Sorry that was the typo, it should be:
> >> complete_sbjct_seq += str(sbjct[sb_start:sb_end]).
> >>
> >> I tried a suggestion by Ivan on the providing tblastn option
> >> [-max_hsps_per_subject 1] but still the output shows up as fragmented
> hits.
> >>
> >> Peter said: "Another approach would be to use the alignment sequence
> >> fragments BLAST gives you (and remove the gap characters)."
> >> With the script I have I can only extract the first fragment only for
> >> each hit. I don't know why string slicing method [sb_start:sb_end] in my
> >> script
> >> does not include start and end positions for subsequent fragments.
> >>
> >> Regards,
> >>
> >> Edson
> >>
> >
> > Hi Edson,
> >
> > Emails can mess up Python indentation, so posting the file online might
> > show something silly we've missed - I find http://gist.github.com works
> > well for this.
> >
> > It would also help if you could share a sample BLAST output file where
> the
> > script is failing, as then people on the list could recreate your problem
> > on their own computer, which is often the first step in solving it.
> >
> > Peter
> >
> >
>
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>


-- 
*Radhouane Aniba*
*Bioinformatics Postdoctoral Research Scientist*

*Institute for Advanced Computer StudiesCenter for Bioinformatics and
Computational Biology* *(CBCB)*

*University of Maryland, College ParkMD 20742*