[Biopython-dev] Binary blast DB reader

[Alexey Morozov]

Yes, DNA support, alias files and so on will be added. I'm not sure about
indexing, though. That may be a nice option to have, but definitely not
default.

2015-03-10 17:17 GMT+08:00 Peter Cock <p.j.a.cock at googlemail.com>:

> Hi Alexey,
>
> I think this would be a very interesting addition to Bio.SeqIO,
> initially a simple iterator for parsing the records one by one
> (like a binary FASTA file), but with more work if we can decode
> the BLAST lookup files efficient random access via the
> Bio.SeqIO.index interface would be great.
>
> Your code currently only looks at protein databases - have
> you tried nucleotide BLAST databases yet? I would expect
> the basic structure to be quite similar...
>
> Also for many uses parsing *.pal (and *.nal) alias files would
> be important (e.g. accessing sequencing from the nr/nt
> databases).
>
> Once you have some functional tests, generalising Python 3
> code to also run on Python 2.6 and 2.7 is not too hard - and
> we would need to do that for inclusion in Biopython. See
> the code in SffIO.py for another example which deals with
> a binary sequence file format:
>
> https://github.com/biopython/biopython/blob/master/Bio/SeqIO/SffIO.py
>
> Peter
>
>
>
> On Tue, Mar 10, 2015 at 7:59 AM, Alexey Morozov
> <alexeymorozov1991 at gmail.com> wrote:
> > Dear colleagues,
> > I have a pretty crude pure Python3 module that reads binary BLAST
> databases
> > (https://github.com/SynedraAcus/BinaryBlast). Is there any chance it'll
> make
> > to main distribuition as SeqIO subclass if I add iterator behaviour and
> fix
> > dirty hacks?
> >
> > --
> > Alexey Morozov,
> > LIN SB RAS, bioinformatics group.
> > Irkutsk, Russia.
> >
> > _______________________________________________
> > Biopython-dev mailing list
> > Biopython-dev at mailman.open-bio.org
> > http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>



-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.
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