[Biopython] Adding SVM in biopython

[Vishnu Chilakamarri]

Hello Peter,

You're right , addition of another machine learning algorithm in biopython
does not seem necessary.Sorry about that. I was actually looking for
contributing to biopython for Google Summer of Code. I was reading about
the lazy parsers idea which seems very interesting. Like you mentioned in
the Biopython Wiki, I started reading about tabix and BAM indexing. Formats
such as FASTA can be converted to BAM and then indexed using tabix. I read
from here about how Tabix works :
http://bioinformatics.oxfordjournals.org/content/27/5/718.full . Apart from
this is there any source from where I can learn more about this? Thanks in
advance.


On Tue, Feb 11, 2014 at 8:12 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Tue, Feb 11, 2014 at 2:23 PM, Vishnu Chilakamarri
> <vishnuc11j93 at gmail.com> wrote:
> > Hello Peter,
> >
> > You're right , addition of another machine learning algorithm in
> biopython
> > does not seem necessary.
>
> Do you want to reply on the list?
>
> > Sorry about that. I was actually looking for
> > contributing to biopython for Google Summer of Code. I was reading about
> the
> > lazy parsers idea which seems very interesting. Like you mentioned in the
> > Biopython Wiki, I started reading about tabix and BAM indexing. Formats
> such
> > as FASTA can be converted to BAM and then indexed using tabix.
>
> Not quite, you compress the FASTA file using bgzip (which uses
> BGZF, a type of GZIP compression). See:
>
> http://blastedbio.blogspot.co.uk/2011/11/bgzf-blocked-bigger-better-gzip.html
>
> > I read from here about how Tabix works :
> > http://bioinformatics.oxfordjournals.org/content/27/5/718.full . Apart
> from
> > this is there any source from where I can learn more about this? Thanks
> in
> > advance.
>
> For BGZF (used in BAM and tabix), my blog post and the Biopython code:
> https://github.com/biopython/biopython/blob/master/Bio/bgzf.py
>
> Peter
>



-- 
Vishnu Chilakamarri
+919049437582
Public Relations Team
BITSAA
B.E. Computer Science + Msc Biological Sciences