[Biopython-dev] [biopython] added unstable Bam parser class (e6343eb)

Kevin Murray k.d.murray.91 at gmail.com
Tue Apr 2 09:09:03 UTC 2013


Hi Tiago,
It is indeed impressive, which makes me suspect I've screwed something up
in my benchmarks. I'll whack them up onto github for closer inspection
sometime tomorrow (Aussie time).

However, in general code:

bam = BamParser("path")
print next(bam)
for mapping in bam:
 pass


Regards
Kevin Murray


On 2 April 2013 19:59, Tiago Antão <tiagoantao at gmail.com> wrote:

> Regarding the performance comparison to pysam: wow! Fantastic!
>
> On Tue, Apr 2, 2013 at 9:52 AM, Kevin Murray <k.d.murray.91 at gmail.com>
> wrote:
> > Hi All,
> >
> > Peter and I have
> > discussed<
> https://github.com/kdmurray91/biopython/commit/e6343ebae50e4ff0633476a5761b47aa5ecacec4#commitcomment-2905033
> >including
> > the SamBam parser he has worked on into the master branch. I've
> > offered to help with test coverage/missing features/testing.
> >
> > The performance is very good; reading sequentially all reads from a 11mb
> > (540k reads) Bam file took:
> > CPython with Kevin's Pure-python parser: 0m17.531s real, 0m17.452s user
> > CPython with Peter's Pure-python parser: 0m5.589s real, 0m5.560s user
> > CPython with pysam: 4m29.240s real, 4m25.576s user
> > Pypy1.9 with Kevin's Pure-python parser: 0m6.125s real, 0m6.056s user
> > Pypy1.9 with Peter's Pure-python parser: 0m1.716s real, 0m1.624s user
> >
> >
> > What are everyone's thoughts on including this into the master branch?
> > (with a BiopythonExperimentalWarning)
> >
> > Regards,
> > Kevin
> >
> >
> >
> > On 2 April 2013 19:09, Peter Cock <notifications at github.com> wrote:
> >
> >> We're experimenting with including experimental code in the stable
> >> releases (modules with an experimental warning on import), so possibly
> yes.
> >> I was never entirely sure if it would be useful given pysam exists (and
> may
> >> well be faster on many jobs), but as this is pure Python it works on
> PyPy
> >> which is interesting (and Jython, but on Java you have access to
> Picard).
> >> Shall we take this dicussion to the dev mailing list?
> >>
> >> —
> >> Reply to this email directly or view it on GitHub<
> https://github.com/kdmurray91/biopython/commit/e6343ebae50e4ff0633476a5761b47aa5ecacec4#commitcomment-2925593
> >
> >> .
> >>
> >
> > _______________________________________________
> > Biopython-dev mailing list
> > Biopython-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython-dev
>
>
>
> --
> “Grant me chastity and continence, but not yet” - St Augustine
>




More information about the Biopython-dev mailing list