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

[Kevin Murray]

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
> >
> >> .
> >>
> >
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>
>
>
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>