[BioRuby] New biogems for IonTorrent, pileup files, pfam and hmmer

[Francesco Strozzi]

Hi Ben,
thanks for the amazing work! I'm not using Ion Torrent atm but I
eventually will and it's good to see there is something already setup.

Francesco

On Fri, May 18, 2012 at 7:40 AM, Ben Woodcroft <donttrustben at gmail.com> wrote:
> Hi guys,
>
> Here's some blatant advertising for some code I've recently written in
> biogem form.
>
> bio-gag: "gag error" is the term I've coined to describe an error that
> various people have observed on certain sequencing kits with IonTorrent,
> though it has not previously been characterised very well that I know of
> (we noticed that the errors seemed to occur at GAG positions in the reads
> that were supposed to be GAAG). This biogem tries to find and fix these
> errors. It isn't benchmarked for accuracy but worked well enough for my
> lab's own purposes. Actually to be honest we've only used an older version
> of the software on real data and the logic has a little since given some
> recent evidence we have, but I thought I'd push it out with the latest and
> greatest error model.
> https://github.com/wwood/bioruby-gag
>
> bio-pileup_iterator: To find gag errors bio-gag iterates through pileup
> files looking for particular patterns e.g. strand bias of insertions. This
> gem can be used to iterate through pileup files one position (one line) at
> a time, building up the sequence of each read as it goes, recording their
> direction etc. Probably not the fastest piece of code in the world, sorry.
> I'm not sure whether this should/can be incorporated into bio-samtools? It
> adds functionality - there's no duplication (I don't think).
> https://github.com/wwood/bioruby-pileup_iterator
>
> bio-hmmer_model: This is a parser of HMM files e.g. from PFAM according to
> the hmmer v3 manual.
> https://github.com/wwood/bioruby-hmmer_model
>
> bio-hmmer3_report: Parsing of HMMER3 result files. Currently only handles
> tabular format files - the guts of this were written by Christian - see
> yesterday's thread for details. I'm hoping to add regular (non-tabular)
> format parsing in the near future, but no promises.
> https://github.com/wwood/bioruby-hmmer3_report
>
> I'm sure there is bugs and deficiencies - apologies in advance.
>
> Enjoy,
> ben
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-- 

Francesco