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

[Raoul Bonnal]

My lab (Alberto) will try your HMM parsers because we are going to annotate
a lot of stuff coming form NGS ^_^


On 18/05/12 10.01, "Francesco Strozzi" <francesco.strozzi at gmail.com> wrote:

> 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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> 
>