[BioRuby] blatanalyzer.rb

[Davide Rambaldi]

Hi,

    I have published a first version of my command-line "application"  
that use BioRuby: blatanalyzer at http://rubyforge.org/projects/ 
blatanalyzer/.

Blatanalyzer is a software to analize the output of blat software  
alignment (PSL files): list query names,sort by identity, coverage,  
score, span. convert to: gff, gtf formats generate: report tables,  
PSL, GFF and GTF files

Available Actions: gff, list, cut, duplicates, gtf, report,  
singletons, table, summary

gff,gtf: conversion to gff,gtf

list: generate list of query names

cut: extract psl alignments over/under a given threshold (identity,  
span, coverage, score)

report, table, summary:
generate pretty reports, table is like the web-blat output table,  
report is a custom table with coverage and span, summary print a list  
of query names with number of alignments and number of distinct  
chromosomes target.

more actions coming...

basically is composed by:

- an OptionParser class
- a Bio::Blat::Application class (implement actions)
- a Bio::Blat::Analyzer class (subclass of Bio::Blat::Report)

Any suggestion is really appreciated!

Davide Rambaldi,
Bioinformatics PhD student.
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Bioinformatic Group IFOM-IEO Campus
Via Adamello 16, Milano
I-20139 Italy

[t] +39 02574303 066
[e] davide.rambaldi at ifom-ieo-campus.it
[i] http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi  
(homepage)
[i] http://www.semm.it             (PhD school)
[i] http://www.btbs.unimib.it/     (Master)

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