[BioRuby] blatanalyzer.rb
Davide Rambaldi
davide.rambaldi at ifom-ieo-campus.it
Mon Sep 8 12:31:45 UTC 2008
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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