Mercurial > repos > biowebdb > flowgram
view sffextract.rb @ 2:ce049751b625 draft default tip
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author | biowebdb |
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date | Tue, 01 Apr 2014 09:16:51 -0400 |
parents | d27bec235ad9 |
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#!/usr/bin/ruby ########################################################## ## Wrapper to convert SFF to Fasta ## ## Author: Biowebdb, 2014 ## ## This tool needs sff_extraxt version 0.28 or higher ## in path directory or $SFF_EXTRACT ## ## This tool need Biowebdb Ruby Lib ## (http://biowebdb.org) ## ########################################################## require "logger" require "#{ENV['biowebdb']}/bioinformatics/Bioinformatics" c = Bioinformatics.program "Sff" c.logger(Logger.new(STDOUT)) c.workPath="/tmp/" c.input = ARGV[0] if ARGV.size == 2 c.format = 'FASTQ' else c.format = 'FASTA' end c.outputDir = "/tmp/#{Time.new.strftime("%Y%m%d%H%M%S")}" c.execute(c.lineCommand) basename = File.basename(c.input, '.*') if c.format == 'FASTQ' Kernel.system("mv #{c.outputDir}/*.fastq #{ARGV[1]}") else Kernel.system("mv #{c.output} #{ARGV[1]}") Kernel.system("mv #{c.outputQual} #{ARGV[2]}") end