# HG changeset patch
# User biowebdb
# Date 1396289421 14400
# Node ID d27bec235ad97dbf15b267c342b2f8fb03907df6

Uploaded

diff -r 000000000000 -r d27bec235ad9 sffextract.rb
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sffextract.rb	Mon Mar 31 14:10:21 2014 -0400
@@ -0,0 +1,36 @@
+#!/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
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