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1 #!/usr/bin/ruby
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2 ##########################################################
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3 ## Wrapper to convert SFF to Fasta
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4 ##
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5 ## Author: Biowebdb, 2014
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6 ##
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7 ## This tool needs sff_extraxt version 0.28 or higher
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8 ## in path directory or $SFF_EXTRACT
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9 ##
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10 ## This tool need Biowebdb Ruby Lib
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11 ## (http://biowebdb.org)
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12 ##
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13 ##########################################################
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14 require "logger"
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15 require "#{ENV['biowebdb']}/bioinformatics/Bioinformatics"
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16
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17 c = Bioinformatics.program "Sff"
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18 c.logger(Logger.new(STDOUT))
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19 c.workPath="/tmp/"
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20 c.input = ARGV[0]
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21 if ARGV.size == 2
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22 c.format = 'FASTQ'
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23 else
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24 c.format = 'FASTA'
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25 end
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26 c.outputDir = "/tmp/#{Time.new.strftime("%Y%m%d%H%M%S")}"
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27 c.execute(c.lineCommand)
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28
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29 basename = File.basename(c.input, '.*')
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30
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31 if c.format == 'FASTQ'
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32 Kernel.system("mv #{c.outputDir}/*.fastq #{ARGV[1]}")
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33 else
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34 Kernel.system("mv #{c.output} #{ARGV[1]}")
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35 Kernel.system("mv #{c.outputQual} #{ARGV[2]}")
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36 end |
