/usr/bin/fix-trinity-output is in ruby-fix-trinity-output 1.0.0-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 | #!/usr/bin/ruby
# fix bullshit trinity output files
require 'trollop'
require 'fix-trinity-output'
ARGV[0] = "--help" if ARGV.length() == 0
opts = Trollop::options do
banner <<-EOS
fix-trinity-output v1.0
Trinity outputs fastq files that have been 'corrected'
Unfortunately these files are no longer properly paired and therefore
can't be used in most aligners such as bowtie2 and snap
This script attempts to fix that and produce 2 properly paired fastq
files and a fastq file containing single reads
Options:
EOS
opt :left, "fastq file of left reads", :type => String, :required => true
opt :right, "fastq file of right reads", :type => String, :required => true
opt :output, "output prefix", :type => String, :required => true
end
left = File.expand_path(opts.left)
right = File.expand_path(opts.right)
if left and right
if !File.exist?(left)
Trollop::die "#{left} not found"
end
if !File.exist?(right)
Trollop::die "#{right} not found"
end
end
fixer = Fixer.new
fixer.run(left, right, opts.output)
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