merge is_this_sra_16s.rb

sralites_to_acacia.rb

@@ -0,0 +1,99 @@
+#!/usr/bin/env ruby
+
+require 'optparse'
+require 'bio-logger'
+require 'progressbar'
+
+$LOAD_PATH.unshift('/home/ben/git/bioruby-sra_fastq_dumper/lib')
+require 'bio-sra_fastq_dumper'
+
+SCRIPT_NAME = File.basename(__FILE__); LOG_NAME = SCRIPT_NAME.gsub('.rb','')
+
+# Parse command line options into the options hash
+options = {
+  :logger => 'stdout',
+}
+o = OptionParser.new do |opts|
+  opts.banner = "
+    Usage: #{SCRIPT_NAME} <arguments>
+    
+    Take a directory of .lite.sra files, and correct them using acacia, outputing the results in a second directory filled with directories (one for each sra lite file) \n\n"
+
+    opts.on("-i", "--input-directory DIRECTORY", "a directory full of SRA .lite.sra files [required]") do |arg|
+      options[:in_directory] = File.absolute_path(arg)
+    end
+    opts.on("-o", "--output-directory DIRECTORY", "a directory to put output files in [required]") do |arg|
+      options[:out_directory] = File.absolute_path(arg)
+    end
+
+  # logger options
+  opts.on("-q", "--quiet", "Run quietly, set logging to ERROR level [default INFO]") do |q|
+    Bio::Log::CLI.trace('error')
+  end
+  opts.on("--logger filename",String,"Log to file [default #{options[:logger]}]") do | name |
+    options[:logger] = name
+  end
+  opts.on("--trace options",String,"Set log level [default INFO]. e.g. '--trace debug' to set logging level to DEBUG") do | s |
+    Bio::Log::CLI.trace(s)
+  end
+end
+o.parse!
+if ARGV.length != 0 or options[:in_directory].nil? or options[:out_directory].nil?
+  $stderr.puts o
+  exit 1
+end
+# Setup logging. bio-logger defaults to STDERR not STDOUT, I disagree
+Bio::Log::CLI.logger(options[:logger]); log = Bio::Log::LoggerPlus.new(LOG_NAME); Bio::Log::CLI.configure(LOG_NAME)
+
+
+# Collect a list of the input sra lite files to process, advise
+log.debug "Inspecting #{options[:in_directory]}"
+sralites = Dir.entries(options[:in_directory]).select{|s| s.match(/\.lite\.sra$/)}
+log.info "Found #{sralites.length} SRA lite files in #{options[:in_directory]}"
+
+# Setup progress bar
+progress = ProgressBar.new('acacia', sralites.length)
+
+# For each input file,
+sralites.each do |sralite|
+  # convert to a fastq file in a temporary directory
+  Bio::FastqDumper.dump_in_tmpdir(File.join options[:in_directory], sralite) do |fastq|
+    # mkdir and cd to an aptly named direct in the output folder
+    outdir = File.join(options[:out_directory], sralite)
+    if File.exist?(outdir)
+      log.info "Skipping SRA file #{sralite}, since it already appears to be processed (output directory exists)"
+      next
+    end
+    log.debug "Creating directory #{options[:out_directory]}"
+    Dir.mkdir outdir
+    # Dir.chdir options[:in_directory] #acacia cannot handle the fastq file not being in the current directory, I think
+
+    # Run acacia and output the files into the working directory
+    f = 
+    acacia_command = [
+      'java',
+      '-jar',
+      #'/srv/whitlam/home/projects/DATA_MODELLING/acacia-1.50.b04.jar'
+      '/home/ben/bioinfo/acacia/acacia-1.50.b05.jar',
+      %w(-DFASTA=FALSE -DFASTQ=TRUE),
+      "-DOUTPUT_DIR=#{outdir}",
+      %w(-DOUTPUT_PREFIX=acacia -DMID_FILE=null),
+      "-DFASTQ_LOCATION=#{File.absolute_path fastq}"
+    ].flatten
+    log.debug "Running acacia with '#{acacia_command}'"
+    Bio::Command.call_command_open3(acacia_command) do |stdin, stdout, stderr|
+      err = stderr.read
+      raise err if err != ''
+      p stdout
+    end
+    puts `ls`
+
+    progress.inc
+  end
+end
+progress.finish
+
+
+
+
+