Merge branch 'master' of github.com:wwood/bbbin

fasta_to_fastq.rb

@@ -0,0 +1,38 @@
+#!/usr/bin/env ruby
+
+require 'optparse'
+require 'bio-logger'
+require 'bio/kseq'
+
+SCRIPT_NAME = File.basename(__FILE__); LOG_NAME = SCRIPT_NAME.gsub('.rb','')
+
+# Parse command line options into the options hash
+options = {
+  :logger => 'stderr',
+  :log_level => 'info',
+}
+o = OptionParser.new do |opts|
+  opts.banner = "
+    Usage: #{SCRIPT_NAME} <arguments>
+
+Converts a FASTA file into the same file except in FASTQ format with dummy quality scores.\n\n"
+
+  # logger options
+  opts.separator "\nVerbosity:\n\n"
+  opts.on("-q", "--quiet", "Run quietly, set logging to ERROR level [default INFO]") {options[:log_level] = 'error'}
+  opts.on("--logger filename",String,"Log to file [default #{options[:logger]}]") { |name| options[:logger] = name}
+  opts.on("--trace options",String,"Set log level [default INFO]. e.g. '--trace debug' to set logging level to DEBUG"){|s| options[:log_level] = s}
+end; o.parse!
+# Setup logging
+Bio::Log::CLI.logger(options[:logger]); Bio::Log::CLI.trace(options[:log_level]); log = Bio::Log::LoggerPlus.new(LOG_NAME); Bio::Log::CLI.configure(LOG_NAME); log.outputters[0].formatter = Log4r::PatternFormatter.new(:pattern => "%5l %c %d: %m", :date_pattern => '%d/%m %T')
+
+
+# Convert FASTQ to FASTA
+kseq = Bio::Kseq.new(ARGV[0])
+while kseq.read! # returns truthy values when there is an entry
+  puts "@" + kseq.name
+  puts kseq.seq
+  puts '+'
+  puts 'A'*kseq.seq.length
+end
+