fasta_util in fasta_util-0.2.2

- old
+ new
@@ -1,4 +1,88 @@
 #!/usr/bin/env ruby
-require 'fasta_util'
+require 'thor'
+require 'bio'
 
+class FastaUtility < Thor
+  include Thor::Actions
+  Struct.new("Stats", :sum, :l50, :n50, :count, :mean, :median)
+  
+  no_tasks do
+    def stats(lengths)
+      lengths = lengths.sort{|a, b| b <=> a}
+      stats = Struct::Stats.new
+      
+      temp_sum = 0
+      stats[:sum] = lengths.inject(:+)
+      stats[:l50] = lengths.find{|length| (temp_sum += length) > stats[:sum]/2.0}
+      stats[:n50] = lengths.count{|length| length >= stats[:l50]}
+      stats[:mean] = stats[:sum].to_f/lengths.length
+      stats[:median] = (lengths.length % 2 == 0) ? (lengths[lengths.length/2-1] + lengths[lengths.length/2])/2.0 : lengths[lengths.length/2]
+      stats[:count] = lengths.count
+      return stats
+    end
+    
+    def format(stats)
+      output = []
+      buffer_length = stats.members.map{|key| key.length}.max
+      stats.each_pair do |key, value|
+        numtype = value.is_a?(Float) ? "f" : "d"
+        output << "  %-#{buffer_length}s: %#{numtype}" % [key.to_s.capitalize, value]
+      end
+      output.join("\n")
+    end
+  end
+  
+  desc "filecheck", "Checks to see if a given file exists. Used internally, don't worry about it too much", :hide => true
+  def filecheck(filename)
+    say "The file '#{filename}' doesn't seem to exist!", :red unless File.exists?(filename)
+  end
+  
+  desc "lengths", "Print a set of summary statistics for the given fasta file, including L50, N50, sum and count."
+  method_options [:cutoff, '-c'] => 0
+  def lengths(filename)
+    invoke :filecheck
+    lengths =  Bio::FlatFile.open(filename).map{|entry| (entry.seq[-1,1] == "*") ? entry.length - 1 : entry.length}
+    
+    say "All entries", :green
+    puts format(stats(lengths))
+    if options.cutoff > 0
+      say "Entries with length >= #{options.cutoff}", :green
+      puts format(stats(lengths.find_all{|l| l >= options.cutoff}))
+    end
+  end
+  
+  desc "filter FILENAME [options]", "Impose a filter or set of filters on entries in a fasta file."
+  long_desc "Impose a filter or set of filters on entries in a fasta file where each sequence in the file has to pass all of the filters to be printed."
+  method_option :length_cutoff, :aliases => '-l', :type => :numeric, :default => 0,  :desc => 'Only entries with length >= cutoff will be returned.'
+  method_option :inverse_match,  :aliases => '-v', :type => :boolean, :desc => "Return the inverse of the match after all the other filters have been applied."
+  method_option :defline_grep,  :aliases => '-d', :type => :string,  :default => '', :desc => "A regular expression, used to search the entry's definition line."
+  def filter(filename)
+    invoke :filecheck
+    Bio::FlatFile.open(filename).each do |entry|
+      passed = true
+      passed &&= (entry.length >= options.length_cutoff)
+      passed &&= (entry.definition.match(Regexp.new(options.defline_grep)))
+      passed = !passed if options.inverse_match
+      puts entry if passed
+    end
+  end
+  
+  desc "clean FILENAME [options]", "Clean up a fasta file"
+  method_option :wrap_width, :aliases => '-w', :type => :numeric, :desc => 'Wrap the fasta to N columns'
+  def clean(filename)
+    invoke :filecheck
+    Bio::FlatFile.open(filename).each do |entry|
+      puts entry.to_biosequence.output(:fasta, :header => entry.definition, :width => options.wrap_width)
+    end
+  end
+  
+  
+  desc "sort FILENAME [options]", "Sorts a fasta file according to criteria"
+  def sort(filename)
+    invoke :filecheck
+    Bio::FlatFile.open(filename).to_a.sort{|a,b| b.length <=> a.length}.each do |entry|
+      puts entry
+    end
+  end
+end
 FastaUtility.start