fasta_util 0.2.1 → 0.2.2

data/VERSION

@@ -1 +1 @@
-0.2.1
+0.2.2

data/bin/fasta_util

@@ -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

data/fasta_util.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{fasta_util}
-  s.version = "0.2.1"
+  s.version = "0.2.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["robsyme"]
-  s.date = %q{2011-02-17}
+  s.date = %q{2011-02-18}
   s.default_executable = %q{fasta_util}
   s.description = %q{Easy fasta filtering, wrapping, calculating common statistics, sorting etc. Based on the fasta_tool script that I think was written by Jason Stajich.}
   s.email = %q{rob.syme@gmail.com}
@@ -28,7 +28,6 @@ Gem::Specification.new do |s|
     "VERSION",
     "bin/fasta_util",
     "fasta_util.gemspec",
-    "lib/fasta_util.rb",
     "test/helper.rb",
     "test/test_fasta_util.rb"
   ]

metadata

@@ -2,7 +2,7 @@
 name: fasta_util
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 0.2.1
+  version: 0.2.2
 platform: ruby
 authors: 
 - robsyme
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-02-17 00:00:00 +08:00
+date: 2011-02-18 00:00:00 +08:00
 default_executable: fasta_util
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -109,7 +109,6 @@ files:
 - VERSION
 - bin/fasta_util
 - fasta_util.gemspec
-- lib/fasta_util.rb
 - test/helper.rb
 - test/test_fasta_util.rb
 has_rdoc: true
@@ -126,7 +125,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: -728010957941595934
+      hash: -443172315906729972
       segments: 
       - 0
       version: "0"

data/lib/fasta_util.rb

@@ -1,86 +0,0 @@
-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