lederhosen 0.0.2 → 0.0.3

data/lib/lederhosen/cli.rb

@@ -1,212 +1,15 @@
 module Lederhosen
   class CLI < Thor
-  
-    ##
-    # QUALITY TRIMMING
-    #
-    desc "trim Illumina QSEQ files", "--reads_dir=reads/* --out_dir=trimmed.fasta"
-    method_options :reads_dir => :string, :out_dir => :string
-    def trim
 
-      raw_reads = options[:reads_dir]
-      out_dir = options[:out_dir] || 'trimmed/'
-
-      `mkdir -p #{out_dir}`
-
-      raw_reads = Helpers.get_grouped_qseq_files raw_reads
-      puts "found #{raw_reads.length} pairs of reads"
-      puts "trimming!"
-
-      pbar = ProgressBar.new "trimming", raw_reads.length
-
-      raw_reads.each do |a|
-        pbar.inc
-        out = File.join(out_dir, "#{File.basename(a[0])}.fasta")
-        # TODO get total and trimmed
-        total, trimmed = Helpers.trim_pairs a[1][0], a[1][1], out, :min_length => 70
-      end
-
-      pbar.finish
-    end
-
-    ##
-    # PAIRED-END READ WORK-AROUND (JOIN THEM)
-    #
-    desc "join reads end-to-end", "--trimmed=trimmed/*.fasta --output=joined.fasta"
-    method_options :trimmed => :string, :output => :string
-    def join
-      puts "joining!"
-
-      trimmed = Dir[options[:trimmed] || 'trimmed/*.fasta']
-      output = options[:output] || 'joined.fasta'
-
-      fail "no reads in #{trimmed}" if trimmed.length == 0
-
-      output = File.open(output, 'w')
-
-      pbar = ProgressBar.new "joining", trimmed.length
-
-      trimmed.each do |fasta_file|
-        pbar.inc
-        records = Dna.new File.open(fasta_file)
-        records.each_slice(2) do |r, l|
-          output.puts ">#{r.name}:#{File.basename(fasta_file, '.fasta')}\n#{r.sequence.reverse+l.sequence}"
-        end
+    no_tasks do
+      # just print string to STDERR
+      def ohai(s)
+        $stderr.puts s
       end
-      pbar.finish
     end
 
-    ##
-    # SORT JOINED READS BY LENGTH
-    #
-    desc "sort fasta file by length", "--input=joined.fasta --output=sorted.fasta"
-    method_options :input => :string, :output => :string
-    def sort
-      input = options[:input] || 'joined.fasta'
-      output = options[:output] || 'sorted.fasta'
-      `uclust --mergesort #{input} --output #{output}`
-    end
-
-    ##
-    # FINALLY, CLUSTER!
-    #
-    desc "cluster fasta file", "--input=sorted.fasta --identity=0.80 --output=clusters.uc"
-    method_options :input => :string, :output => :string, :identity => :float
-    def cluster
-      identity = options[:identity] || 0.8
-      output = options[:output] || 'clusters.uc'
-      input = options[:input] || 'sorted.fasta'
-
-      cmd = [
-        'uclust',
-        "--input #{input}",
-        "--uc #{output}",
-        "--id #{identity}",
-      ].join(' ')
-      exec cmd
-    end
-
-    ##
-    # MAKE TABLES
-    #
-    desc "otu_tables generates otu tables & representative reads", "--clusters=clusters.uc --output=otu_prefix --joined=joined.fasta"
-    method_options :clusters => :string, :output => :string, :joined => :string
-    def otu_table
-      input = options[:clusters] || 'clusters.uc'
-      output = options[:output] || 'otus'
-      joined_reads = options[:joined] || 'joined.fasta'
-
-      clusters = Hash.new
-
-      # Load cluster table!
-      clusters = Helpers.load_uc_file(input)
-
-      clusters_total = clusters[:count_data].values.collect{ |x| x[:total] }.inject(:+)
-
-      # Get representative sequences!
-      reads_total = 0
-      representatives = {}
-      clusters[:count_data].each{ |k, x| representatives[x[:seed]] = k }
-
-      out_handle = File.open("#{output}.fasta", 'w')
-
-      File.open(joined_reads) do |handle|
-        records = Dna.new handle
-        records.each do |dna|
-          reads_total += 1
-          if !representatives[dna.name].nil?
-            dna.name = "#{dna.name}:cluster_#{representatives[dna.name]}"
-            out_handle.puts dna
-          end
-        end
-      end
-
-      out_handle.close
-
-      # Print some statistics
-      puts "reads in clusters:  #{clusters_total}"    
-      puts "number of reads:    #{reads_total}"
-      puts "unique clusters:    #{clusters.keys.length}"
-
-      # print OTU abundancy matrix
-      csv = Helpers.cluster_data_as_csv(clusters)
-      File.open("#{output}.csv", 'w') do |h|
-        h.puts csv
-      end
-
-    end
-
-    ##
-    # Create a fasta file with nucleotide sequences for each cluster larger than a cutoff
-    #
-    desc "output separate fasta file containing sequences belonging to each cluster", "--clusters=clusters.uc --reads=joined.fasta --min-clst-size=100"
-    method_options :clusters => :string, :reads=> :string, :buffer_size => :int, :min_clst_size => :int, :out_dir => :string
-    def split
-      clusters = options[:clusters] || 'clusters.uc'
-      reads    = options[:reads]    || 'joined.fasta'
-      out_dir  = options[:out_dir]        || 'clusters_split'
-      buffer_size = (options[:buffer_size] || 1000).to_i
-      min_clst_size = (options[:min_clst_size] || 100).to_i
-      finalize_every = 100_000
-
-      `mkdir -p #{out_dir}/`
-
-      puts "loading #{clusters}"
-
-      # Load read id -> cluster
-      read_to_clusterid = Hash.new
-
-      # keep track of cluster sizes
-      cluster_counts    = Hash.new { |h, k| h[k] = 0}
-
-      File.open(clusters)do |handle|
-        handle.each do |line|
-          line = line.strip.split
-          cluster_nr = line[1]
-          if line[0] == 'S' || line[0] == 'H'
-            read = line[8]
-          else
-            next
-          end
-          read_to_clusterid[read] = cluster_nr
-          cluster_counts[cluster_nr] += 1
-        end
-      end
-
-      read_to_clusterid.delete_if do |read, cluster_nr|
-        cluster_counts[cluster_nr] < min_clst_size
-      end
-
-      total_reads = read_to_clusterid.length
-      total_clusters = read_to_clusterid.values.uniq.length
-      puts "#{total_reads} reads in #{total_clusters} clusters"
-
-      puts "writing out fasta files"
-
-      pbar = ProgressBar.new "writing", total_reads
-
-      # Write reads to individual fasta files using Buffer
-      buffer = Buffer.new :buffer_max => buffer_size
-      File.open(reads) do |handle|
-        records = Dna.new handle
-        $stderr.puts "reads = #{reads}"
-        records.each_with_index do |record, i|
-          cluster_id = read_to_clusterid[record.name]
-          if cluster_id
-            pbar.inc
-            filename = File.join(out_dir, cluster_id + '.fasta')
-            buffer[filename] << record
-            buffer.finalize if (i%finalize_every == 0)
-          end
-        end
-      end
-
-      pbar.finish
-      puts "finalizing output"
-      buffer.finalize # finish writing out
+  end # class CLI
 
-      puts "done"
-    end
+end # module
 
-  end # class CLI
-end # module
+Dir.glob(File.join(File.dirname(__FILE__), 'tasks', '*.rb')).each { |f| require f }

data/lib/version.rb

@@ -1,3 +1,3 @@
 module Lederhosen
-  VERSION = '0.0.2'
+  VERSION = '0.0.3'
 end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: lederhosen
 version: !ruby/object:Gem::Version 
-  hash: 27
+  hash: 25
   prerelease: 
   segments: 
   - 0
   - 0
-  - 2
-  version: 0.0.2
+  - 3
+  version: 0.0.3
 platform: ruby
 authors: 
 - Austin G. Davis-Richardson