lederhosen 1.8.0 → 1.8.1

data/lederhosen.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "lederhosen"
-  s.version = "1.8.0"
+  s.version = "1.8.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Austin G. Davis-Richardson"]
@@ -34,7 +34,6 @@ Gem::Specification.new do |s|
     "lib/lederhosen/tasks/otu_table.rb",
     "lib/lederhosen/tasks/split_fasta.rb",
     "lib/lederhosen/tasks/version.rb",
-    "lib/lederhosen/trimmer.rb",
     "lib/lederhosen/version.rb",
     "readme.md",
     "scripts/illumina_pipeline/.gitignore",

data/lib/lederhosen/version.rb

@@ -3,7 +3,7 @@ module Lederhosen
     MAJOR = 1
     MINOR = 8
     CODENAME = 'Karottensaft' # changes for minor versions
-    PATCH = 0
+    PATCH = 1
 
     STRING = [MAJOR, MINOR, PATCH].join('.')
   end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: lederhosen
 version: !ruby/object:Gem::Version
-  version: 1.8.0
+  version: 1.8.1
   prerelease: 
 platform: ruby
 authors:
@@ -132,7 +132,6 @@ files:
 - lib/lederhosen/tasks/otu_table.rb
 - lib/lederhosen/tasks/split_fasta.rb
 - lib/lederhosen/tasks/version.rb
-- lib/lederhosen/trimmer.rb
 - lib/lederhosen/version.rb
 - readme.md
 - scripts/illumina_pipeline/.gitignore
@@ -167,7 +166,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -1539752797284012594
+      hash: 4470842345198425739
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:

data/lib/lederhosen/trimmer.rb

@@ -1,225 +0,0 @@
-module Lederhosen
-module Trimmer
-
-##
-# Code used for sequence trimming
-#
-# - PairedTrimmer
-# - HuangTrimmer
-# - ProbabilityTrimmer
-# - QSEQTrimmer
-#
-# Some major refactoring needs to get done here
-#
-
-# HaungTrimmer
-#
-# class that has the trim function. Used in mixins
-# this trim function is based on the function documented
-# in the paper:
-#   Huang X, Wang J, Aluru S, Yang SP, Hillier L. (2003). PCAP:
-#   a whole-genome assembly program. Genome Res 13:
-#   2164–2170.
-#
-# The implementation is a direct copy from the perl implementation
-# implemented in Pangea 1.0:
-#   PANGEA: pipeline for analysis of next generation amplicons
-#   A Giongo, DB Crabb, AG Davis-Richardson - ISME , 2010
-#
-class HuangTrimmer
-
-  def initialize(args={})
-    @min = args[:min]
-    @offset = args[:offset]
-  end
-
-  def trim_seq(dna)
-
-    _sum, _max, first, last, start, _end = 0, 0, 0, 0, 0
-
-    dna.quality.each_byte.each_with_index do |b, a|
-      _sum += (b - @offset - @min)
-      if _sum > _max
-        _max = _sum
-        _end = a
-        start = first
-      elsif _sum < 0
-        _sum = 0
-        first = a
-      end
-    end
-
-    begin
-      dna.sequence[start, _end - start].gsub('.', 'N')
-    rescue
-      nil
-    end
-  end
-end
-
-#
-# return the longest string starting from the left side
-# where the PROBABILITY OF ERROR as computed from the PHRED
-# scores does not go above a certain cutoff
-# (default is 0.005)
-#
-class ProbabilityTrimmer
-
-  def initialize(args = {})
-    @cutoff = args[:cutoff] || 0.005
-    @min = args[:min]
-    @seqtech = args[:seq_tech] || fail
-    # must be illumina, sanger or solexa
-  end
-
-  def trim_seq(dna)
-    trim_coord = dna.sequence.size
-    probabilities = dna.send(:"#{@seqtech}_probabilities")
-    probabilities.each_with_index do |q, i|
-      if q > @cutoff
-        trim_coord = i
-        break
-      end
-    end
-
-    begin
-      dna.sequence[0..trim_coord].gsub('.', 'N')
-    rescue
-      nil
-    end
-  end
-end
-
-#
-# Base class for trimming paired-end reads
-#
-class PairedTrimmer < Enumerator
-
-  def initialize(args = {})
-    @pretrim    = args[:pretrim]
-    # TODO
-    # need to be able to trim from left, right of pairs
-    # thinking about specifying a "trimming language"
-    #
-    # Something like:
-    #
-    # --trim="5L0 0L3"
-    # --trim="0L4 2L6"
-    #
-    # also thinking about breaking all of this trimming stuff
-    # out into its own package. (to be more unixy and stuff ;)
-    #
-    @min_length = args[:min_length] || 70
-    @min         = args[:min] || 20
-    @offset      = args[:cutoff] || 64 # XXX should both be called 'cutoff'
-    @left_trim   = args[:left_trim] || 0 # trim adapter sequence
-    @skip_ambig  = args[:skip_ambiguous] || false
-    @trimmer     = args[:trimmer] || ProbabilityTrimmer.new(:min => @min,
-                                                           :offset => @offset,
-                                                           :seq_tech =>
-                                                           :illumina)
-  end
-
-  def each(&block)
-
-    skipped_because_singleton = 0
-    skipped_because_length = 0
-    skipped_because_ambig = 0
-
-    @paired_iterator.each_with_index do |a, i|
-      seqa = @trimmer.trim_seq(a[0])[@left_trim..-1] rescue nil # trim adapter sequence
-      seqb = @trimmer.trim_seq a[1]
-
-      # make sure sequences are good
-      # (both pairs survived and both are at least min_length long)
-      # optionally skip reads that contain ambiguous nucleotides (N)
-      if [seqa, seqb].include? nil
-        skipped_because_singleton += 1
-      elsif !(seqb.length >= @min_length && seqa.length >= @min_length)
-        skipped_because_length += 1
-      elsif @skip_ambig and (seqb =~ /N/ or seqa =~ /N/)
-        skipped_because_ambig
-      else # reads are good
-        #
-        # TODO
-        # this is experiment specific. I save memory down the road
-        # by having both of the reads in the forward orientation
-        # but depending on the sequencing technology/pipeline
-        # this may change.
-        #
-        # I'm planning on removing the trimming steps from lederhosen
-        # for their own gem. With that, this will go too.
-        #
-        seqb = reverse_complement(seqb)
-        
-        # Create and yield new fasta objects
-        # Perhaps this is slow?
-        a = Fasta.new :name => "#{i}:0", :sequence => seqa
-        b = Fasta.new :name => "#{i}:1", :sequence => seqb
-        block.yield a
-        block.yield b
-      end
-    end
-  end
-
-  # reverse complement a DNA sequence
-  # assumes only GATCN nucleotides
-  def reverse_complement(s)
-    s.reverse.tr('GATCNgatcn','CTAGNctagn')
-  end
-end
-
-#
-# Yields trimmed fasta records given an input
-# interleaved, paired-end fastq file
-#
-class InterleavedTrimmer < PairedTrimmer
-
-  def initialize(interleaved_file, args = {})
-    # create an iterator that yields paired records
-    # as an array
-
-    handle =
-      begin
-        Zlib::GzipReader.open(interleaved_file)
-      rescue Zlib::GzipFile::Error
-        File.open(interleaved_file)
-      end
-
-    reads = Dna.new handle
-    @paired_iterator = reads.each_slice(2)
-
-    super(args)
-  end
-end
-
-#
-# Yield trimmed fasta records given an two separate
-# paired QSEQ files
-#
-class QSEQTrimmer < PairedTrimmer
-  def initialize(left_file, right_file, args = {})
-    # create an iterator that yields paired records
-    # as an array
-
-    left_handle, right_handle =
-      begin
-        [ Zlib::GzipReader.open(left_file), Zlib::GzipReader.open(right_file)]
-      rescue Zlib::GzipFile::Error
-        [ File.open(left_file), File.open(right_file) ]
-      end
-
-    left_file_reads  = Dna.new left_handle
-    right_reads = Dna.new right_handle
-
-    @paired_iterator = left_file_reads.zip(right_reads)
-
-    super(args)
-
-    left_handle.close
-    right_handle.close
-  end
-end
-
-end # module Trimmer
-end # module Lederhosen