BioDSL 1.0.0

data/lib/BioDSL/csv.rb

@@ -0,0 +1,307 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                #
+#                                                                              #
+# This program is free software; you can redistribute it and/or                #
+# modify it under the terms of the GNU General Public License                  #
+# as published by the Free Software Foundation; either version 2               #
+# of the License, or (at your option) any later version.                       #
+#                                                                              #
+# This program is distributed in the hope that it will be useful,              #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of               #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                #
+# GNU General Public License for more details.                                 #
+#                                                                              #
+# You should have received a copy of the GNU General Public License            #
+# along with this program; if not, write to the Free Software                  #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301,    #
+# USA.                                                                         #
+#                                                                              #
+# http://www.gnu.org/copyleft/gpl.html                                         #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# This software is part of BioDSL (www.github.com/maasha/BioDSL).              #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+# Monkey patching Array to add convert_types method.
+class Array
+  # Method that converts variable types given an array of types.
+  # Example: ["fish", 0.0, 1].convert_types([:to_s, :to_f, :to_i])
+  def convert_types(types)
+    if size != types.size
+      fail ArgumentError, "Array and types size mismatch: #{size} != " \
+        "#{types.size}"
+    end
+
+    types.each_with_index do |type, i|
+      self[i] = self[i].send(type)
+    end
+
+    self
+  end
+end
+
+module BioDSL
+  class CSVError < StandardError; end
+
+  # rubocop: disable ClassLength
+
+  # Class for manipulating CSV or table files.
+  # Allow reading and writing of gzip and bzip2 data.
+  # Auto-convert data types.
+  # Returns lines, arrays or hashes.
+  class CSV
+    def self.open(*args)
+      io = IO.open(*args)
+
+      if block_given?
+        yield new(io)
+      else
+        return new(io)
+      end
+    end
+
+    # Method that reads all CSV data from a file into an array of arrays (array
+    # of rows) which is returned. In the default mode all columns are read.
+    # Using the select option subselects the columns based on a given Array or
+    # if a heder line is present a given Hash. Visa versa for the reject option.
+    # Header lines are prefixed with '#' and are returned if the include_header
+    # option is given.
+    #
+    # Options:
+    #   * include_header
+    #   * delimiter.
+    #   * select.
+    #   * reject.
+    def self.read_array(file, options = {})
+      data = []
+
+      open(file) do |ios|
+        ios.each_array(options) { |row| data << row }
+      end
+
+      data
+    end
+
+    # Method that reads all CSV data from a file into an array of hashes (array
+    # of rows) which is returned. In the default mode all columns are read.
+    # Using the select option subselects the columns based on a given Array or
+    # if a heder line is present a given Hash. Visa versa for the reject option.
+    # Header lines are prefixed with '#'.
+    #
+    # Options:
+    #   * delimiter.
+    #   * select.
+    #   * reject.
+    def self.read_hash(file, options = {})
+      data = []
+
+      open(file) do |ios|
+        ios.each_hash(options) { |row| data << row }
+      end
+
+      data
+    end
+
+    # Constructor method for CSV.
+    def initialize(io)
+      @io        = io
+      @delimiter = "\s"
+      @header    = nil
+      @fields    = nil
+      @types     = nil
+    end
+
+    # Method to skip a given number or non-empty lines.
+    def skip(num)
+      while num != 0 && (line = @io.gets)
+        line.chomp!
+
+        num -= 1 unless line.empty?
+      end
+    end
+
+    # Method to iterate over a CSV IO object yielding arrays or an enumerator
+    #   CSV.each_array(options={}) { |item| block } -> ary
+    #   CSV.each_array(options={})                  -> Enumerator
+    #
+    # Options:
+    #   * :include_header -
+    #   * :delimiter      -
+    #   * :select         -
+    #   * :reject         -
+    def each_array(options = {})
+      return to_enum :each_array unless block_given?
+
+      delimiter = options[:delimiter] || @delimiter
+
+      @io.each do |line|
+        line.chomp!
+        next if line.empty?
+
+        fields = line.split(delimiter)
+
+        if line[0] == '#'
+          get_header(fields, options) unless @header
+          get_fields(fields, options) unless @fields
+
+          yield @header.map(&:to_s) if options[:include_header]
+        else
+          get_header(fields, options) unless @header
+          get_fields(fields, options) unless @fields
+
+          fields = fields.values_at(*@fields) if @fields
+
+          determine_types(fields) unless @types
+
+          yield fields.convert_types(@types)
+        end
+      end
+
+      self
+    end
+
+    # Method to iterate over a CSV IO object yielding hashes or an enumerator
+    #   CSV.each_hash(options={}) { |item| block } -> hash
+    #   CSV.each_hash(options={})                  -> Enumerator
+    #
+    # Options:
+    #   * :delimiter      -
+    #   * :select         -
+    #   * :reject         -
+    def each_hash(options = {})
+      each_array(options) do |array|
+        hash = {}
+
+        array.convert_types(@types).each_with_index do |field, i|
+          hash[@header[i]] = field
+        end
+
+        yield hash
+      end
+
+      self
+    end
+
+    private
+
+    # Method to set the @header given a list of fields (a row).
+    # Options:
+    #   * :select - list of column indexes, names or a range to select.
+    #   * :reject - list of column indexes, names or a range to reject.
+    def get_header(fields, options)
+      if fields[0][0] == '#'
+        fields[0] = fields[0][1..-1]
+        @header = fields.map(&:to_sym)
+      else
+        @header = []
+        fields.each_with_index { |_field, i| @header << "V#{i}".to_sym }
+      end
+
+      if options[:select]
+        if options[:select].first.is_a? Fixnum
+          if options[:select].max >= @header.size
+            fail CSVError, "Selected columns out of bounds: #{options[:select].
+              select { |c| c >= @header.size }}"
+          end
+        else
+          options[:select].each do |value|
+            unless @header.include? value.to_sym
+              fail CSVError, "Selected value: #{value} not in header: " \
+                " #{@header}"
+            end
+          end
+        end
+      elsif options[:reject]
+        if options[:reject].first.is_a? Fixnum
+          if options[:reject].max >= @header.size
+            fail CSVError, "Rejected columns out of bounds: #{options[:reject].
+              reject { |c| c >= @header.size }}"
+          end
+        else
+          options[:reject].map do |value|
+            unless @header.include? value.to_sym
+              fail CSVError, "Rejected value: #{value} not found in header: " \
+                "#{@header}"
+            end
+          end
+        end
+      end
+
+      @header
+    end
+
+    # Method to determine the indexes of fields to be parsed and store these in
+    # @fields.
+    # Options:
+    #   * :select - list of column indexes, names or a range to select.
+    #   * :reject - list of column indexes, names or a range to reject.
+    def get_fields(fields, options)
+      if options[:select]
+        if options[:select].first.is_a? Fixnum
+          @fields = options[:select]
+        else
+          fail CSVError, 'No header found' unless @header
+
+          fields = []
+
+          options[:select].each do |value|
+            fields << @header.index(value.to_sym)
+          end
+
+          @fields = fields
+        end
+
+        @header = @header.values_at(*@fields)
+      elsif options[:reject]
+        if options[:reject].first.is_a? Fixnum
+          reject = if options[:reject].is_a?(Range)
+                     options[:reject].to_a
+                   else
+                     options[:reject]
+                   end
+          @fields = (0...fields.size).to_a - reject
+        else
+          fail CSVError, 'No header found' unless @header
+
+          reject = options[:reject].map(&:to_sym)
+
+          @fields = @header.map.with_index.to_h.
+                    delete_if { |k, _| reject.include? k }.values
+        end
+
+        @header = @header.values_at(*@fields)
+      end
+    end
+
+    # Method that determines the data types used in an array of fields.
+    def determine_types(fields)
+      types = []
+
+      fields.each do |field|
+        field = field.to_num
+
+        if field.is_a? Fixnum
+          types << :to_i
+        elsif field.is_a? Float
+          types << :to_f
+        elsif field.is_a? String
+          types << :to_s
+        else
+          types << nil
+        end
+      end
+
+      @types = types
+    end
+
+    # IO class for CSV.
+    class IO < Filesys
+      def gets
+        @io.gets
+      end
+    end
+  end
+end

data/lib/BioDSL/debug.rb

@@ -0,0 +1,42 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                #
+#                                                                              #
+# This program is free software; you can redistribute it and/or                #
+# modify it under the terms of the GNU General Public License                  #
+# as published by the Free Software Foundation; either version 2               #
+# of the License, or (at your option) any later version.                       #
+#                                                                              #
+# This program is distributed in the hope that it will be useful,              #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of               #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                #
+# GNU General Public License for more details.                                 #
+#                                                                              #
+# You should have received a copy of the GNU General Public License            #
+# along with this program; if not, write to the Free Software                  #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301,    #
+# USA.                                                                         #
+#                                                                              #
+# http://www.gnu.org/copyleft/gpl.html                                         #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# This software is part of the BioDSL framework (www.BioDSL.org).        #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+# Namespace for BioDSL.
+module BioDSL
+  # Class variabel visible across the BioDSL module scope.
+  @@debug = false
+
+  # Class variable getter method.
+  def self.debug
+    @@debug
+  end
+
+  # Class variable setter method.
+  def self.debug=(x)
+    @@debug = x
+  end
+end

data/lib/BioDSL/fasta.rb

@@ -0,0 +1,133 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                                #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                  #
+#                                                                                #
+# This program is free software; you can redistribute it and/or                  #
+# modify it under the terms of the GNU General Public License                    #
+# as published by the Free Software Foundation; either version 2                 #
+# of the License, or (at your option) any later version.                         #
+#                                                                                #
+# This program is distributed in the hope that it will be useful,                #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of                 #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                  #
+# GNU General Public License for more details.                                   #
+#                                                                                #
+# You should have received a copy of the GNU General Public License              #
+# along with this program; if not, write to the Free Software                    #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. #
+#                                                                                #
+# http://www.gnu.org/copyleft/gpl.html                                           #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                                #
+# This software is part of BioDSL (www.BioDSL.org).                        #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+module BioDSL
+  # Error class for all exceptions to do with FASTA.
+  class FastaError < StandardError; end
+
+  class Fasta
+    def self.open(*args)
+      ios = IO.open(*args)
+
+      if block_given?
+        begin
+          yield self.new(ios)
+        ensure
+          ios.close
+        end
+      else
+        return self.new(ios)
+      end
+    end
+
+    def self.read(*args)
+      entries = []
+
+      Fasta.open(*args) do |ios|
+        ios.each do |entry|
+          entries << entry
+        end
+      end
+
+      entries
+    end
+
+    attr_accessor :seq_name, :seq
+
+    def initialize(io)
+      @io        = io
+      @seq_name  = nil
+      @seq       = ""
+      @got_first = nil
+      @got_last  = nil
+    end
+
+    def each
+      while entry = next_entry
+        yield entry
+      end
+    end
+
+    def puts(*args)
+      @io.puts(*args)
+    end
+
+    # Method to get the next FASTA entry form an ios and return this
+    # as a Seq object. If no entry is found or eof then nil is returned.
+    def next_entry
+      @io.each do |line|
+        line.chomp!
+
+        next if line.empty?
+
+        if line[0] == '>'
+          if not @got_first and not @seq.empty?
+            raise FastaError, "Bad FASTA format -> content before Fasta header: #{@seq}" unless @seq.empty?
+          end
+
+          @got_first = true
+
+          if @seq_name
+            entry     = Seq.new(seq_name: @seq_name, seq: @seq)
+            @seq_name = line[1 .. -1]
+            @seq      = ""
+
+            raise FastaError, "Bad FASTA format -> truncated Fasta header: no content after '>'" if @seq_name.empty?
+
+            return entry
+          else
+            @seq_name = line[1 .. -1]
+
+            raise FastaError, "Bad FASTA format -> truncated Fasta header: no content after '>'" if @seq_name.empty?
+          end
+        else
+          @seq << line
+        end
+      end
+
+      if @seq_name
+        @got_last = true
+        entry     = Seq.new(seq_name: @seq_name, seq: @seq)
+        @seq_name = nil
+        return entry
+      end
+
+      if not @got_last and not @seq.empty?
+        raise FastaError, "Bad FASTA format -> content witout Fasta header: #{@seq}"
+      end
+
+      nil
+    end
+
+    class IO < Filesys
+      def each
+        while not @io.eof?
+          yield @io.gets
+        end
+      end
+    end
+  end
+end

data/lib/BioDSL/fastq.rb

@@ -0,0 +1,77 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                                #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                  #
+#                                                                                #
+# This program is free software; you can redistribute it and/or                  #
+# modify it under the terms of the GNU General Public License                    #
+# as published by the Free Software Foundation; either version 2                 #
+# of the License, or (at your option) any later version.                         #
+#                                                                                #
+# This program is distributed in the hope that it will be useful,                #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of                 #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                  #
+# GNU General Public License for more details.                                   #
+#                                                                                #
+# You should have received a copy of the GNU General Public License              #
+# along with this program; if not, write to the Free Software                    #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. #
+#                                                                                #
+# http://www.gnu.org/copyleft/gpl.html                                           #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                                #
+# This software is part of BioDSL (www.BioDSL.org).                        #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+module BioDSL
+  # Error class for all exceptions to do with FASTQ.
+  class FastqError < StandardError; end
+
+  # Class for parsing FASTQ entries from an ios and return as Seq objects.
+  class Fastq < BioDSL::Filesys
+    def self.open(*args)
+      ios = IO.open(*args)
+
+      if block_given?
+        begin
+          yield self.new(ios)
+        ensure
+          ios.close
+        end
+      else
+        return self.new(ios)
+      end
+    end
+
+    def initialize(io)
+      @io        = io
+    end
+
+    def each
+      while entry = next_entry
+        yield entry
+      end
+    end
+
+    # Method to get the next FASTQ entry from an ios and return this
+    # as a Seq object. If no entry is found or eof then nil is returned.
+    def next_entry
+      return nil if @io.eof?
+      seq_name = @io.gets[1 .. -2]
+      seq      = @io.gets.chomp
+      @io.gets
+      qual     = @io.gets.chomp
+
+      Seq.new(seq_name: seq_name, seq: seq, qual: qual)
+    end
+
+    class IO < Filesys
+      def each
+        while not @io.eof?
+          yield @io.gets
+        end
+      end
+    end
+  end
+end

data/lib/BioDSL/filesys.rb

@@ -0,0 +1,137 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                                #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                  #
+#                                                                                #
+# This program is free software; you can redistribute it and/or                  #
+# modify it under the terms of the GNU General Public License                    #
+# as published by the Free Software Foundation; either version 2                 #
+# of the License, or (at your option) any later version.                         #
+#                                                                                #
+# This program is distributed in the hope that it will be useful,                #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of                 #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                  #
+# GNU General Public License for more details.                                   #
+#                                                                                #
+# You should have received a copy of the GNU General Public License              #
+# along with this program; if not, write to the Free Software                    #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. #
+#                                                                                #
+# http://www.gnu.org/copyleft/gpl.html                                           #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                                #
+# This software is part of BioDSL (www.BioDSL.org).                        #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+module BioDSL
+  # Error class for all exceptions to do with Filesys.
+  class FilesysError < StandardError; end
+
+  class Filesys
+    require 'open3'
+
+    include Enumerable
+
+    # Cross-platform way of finding an executable in the $PATH.
+    #
+    #   which('ruby') #=> /usr/bin/ruby
+    def self.which(cmd)
+      exts = ENV['PATHEXT'] ? ENV['PATHEXT'].split(';') : ['']
+
+      ENV['PATH'].split(File::PATH_SEPARATOR).each do |path|
+        exts.each { |ext|
+          exe = File.join(path, "#{cmd}#{ext}")
+          return exe if File.executable?(exe) && !File.directory?(exe)
+        }
+      end
+
+      nil
+    end
+
+    # Class method that returns a path to a unique temporary file.
+    # If no directory is specified reverts to the systems tmp directory.
+    def self.tmpfile(tmp_dir = ENV["TMPDIR"])
+      time = Time.now.to_i
+      user = ENV["USER"]
+      pid  = $$
+      path = tmp_dir + [user, time + pid, pid].join("_") + ".tmp"
+      path
+    end
+
+    def self.open(*args)
+      file    = args.shift
+      mode    = args.shift
+      options = args.shift || {}
+
+      if mode == 'w'
+        case options[:compress]
+        when :gzip
+          ios, = Open3.pipeline_w("gzip -f", out: file)
+        when :bzip, :bzip2
+          ios, = Open3.pipeline_w("bzip2 -c", out: file)
+        else 
+          ios = File.open(file, mode, options)
+        end
+      else
+        type = (file.respond_to? :path) ? `file -Lk #{file.path}` : `file -Lk #{file}`
+        case type
+        when /gzip/
+          ios = IO.popen("gzip -cd #{file}")
+        when /bzip/
+          ios = IO.popen("bzcat #{file}")
+        else
+          ios = File.open(file, mode, options)
+        end
+      end
+
+      if block_given?
+        begin
+          yield self.new(ios)
+        ensure
+          ios.close
+        end
+      else
+        return self.new(ios)
+      end
+    end
+
+    attr_reader :io
+
+    def initialize(ios)
+      @io = ios
+    end
+
+    def gets
+      @io.gets
+    end
+
+    def puts(*args)
+      @io.puts(*args)
+    end
+
+    def read
+      @io.read
+    end
+
+    def write(arg)
+      @io.write arg
+    end
+
+    def close
+      @io.close
+    end
+
+    def eof?
+      @io.eof?
+    end
+
+    # Iterator method for parsing entries.
+    def each
+      return to_enum :each unless block_given?
+
+      @io.each { |line| yield line }
+    end
+  end
+end
+