bioroebe 0.12.24 → 0.13.31

data/lib/bioroebe/toplevel_methods/levensthein.rb

@@ -1,63 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-module Bioroebe
-
-  # ========================================================================= #
-  # === Bioroebe.min3
-  # ========================================================================= #
-  def self.min3(a, b, c)
-    if a < b && a < c
-      a
-    elsif b < c
-      b
-    else
-      c
-    end
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.levenshtein_distance
-  # ========================================================================= #
-  def self.levenshtein_distance(str1, str2)
-    n = str1.length
-    m = str2.length
-
-    return m if n.zero?
-    return n if m.zero?
-
-    x = nil
-    d = (0 .. m).to_a # Get the distance.
-
-    # ======================================================================= #
-    # To avoid duplicating an enumerable object, create it outside of the
-    # loop.
-    # ======================================================================= #
-    str2_codepoints = str2.codepoints
-
-    str1.each_codepoint.with_index(1) { |char1, i|
-      j = 0
-      while j < m
-        cost = (char1 == str2_codepoints[j]) ? 0 : 1
-        x = min3(
-          d[j + 1] + 1, # insertion
-          i + 1,        # deletion
-          d[j] + cost   # substitution
-        )
-        d[j] = i
-        i = x
-        j += 1
-      end
-      d[m] = x
-    }
-    x # Return the cost here.
-  end
-
-end
-
-if __FILE__ == $PROGRAM_NAME
-  alias e puts
-  e 'Difference between "shevy" and "chevy" is: '+
-     Bioroebe.levenshtein_distance('shevy', 'chevy').to_s # => 1  
-end # rb levensthein.rb

data/lib/bioroebe/toplevel_methods/log_directory.rb

@@ -1,109 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# This file keeps track of where we will store output generated by
-# the Bioroebe project.
-# =========================================================================== #
-# require 'bioroebe/toplevel_methods/log_directory.rb'
-# Bioroebe.download_dir?
-# =========================================================================== #
-module Bioroebe
-
-  # ========================================================================= #
-  # === @log_directory
-  #
-  # Keep track where to log output into, through this variable.
-  # ========================================================================= #
-  @log_directory = nil
-
-  # ========================================================================= #
-  # === Bioroebe.log_directory?
-  #
-  # This method will keep track over where we will store output,
-  # related to the Bioroebe project.
-  # ========================================================================= #
-  def self.log_directory?
-    @log_directory
-  end; self.instance_eval { alias log_dir                log_directory? } # === Bioroebe.log_dir
-       self.instance_eval { alias store_here?            log_directory? } # === Bioroebe.store_here?
-       self.instance_eval { alias save_dir?              log_directory? } # === Bioroebe.save_dir?
-       self.instance_eval { alias log_dir?               log_directory? } # === Bioroebe.log_dir?
-       self.instance_eval { alias project_log_directory? log_directory? } # === Bioroebe.project_log_directory?
-
-  require 'bioroebe/constants/base_directory.rb'
-  # ========================================================================= #
-  # === Bioroebe.set_log_dir
-  #
-  # This method will set the log-directory for the Bioroebe project.
-  #
-  # Usually this will be in the user's home directory, and then a
-  # 'Bioroebe/' suffix appended. The default input-value is the
-  # symbol :default.
-  #
-  # The user can set to use another log-directory through this method.
-  # ========================================================================= #
-  def self.set_log_directory(
-      i = :default
-    )
-    case i # case tag
-    # ======================================================================= #
-    # === :default
-    #
-    # This is the default value.
-    # ======================================================================= #
-    when :default
-      i = ::Bioroebe.base_directory?
-    end
-    unless i.end_with? '/'
-      i = i.dup if i.frozen?
-      i << '/'
-    end
-    @log_directory = i
-  end; self.instance_eval { alias set_log_dir set_log_directory } # === Bioroebe.set_log_dir
-
-  # ========================================================================= #
-  # === Initialize it at once, with the default value.
-  # ========================================================================= #
-  _ = :default # Uses the default path.
-  if ENV.has_key? 'BIOROEBE_DEFAULT_LOG_DIRECTORY'
-    _ = ENV['BIOROEBE_DEFAULT_LOG_DIRECTORY']
-  end
-  set_log_directory(_)
-
-  # ========================================================================= #
-  # === Bioroebe.download_directory?
-  # ========================================================================= #
-  def self.download_directory?
-    "#{@log_directory}Downloads/"
-  end; self.instance_eval { alias download_dir? download_directory? } # === Bioroebe.download_dir?
-
-  # ========================================================================= #
-  # === LOCAL_DIRECTORY_FOR_UNIPROT
-  #
-  # This denotes the directory for uniprot-files.
-  # ========================================================================= #
-  LOCAL_DIRECTORY_FOR_UNIPROT = "#{@log_directory}uniprot/"
-
-  # ========================================================================= #
-  # === Bioroebe::AUTOGENERATED_SQL_FILES_DIR
-  # ========================================================================= #
-  AUTOGENERATED_SQL_FILES_DIR =
-    "#{@log_directory}autogenerated_sql_files/" # Where to store .sql files.
-
-  # ========================================================================= #
-  # === Bioroebe.fasta_directory?
-  #
-  # This method will return a path such as "/root/Bioroebe/fasta/".
-  # ========================================================================= #
-  def self.fasta_directory?
-    "#{::Bioroebe.log_directory?}fasta/"
-  end
-
-end
-
-if __FILE__ == $PROGRAM_NAME
-  alias e puts
-  e Bioroebe.log_directory?
-  e Bioroebe.download_directory?  
-end

data/lib/bioroebe/toplevel_methods/longest_common_substring.rb

@@ -1,55 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/toplevel_methods/longest_common_substring.rb'
-# =========================================================================== #
-module Bioroebe
-
-  # ========================================================================= #
-  # === Bioroebe.longest_common_substring
-  #
-  # This method will return the longest common substring. There may be
-  # more than one solution, though.
-  #
-  # Note that this method was specifically written for Rosalind, so it
-  # may not be too overly useful for most general tasks. For example,
-  # it is not optimised for speed, so you should probably not use
-  # it for very long sequences.
-  # ========================================================================= #
-  def self.longest_common_substring(sequences)
-    if sequences and !sequences.empty? and File.file?(sequences.first)
-      require 'bioroebe/requires/require_all_fasta_and_fastq_files.rb'
-      hash = parse_fasta_quietly(sequences.first).hash?
-      sequences = hash.values.map {|entry| entry.delete("\n") }
-    end
-    # ======================================================================= #
-    # First obtain a handle towards the shortest sequence.
-    # ======================================================================= #
-    shortest_sequence = sequences.min_by(&:length)
-    maxlen = shortest_sequence.length
-    maxlen.downto(1) {|len|
-      0.upto(maxlen - len) { |start|
-        substring = shortest_sequence.to_s[start,len]
-        if sequences.all? {|seq| seq.to_s.include? substring }
-          return shortest_sequence.class.new(substring)
-        end
-      }
-    }
-    return nil
-  end
-
-end
-
-if __FILE__ == $PROGRAM_NAME
-  alias e puts
-  if ARGV.empty?
-    e Bioroebe.longest_common_substring(
-      %w( GATTACA TAGACCA ATACA )
-    )
-  else
-    e Bioroebe.longest_common_substring(ARGV)
-  end
-end # longestcommonsubstring
-    # longestcommonsubstring ATTTTT ATTT
-    # longestcommonsubstring /rosalind_lcsm.txt

data/lib/bioroebe/toplevel_methods/map_ncbi_entry_to_eutils_id.rb

@@ -1,88 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/toplevel_methods/map_ncbi_entry_to_eutils_id.rb'
-# =========================================================================== #
-module Bioroebe
-
-  # ========================================================================= #
-  # === Bioroebe.map_ncbi_entry_to_eutils_id
-  #
-  # This is a general "URL mapper" from certain NCBI IDs to specific
-  # nucleotide sequences. Only some URLs will be mapped, in particular
-  # those that I use more frequently.
-  #
-  # The method was created specifically to allow simpler input via
-  # the commandline and the bioshell - it is easier to remember
-  # a name such as "rhinovirus" as opposed to the NC entry, which
-  # is "NC_038311".
-  #
-  # Usage examples:
-  #
-  #   Bioroebe.map_ncbi_entry_to_eutils_id 'rhinovirus'
-  #   Bioroebe.map_ncbi_entry_to_eutils_id 'T6'
-  # 
-  # ========================================================================= #
-  def self.map_ncbi_entry_to_eutils_id(
-      i = 'NC_001416.1.fasta'
-    )
-    case i
-    # ======================================================================= #
-    # === Lambda phage genome
-    # ======================================================================= #
-    when /^-?-?NC_001416.1.fasta$/i,
-         'lambda'
-      i = '9626243'
-    # ======================================================================= #
-    # === P1
-    # ======================================================================= #
-    when 'NC_005856.1.fasta',
-         'P1'
-      i = '46401626'
-    # ======================================================================= #
-    # === P2
-    # ======================================================================= #
-    when 'NC_041848.1.fasta',
-         'P2'
-      i = '1631913463'
-    # ======================================================================= #
-    # === T12
-    # ======================================================================= #
-    when 'NC_028700.1.fasta',
-         'T12'
-      i = '966201481'
-    # ======================================================================= #
-    # === T2
-    # ======================================================================= #
-    when 'AP018813.1.fasta',
-         'T2'
-      i = 'AP018813.1'
-    # ======================================================================= #
-    # === T4
-    # ======================================================================= #
-    when 'NC_000866.4.fasta',
-         'T4'
-      i = 'NC_000866.4'
-    # ======================================================================= #
-    # === T6
-    # ======================================================================= #
-    when 'T6'
-      i = 'MH550421.1'
-    # ======================================================================= #
-    # === rhinovirus
-    # ======================================================================= #
-    when /NC_038311/,
-         'rhinovirus'
-      i = '1464306962'
-    end
-    return i
-  end
-
-end
-
-if __FILE__ == $PROGRAM_NAME
-  alias e puts
-  e Bioroebe.map_ncbi_entry_to_eutils_id 'rhinovirus'
-  e Bioroebe.map_ncbi_entry_to_eutils_id 'T6'
-end

data/lib/bioroebe/toplevel_methods/matches.rb

@@ -1,259 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# Match-related actions on the toplevel "namespace" are collected in this
-# file here.
-# =========================================================================== #
-# require 'bioroebe/toplevel_methods/matches.rb'
-# =========================================================================== #
-module Bioroebe
-
-  require 'bioroebe/constants/regex.rb'
-  require 'bioroebe/toplevel_methods/e.rb'
-  require 'bioroebe/toplevel_methods/download_and_fetch_data.rb'
-  require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
-  require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
-  require 'bioroebe/codons/start_codons.rb'
-
-  # ========================================================================= #
-  # === Bioroebe.determine_n_glycosylation_matches
-  #
-  # This method can be used to determine N-Glycosylation patterns in a
-  # protein.
-  #
-  # The input to this method should be an aminoacid chain - aka a protein
-  # sequence.
-  #
-  # This method will return an Array. This Array holds the indices where
-  # a N-glycosylation pattern begins.
-  #
-  # Usage example:
-  #
-  #   Bioroebe.determine_n_glycosylation_matches # => [85, 118, 142, 306, 395]
-  #
-  # ========================================================================= #
-  def self.determine_n_glycosylation_matches(
-      of_this_protein_sequence =
-        'MKNKFKTQEELVNHLKTVGFVFANSEIYNGLANAWDYGPLGVLLKNNLKNLWWKEFVTKQKDV'\
-        'VGLDSAIILNPLVWKASGHLDNFSDPLIDCKNCKARYRADKLIESFDENIHIAENSSNEEFAK'\
-        'VLNDYEISCPTCKQFNWTEIRHFNLMFKTYQGVIEDAKNVVYLRPETAQGIFVNFKNVQRSMR'\
-        'LHLPFGIAQIGKSFRNEITPGNFIFRTREFEQMEIEFFLKEESAYDIFDKYLNQIENWLVSAC'\
-        'GLSLNNLRKHEHPKEELSHYSKKTIDFEYNFLHGFSELYGIAYRTNYDLSVHMNLSKKDLTYF'\
-        'DEQTKEKYVPHVIEPSVGVERLLYAILTEATFIEKLENDDERILMDLKYDLAPYKIAVMPLVN'\
-        'KLKDKAEEIYGKILDLNISATFDNSGSIGKRYRRQDAIGTIYCLTIDFDSLDDQQDPSFTIRE'\
-        'RNSMAQKRIKLSELPLYLNQKAHEDFQRQCQK'
-    )
-    if of_this_protein_sequence.is_a? Array
-      of_this_protein_sequence.each {|this_sequence|
-        determine_n_glycosylation_matches(this_sequence)
-      }
-    else
-      scanned = of_this_protein_sequence.scan(
-        REGEX_FOR_N_GLYCOSYLATION_PATTERN
-      )
-      scanned.flatten.uniq.map {|substring|
-        of_this_protein_sequence.index(substring)+1 # +1 because ruby starts at 0.
-      }
-    end
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.return_longest_substring_via_LCS_algorithm
-  #
-  # This method will return the longest substring between two different
-  # sequences. It will ignore gaps and will thus not be as sophisticated
-  # as other algorithms.
-  #
-  # This method will return a String.
-  #
-  # Usage example in plain ruby:
-  #
-  #   Bioroebe.return_longest_substring_via_LCS_algorithm 'ATGAAA','ATGCAT' # => 'ATGA'
-  #
-  # ========================================================================= #
-  def self.return_longest_substring_via_LCS_algorithm(
-      sequence1 = ARGV,
-      sequence2 = nil
-    )
-    begin
-      require 'diff/lcs'
-    rescue LoadError; end
-    if sequence1.is_a? Array
-      if sequence1.size > 1
-        sequence2 = sequence1[1]
-        sequence1 = sequence1[0]
-      end
-    end 
-    lcs_object = Diff::LCS.LCS(sequence1, sequence2)
-    return lcs_object.join # Must return a String.
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.return_array_of_sequence_matches
-  #
-  # This method can be used to return an Array of subsequence matches.
-  #
-  # This method will always return an Array - an empty Array if no
-  # subsequence match has been found; and an Array with integer numbers
-  # as indices, to denote which indices contain the subsequence. These
-  # numbers store the start position of the subsequence.
-  #
-  # Keep in mind that for nucleotides we will start at +1, not 0, so
-  # if you see an Array such as [3, 7] as result then this refers to
-  # the nucleotide at position 3 and the nucleotide at position 7.
-  #
-  # Arguments to this method:
-  #
-  # The first argument to this method should be the main sequence.
-  #
-  # The second argument to this method should be the subsequence
-  # that we assume to be part of the main sequence (that is, to
-  # occur within that main sequence at the least once).
-  #
-  # Specific invocation examples, with the last example showing
-  # how an empty Array will be returned:
-  #
-  #   Bioroebe.return_array_of_sequence_matches('ACGTACGTAACG','GTA')   # => [3, 7]
-  #   Bioroebe.return_array_of_sequence_matches('ACGTACGTAACG','GTAAA') # => []
-  #   Bioroebe.return_array_of_sequence_matches('ATGGTGGTGGTGATGATGTGCACTCGGTTCCAGGGGGGTCGTAGGAATTGAGCTAGGACCTCCACTAGGCATCTGGGTTCGAAATTATAAAGGTCAAACGCTACTACCCTGTGTGCTAGCTTTGAAGGGCTGACGCTAGAATTGACGTCGCCGGTGACATTTGCGTCGAGGTGGTAGTAATGTTCCAAGGATGCCGGACGAACGGTACTTACCCTCGTTAGTCAGATCGCCAACCCGAGTCGTCCATGAGGAAAGCGTAATGGAAGAGACCGGGACAGCCCTCCTCAAATGTGCCTGGATACGAGTGATTTACCA','ATG')
-  #
-  # ========================================================================= #
-  def self.return_array_of_sequence_matches(
-      main_sequence,
-      subsequence # ← The subsequence that you wish to match onto the main sequence.
-    )
-    if main_sequence
-      array = []
-      chars = main_sequence.chars
-      if main_sequence.is_a? ::Bioroebe::Sequence
-        main_sequence = main_sequence.sequence?
-      end
-      chars.each_with_index.select {|char, index|
-        if main_sequence[index, subsequence.length] == subsequence
-          array << index+1
-        end
-      }
-      return array
-    else
-      []
-    end
-  end; self.instance_eval { alias return_indices_of_matches return_array_of_sequence_matches } # === Bioroebe.return_indices_of_matches
-       self.instance_eval { alias indices_of_matches        return_array_of_sequence_matches } # === Bioroebe.indices_of_matches
-
-  # ========================================================================= #
-  # === Bioroebe.return_all_substring_matches
-  #
-  # This method will give us back an Array that contains all matching
-  # substrings.
-  #
-  # By default, the method will search for start codons such as ATG
-  # or GTG.
-  # ========================================================================= #
-  def self.return_all_substring_matches(
-      this_string,
-      use_this_as_substring = ::Bioroebe.start_codon?
-    )
-    # ======================================================================= #
-    # We will search for both ATG and AUG though, respectively the
-    # input variants given to us. If the following regex appears to
-    # be complicated to you, here is the old variant for the regex:
-    #
-    #   use_this_regex = /(ATG|AUG)/i
-    #
-    # =================================================================== #
-    if use_this_as_substring.include? 'T'
-      use_this_regex = /(#{use_this_as_substring}|#{use_this_as_substring.tr('T','U')})/i
-    else
-      use_this_regex = /#{use_this_as_substring}/i
-    end
-    result = this_string.to_enum(:scan, use_this_regex).map { |match|
-      [$`.size + 1, match] # +1 because we refer to the nucleotide positions.
-    }
-    return result
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.show_n_glycosylation_motifs
-  #
-  # The argument to this method should be a local file, which
-  # stores the IDs of the proteins. Only use one ID per given
-  # line, though.
-  #
-  # This method has been inspired by this Rosalind task:
-  #
-  #   http://rosalind.info/problems/mprt/
-  #
-  # ========================================================================= #
-  def self.show_n_glycosylation_motifs(
-      from_this_file = 'foobar.fasta'
-    )
-    if from_this_file.is_a? Array
-      from_this_file = from_this_file.first
-    end
-    from_this_file = from_this_file.to_s
-    if File.exist? from_this_file
-      result = ''.dup
-      dataset = File.readlines(from_this_file).reject {|entry| entry.strip.empty? }
-      index = 0
-      dataset.each {|this_id_for_the_protein| index += 1
-        this_id_for_the_protein.strip!
-        # =================================================================== #
-        # Fetch the remote dataset from uniprot.
-        # =================================================================== #
-        e
-        e royalblue(
-            index.to_s.rjust(2)+') '
-          )
-        file_location         = ::Bioroebe.fetch_data_from_uniprot(this_id_for_the_protein)
-        parsed_fasta_sequence = ::Bioroebe::ParseFasta.new(file_location) { :be_quiet }.first_value
-        array_of_indices      = ::Bioroebe.determine_n_glycosylation_matches(parsed_fasta_sequence)
-        # =================================================================== #
-        # Next, this is the output that Rosalind wants to have.
-        # =================================================================== #
-        unless array_of_indices.empty?
-          result << this_id_for_the_protein+"\n"
-          result << array_of_indices.join(' ')+"\n"
-        end
-      }
-      e result # And display that result finally.
-    else
-      no_file_exists_at(from_this_file)
-    end
-  end; self.instance_eval { alias glycosylation show_n_glycosylation_motifs } # === Bioroebe.glycosylation
-
-end
-
-if __FILE__ == $PROGRAM_NAME
-  pp Bioroebe.determine_n_glycosylation_matches
-  Bioroebe.show_n_glycosylation_motifs(ARGV)
-    # ========================================================================= #
-  # Some test-code.
-  # ========================================================================= #
-  require 'colours/autoinclude'
-  input_sequence = 'TGCAGAAAAAAAAAAAGCCCCCCCCGTTTTTTTTATGCCCCCCGCGGGGGGGGATGTGGGGGC'
-  e rev+'The input sequence is:'
-  e
-  e "  #{sfancy(input_sequence)}"
-  e
-  array_matches = Bioroebe.return_all_substring_matches(input_sequence)
-  e 'The first match (for the sequence '+::Bioroebe.start_codon?+') would yield:'
-  e
-  e "  #{sfancy(input_sequence[(array_matches.first.first-1) .. -1])}"
-  e
-  e 'All matches found with a start codon are contained in the following Array:'
-  e
-  print '  '; pp array_matches
-  e
-  e 'Next, testing Bioroebe.return_array_of_sequence_matches(ARGV[0], ARGV[1])'
-  e
-  pp Bioroebe.return_array_of_sequence_matches(ARGV[0], ARGV[1])
-end # determinenglycosylationmatches
-    # determinenglycosylationmatches /UNIPROT.md
-    # determinenglycosylationmatches /HERE.md
-    # determinenglycosylationmatches /ABC.md
-    # determinenglycosylationmatches /rosalind_mprt.txt
-    #
-    # return_array_of_sequence_matches AUGACGTACGTAACG AUG # => [1]
-    # return_array_of_sequence_matches ACGTACGTAACG GTA    # => [3, 7]
-    # rb matches.rb ACGTACGTAACG GTA