rbbt-util 5.44.1 → 6.0.3

data/lib/rbbt/tsv/util.rb

@@ -1,420 +1,420 @@
-require 'rbbt/resource/path'
-module TSV
-
-  def self.stream_column(file, column)
-    header = TSV.parse_header(file)
-    pos = header.fields.index(column) + 1
-    sep2 = header.options[:sep2] || "|"
-    case header.type.to_s
-    when nil, "double"
-      TSV.traverse file, :type => :array, :into => :stream do |line|
-        next if line =~ /^#/
-        line.split("\t")[pos].gsub(sep2, "\n")
-      end
-    when "single"
-      TSV.traverse file, :type => :array, :into => :stream do |line|
-        next if line =~ /^#/
-        line.split("\t")[1]
-      end
-    when "flat"
-      TSV.traverse file, :type => :array, :into => :stream do |line|
-        next if line =~ /^#/
-        line.split("\t")[1..-1] * "\n"
-      end
-    when 'list'
-      TSV.traverse file, :type => :array, :into => :stream do |line|
-        next if line =~ /^#/
-        line.split("\t")[pos]
-      end
-    end
-  end
-
-  def self.guess_id(identifier_file, values, options = {})
-    field_matches = TSV.field_match_counts(identifier_file, values, options)
-    field_matches.sort_by{|field, count| count.to_i}.last
-  end
-
-  def self.field_match_counts(file, values, options = {})
-    options = Misc.add_defaults options, :persist_prefix => "Field_Matches"
-    persist_options = Misc.pull_keys options, :persist
-
-    filename = TSV === file ? file.filename : file
-    path = Persist.persist filename, :string, persist_options.merge(:no_load => true) do
-      tsv = TSV === file ? file : TSV.open(file, options)
-
-      text = ""
-      fields = nil
-      tsv.tap{|e| e.unnamed =  true; fields = e.fields}.through do |gene, names|
-        names.zip(fields).each do |list, format|
-          list = [list] unless Array === list
-          list.delete_if do |name| name.empty? end
-          next if list.empty?
-          text << list.collect{|name| [name, format] * "\t"} * "\n" << "\n"
-        end
-        text << [gene, tsv.key_field] * "\t" << "\n"
-      end
-      text
-    end
-
-    TmpFile.with_file(values.uniq * "\n", false) do |value_file|
-      cmd = "cat '#{ path }' | sed 's/\\t/\\tHEADERNOMATCH/' | grep -w -F -f '#{ value_file }' | sed 's/HEADERNOMATCH//' |sort -u|cut -f 2  |sort|uniq -c|sed 's/^ *//;s/ /\t/'"
-      begin
-        TSV.open(CMD.cmd(cmd), :key_field => 1, :fields => [0], :type => :single, :cast => :to_i)
-      rescue
-        Log.exception $!
-        TSV.setup({}, :type => :single, :cast => :to_i)
-      end
-    end
-  end
-
-  def self.get_filename(file)
-    case
-    when (defined? Step and Step === file)
-      file.path
-    when Path === file
-      file
-    when (String === file and (Open.exists? file or Open.remote? file))
-      file
-    when String === file 
-      "String-#{Misc.digest file}"
-    when file.respond_to?(:filename)
-      file.filename
-    when file.respond_to?(:gets)
-      nil
-    else
-      raise "Cannot get filename from: #{file.inspect}"
-    end
-  end
-
-  def self.abort_stream(file, exception = nil)
-    return if file.nil?
-    if defined? Step and Step === file
-      if exception
-        file.exception exception 
-      else
-        if not (file.aborted? or file.done?)
-          file.abort 
-        end
-      end
-    elsif Hash === file or Array === file
-      return
-    else
-      stream = get_stream(file)
-      stream.abort(exception) if stream.respond_to? :abort
-      AbortedStream.setup(stream, exception) unless stream.respond_to?(:exception) && stream.exception
-    end
-  end
-
-  def self.get_stream(file, open_options = {})
-    case file
-    when Zlib::GzipReader
-      file
-    when (defined? Bgzf and Bgzf)
-      file
-    when TSV
-      file.dumper_stream
-    when TSV::Dumper
-      file.stream
-    when TSV::Parser
-      file.stream
-    when Path
-      file.open(open_options)
-    when (defined? Tempfile and Tempfile)
-      begin
-        pos = file.pos
-        file.rewind if file.respond_to?(:rewind) and pos != 0
-      rescue Exception
-      end
-      file
-    when IO, StringIO, File
-      begin
-        pos = file.pos
-        file.rewind if file.respond_to?(:rewind) and pos != 0
-      rescue
-      end
-      file
-    when String
-      if Open.remote?(file) || Open.ssh?(file) || Open.exist?(file) 
-        Open.open(file, open_options)
-      else
-        StringIO.new file
-      end
-    when (defined? Step and Step)
-      if file.respond_to?(:base_url) 
-        if file.result and IO === file.result
-          file.result
-        else
-          file.join
-          get_stream(file.path, open_options.merge(:nocache => true))
-        end
-      else
-        file.grace
-
-        stream = file.get_stream
-        if stream && ! stream.closed?
-          stream
-        else
-          file.join
-          raise "Aborted stream from Step #{file.path}" if file.aborted?
-          raise "Exception in stream from Step #{file.path}: #{file.messages.last}" if file.error?
-          get_stream(file.path, open_options)
-        end
-      end
-    when Array
-      Misc.open_pipe do |sin|
-        file.each do |l|
-          sin.puts l
-        end
-      end
-    when Set
-      get_stream(file.to_a, open_options)
-    when Enumerable
-      file
-    else
-      raise "Cannot get stream from: #{file.inspect}"
-    end
-  end
-
-  def self.identify_field(key_field, fields, field)
-    case field
-    when nil
-      :key
-    when Symbol
-      field == :key ? field : identify_field(key_field, fields, field.to_s)
-    when Integer
-      field
-    when (fields.nil? and String)
-      raise "No field information available and specified field not numeric: #{ field }" unless field =~ /^\d+$/
-      identify_field(key_field, fields, field.to_i)
-    when String
-      return :key if key_field == field
-      pos = fields.index field
-      return pos if pos
-      return identify_field(key_field, fields, field.to_i) if field =~ /^\d+$/
-      if fields.select{|f| f.include?("(") }.any?
-        simplify_fields = fields.collect do |f|
-          if m = f.match(/(.*)\s+\(.*\)/)
-            m[1]
-          else
-            f
-          end
-        end
-        return identify_field(key_field, simplify_fields, field)
-      end
-      raise "Field '#{ field }' was not found. Options: (#{key_field || "NO_KEY_FIELD"}), #{(fields || ["NO_FIELDS"]) * ", "}" if pos.nil?
-    else
-      raise "Field '#{ field }' was not found. Options: (#{key_field || "NO_KEY_FIELD"}), #{(fields || ["NO_FIELDS"]) * ", "}"
-    end
-  end
-
-
-  
-  def self.header_lines(key_field, fields, entry_hash = nil)
-    if Hash === entry_hash 
-      sep = entry_hash[:sep] ? entry_hash[:sep] : "\t"
-      preamble = entry_hash[:preamble]
-      header_hash = entry_hash[:header_hash]
-    end
-
-    header_hash = "#" if header_hash.nil?
-
-    preamble = "#: " << Misc.hash2string(entry_hash.merge(:key_field => nil, :fields => nil)) << "\n" if preamble.nil? and entry_hash and entry_hash.values.compact.any?
-
-    str = "" 
-    str << preamble.strip << "\n" if preamble and not preamble.empty?
-    if fields
-      if fields.empty?
-        str << header_hash << (key_field || "ID").to_s << "\n" 
-      else
-        str << header_hash << (key_field || "ID").to_s << sep << (fields * sep) << "\n" 
-      end
-    end
-
-    str
-  end
-
-  def identify_field(field)
-    TSV.identify_field(key_field, fields, field)
-  end
-
-  def rename_field(field, new)
-    self.fields = self.fields.collect{|f| f == field ? new : f }
-    self
-  end
-
-  def unzip_replicates
-    raise "Can only unzip replicates in :double TSVs" unless type == :double
-
-    new = {}
-    self.with_unnamed do
-      through do |k,vs|
-        Misc.zip_fields(vs).each_with_index do |v,i|
-          new[k + "(#{i})"] = v
-        end
-      end
-    end
-
-    self.annotate(new)
-    new.type = :list
-
-    new
-  end
-
-  def to_list(&block)
-    new = {}
-    case type
-    when :double
-      if block_given?
-        through do |k,v|
-          if block.arity == 1
-            new[k] = v.collect{|e| yield e}
-          else
-            new[k] = yield k, v
-          end
-        end
-      else
-        through do |k,v|
-          new[k] = v.collect{|e| e.first}
-        end
-      end
-    when :flat
-      through do |k,v|
-        new[k] = [v.first]
-      end
-    when :single
-      through do |k,v|
-        new[k] = [v]
-      end
-    when :list
-      return self
-    end
-    self.annotate(new)
-    new.type = :list
-    new
-  end
-
-  def to_double
-    new = {}
-    case type
-    when :double
-      return self
-    when :flat
-      through do |k,v|
-        new[k] = v.nil? ? [] : [v]
-      end
-    when :single
-      through do |k,v|
-        new[k] = v.nil? ? [[]] : [[v]]
-      end
-    when :list
-      if block_given?
-        through do |k,v|
-          if v.nil?
-            new[k] = nil
-          else
-            new[k] = v.collect{|e| yield e}
-          end
-        end
-      else
-        through do |k,v|
-          if v.nil?
-            new[k] = nil
-          else
-            new[k] = v.collect{|e| [e]}
-          end
-        end
-      end
-    end
-    self.annotate(new)
-    new.type = :double
-    new
-  end
-
-  def to_flat(field = nil)
-    new = {}
-    case type
-    when :double
-      if field.nil?
-        through do |k,v| new[k] = v.first end
-      elsif field == :all
-        through do |k,v| new[k] = v.flatten.compact end
-      else
-        pos = identify_field field
-        through do |k,v| new[k] = v[pos] end
-      end
-    when :flat
-      return self
-    when :single
-      through do |k,v|
-        new[k] = [v]
-      end
-    when :list
-      through do |k,v|
-        new[k] = [v.first]
-      end
-    end
-    self.annotate(new)
-    if new.fields
-      case field
-      when nil
-        new.fields = new.fields[0..0]
-      when :all
-        new.fields = [new.fields * "+"]
-      else
-        new.fields = [field]
-      end
-    end
-    new.type = :flat
-    new
-  end
-
-  def to_single
-    new = {}
-
-    if block_given?
-      through do |k,v|
-        new[k] = yield v
-      end
-    else
-      case type
-      when :double
-        through do |k,v|
-          new[k] = v.first.first
-        end
-      when :flat
-        through do |k,v|
-          new[k] = v.first
-        end
-      when :single
-        return self
-      when :list
-        through do |k,v|
-          new[k] = v.nil? ? nil : v.first
-        end
-      end
-    end
-
-    self.annotate(new)
-    new.type = :single
-    new.fields = [new.fields.first] if new.fields.length > 1
-    new
-  end
-
-
-  def to_onehot(boolean = false)
-    all_values = values.flatten.uniq.collect{|v| v.to_s}.sort
-    index = TSV.setup({}, :key_field => key_field, :fields => all_values, :type => :list)
-    index.cast = :to_i unless boolean
-    through do |key,values|
-      v = all_values.collect{|_v| values.include?(_v)}
-      v = v.collect{|_v| _v ? 1 : 0 } unless boolean
-      index[key] = v
-    end
-    index
-  end
-
-  def merge(other)
-    self.annotate(super(other))
-  end
-end
-
+#require 'rbbt/resource/path'
+#module TSV
+#
+#  def self.stream_column(file, column)
+#    header = TSV.parse_header(file)
+#    pos = header.fields.index(column) + 1
+#    sep2 = header.options[:sep2] || "|"
+#    case header.type.to_s
+#    when nil, "double"
+#      TSV.traverse file, :type => :array, :into => :stream do |line|
+#        next if line =~ /^#/
+#        line.split("\t")[pos].gsub(sep2, "\n")
+#      end
+#    when "single"
+#      TSV.traverse file, :type => :array, :into => :stream do |line|
+#        next if line =~ /^#/
+#        line.split("\t")[1]
+#      end
+#    when "flat"
+#      TSV.traverse file, :type => :array, :into => :stream do |line|
+#        next if line =~ /^#/
+#        line.split("\t")[1..-1] * "\n"
+#      end
+#    when 'list'
+#      TSV.traverse file, :type => :array, :into => :stream do |line|
+#        next if line =~ /^#/
+#        line.split("\t")[pos]
+#      end
+#    end
+#  end
+#
+#  def self.guess_id(identifier_file, values, options = {})
+#    field_matches = TSV.field_match_counts(identifier_file, values, options)
+#    field_matches.sort_by{|field, count| count.to_i}.last
+#  end
+#
+#  def self.field_match_counts(file, values, options = {})
+#    options = IndiferentHash.add_defaults options, :persist_prefix => "Field_Matches"
+#    persist_options = IndiferentHash.pull_keys options, :persist
+#
+#    filename = TSV === file ? file.filename : file
+#    path = Persist.persist filename, :string, persist_options.merge(:no_load => true) do
+#      tsv = TSV === file ? file : TSV.open(file, options)
+#
+#      text = ""
+#      fields = nil
+#      tsv.tap{|e| e.unnamed =  true; fields = e.fields}.through do |gene, names|
+#        names.zip(fields).each do |list, format|
+#          list = [list] unless Array === list
+#          list.delete_if do |name| name.empty? end
+#          next if list.empty?
+#          text << list.collect{|name| [name, format] * "\t"} * "\n" << "\n"
+#        end
+#        text << [gene, tsv.key_field] * "\t" << "\n"
+#      end
+#      text
+#    end
+#
+#    TmpFile.with_file(values.uniq * "\n", false) do |value_file|
+#      cmd = "cat '#{ path }' | sed 's/\\t/\\tHEADERNOMATCH/' | grep -w -F -f '#{ value_file }' | sed 's/HEADERNOMATCH//' |sort -u|cut -f 2  |sort|uniq -c|sed 's/^ *//;s/ /\t/'"
+#      begin
+#        TSV.open(CMD.cmd(cmd), :key_field => 1, :fields => [0], :type => :single, :cast => :to_i)
+#      rescue
+#        Log.exception $!
+#        TSV.setup({}, :type => :single, :cast => :to_i)
+#      end
+#    end
+#  end
+#
+#  def self.get_filename(file)
+#    case
+#    when (defined? Step and Step === file)
+#      file.path
+#    when Path === file
+#      file
+#    when (String === file and (Open.exists? file or Open.remote? file))
+#      file
+#    when String === file 
+#      "String-#{Misc.digest file}"
+#    when file.respond_to?(:filename)
+#      file.filename
+#    when file.respond_to?(:gets)
+#      nil
+#    else
+#      raise "Cannot get filename from: #{file.inspect}"
+#    end
+#  end
+#
+#  def self.abort_stream(file, exception = nil)
+#    return if file.nil?
+#    if defined? Step and Step === file
+#      if exception
+#        file.exception exception 
+#      else
+#        if not (file.aborted? or file.done?)
+#          file.abort 
+#        end
+#      end
+#    elsif Hash === file or Array === file
+#      return
+#    else
+#      stream = get_stream(file)
+#      stream.abort(exception) if stream.respond_to? :abort
+#      AbortedStream.setup(stream, exception) unless stream.respond_to?(:exception) && stream.exception
+#    end
+#  end
+#
+#  def self.get_stream(file, open_options = {})
+#    case file
+#    when Zlib::GzipReader
+#      file
+#    when (defined? Bgzf and Bgzf)
+#      file
+#    when TSV
+#      file.dumper_stream
+#    when TSV::Dumper
+#      file.stream
+#    when TSV::Parser
+#      file.stream
+#    when Path
+#      file.open(open_options)
+#    when (defined? Tempfile and Tempfile)
+#      begin
+#        pos = file.pos
+#        file.rewind if file.respond_to?(:rewind) and pos != 0
+#      rescue Exception
+#      end
+#      file
+#    when IO, StringIO, File
+#      begin
+#        pos = file.pos
+#        file.rewind if file.respond_to?(:rewind) and pos != 0
+#      rescue
+#      end
+#      file
+#    when String
+#      if Open.remote?(file) || Open.ssh?(file) || Open.exist?(file) 
+#        Open.open(file, open_options)
+#      else
+#        StringIO.new file
+#      end
+#    when (defined? Step and Step)
+#      if file.respond_to?(:base_url) 
+#        if file.result and IO === file.result
+#          file.result
+#        else
+#          file.join
+#          get_stream(file.path, open_options.merge(:nocache => true))
+#        end
+#      else
+#        file.grace
+#
+#        stream = file.get_stream
+#        if stream && ! stream.closed?
+#          stream
+#        else
+#          file.join
+#          raise "Aborted stream from Step #{file.path}" if file.aborted?
+#          raise "Exception in stream from Step #{file.path}: #{file.messages.last}" if file.error?
+#          get_stream(file.path, open_options)
+#        end
+#      end
+#    when Array
+#      Misc.open_pipe do |sin|
+#        file.each do |l|
+#          sin.puts l
+#        end
+#      end
+#    when Set
+#      get_stream(file.to_a, open_options)
+#    when Enumerable
+#      file
+#    else
+#      raise "Cannot get stream from: #{file.inspect}"
+#    end
+#  end
+#
+#  def self.identify_field(key_field, fields, field)
+#    case field
+#    when nil
+#      :key
+#    when Symbol
+#      field == :key ? field : identify_field(key_field, fields, field.to_s)
+#    when Integer
+#      field
+#    when (fields.nil? and String)
+#      raise "No field information available and specified field not numeric: #{ field }" unless field =~ /^\d+$/
+#      identify_field(key_field, fields, field.to_i)
+#    when String
+#      return :key if key_field == field
+#      pos = fields.index field
+#      return pos if pos
+#      return identify_field(key_field, fields, field.to_i) if field =~ /^\d+$/
+#      if fields.select{|f| f.include?("(") }.any?
+#        simplify_fields = fields.collect do |f|
+#          if m = f.match(/(.*)\s+\(.*\)/)
+#            m[1]
+#          else
+#            f
+#          end
+#        end
+#        return identify_field(key_field, simplify_fields, field)
+#      end
+#      raise "Field '#{ field }' was not found. Options: (#{key_field || "NO_KEY_FIELD"}), #{(fields || ["NO_FIELDS"]) * ", "}" if pos.nil?
+#    else
+#      raise "Field '#{ field }' was not found. Options: (#{key_field || "NO_KEY_FIELD"}), #{(fields || ["NO_FIELDS"]) * ", "}"
+#    end
+#  end
+#
+#
+#  
+#  def self.header_lines(key_field, fields, entry_hash = nil)
+#    if Hash === entry_hash 
+#      sep = entry_hash[:sep] ? entry_hash[:sep] : "\t"
+#      preamble = entry_hash[:preamble]
+#      header_hash = entry_hash[:header_hash]
+#    end
+#
+#    header_hash = "#" if header_hash.nil?
+#
+#    preamble = "#: " << Misc.hash2string(entry_hash.merge(:key_field => nil, :fields => nil)) << "\n" if preamble.nil? and entry_hash and entry_hash.values.compact.any?
+#
+#    str = "" 
+#    str << preamble.strip << "\n" if preamble and not preamble.empty?
+#    if fields
+#      if fields.empty?
+#        str << header_hash << (key_field || "ID").to_s << "\n" 
+#      else
+#        str << header_hash << (key_field || "ID").to_s << sep << (fields * sep) << "\n" 
+#      end
+#    end
+#
+#    str
+#  end
+#
+#  def identify_field(field)
+#    TSV.identify_field(key_field, fields, field)
+#  end
+#
+#  def rename_field(field, new)
+#    self.fields = self.fields.collect{|f| f == field ? new : f }
+#    self
+#  end
+#
+#  def unzip_replicates
+#    raise "Can only unzip replicates in :double TSVs" unless type == :double
+#
+#    new = {}
+#    self.with_unnamed do
+#      through do |k,vs|
+#        Misc.zip_fields(vs).each_with_index do |v,i|
+#          new[k + "(#{i})"] = v
+#        end
+#      end
+#    end
+#
+#    self.annotate(new)
+#    new.type = :list
+#
+#    new
+#  end
+#
+#  def to_list(&block)
+#    new = {}
+#    case type
+#    when :double
+#      if block_given?
+#        through do |k,v|
+#          if block.arity == 1
+#            new[k] = v.collect{|e| yield e}
+#          else
+#            new[k] = yield k, v
+#          end
+#        end
+#      else
+#        through do |k,v|
+#          new[k] = v.collect{|e| e.first}
+#        end
+#      end
+#    when :flat
+#      through do |k,v|
+#        new[k] = [v.first]
+#      end
+#    when :single
+#      through do |k,v|
+#        new[k] = [v]
+#      end
+#    when :list
+#      return self
+#    end
+#    self.annotate(new)
+#    new.type = :list
+#    new
+#  end
+#
+#  def to_double
+#    new = {}
+#    case type
+#    when :double
+#      return self
+#    when :flat
+#      through do |k,v|
+#        new[k] = v.nil? ? [] : [v]
+#      end
+#    when :single
+#      through do |k,v|
+#        new[k] = v.nil? ? [[]] : [[v]]
+#      end
+#    when :list
+#      if block_given?
+#        through do |k,v|
+#          if v.nil?
+#            new[k] = nil
+#          else
+#            new[k] = v.collect{|e| yield e}
+#          end
+#        end
+#      else
+#        through do |k,v|
+#          if v.nil?
+#            new[k] = nil
+#          else
+#            new[k] = v.collect{|e| [e]}
+#          end
+#        end
+#      end
+#    end
+#    self.annotate(new)
+#    new.type = :double
+#    new
+#  end
+#
+#  def to_flat(field = nil)
+#    new = {}
+#    case type
+#    when :double
+#      if field.nil?
+#        through do |k,v| new[k] = v.first end
+#      elsif field == :all
+#        through do |k,v| new[k] = v.flatten.compact end
+#      else
+#        pos = identify_field field
+#        through do |k,v| new[k] = v[pos] end
+#      end
+#    when :flat
+#      return self
+#    when :single
+#      through do |k,v|
+#        new[k] = [v]
+#      end
+#    when :list
+#      through do |k,v|
+#        new[k] = [v.first]
+#      end
+#    end
+#    self.annotate(new)
+#    if new.fields
+#      case field
+#      when nil
+#        new.fields = new.fields[0..0]
+#      when :all
+#        new.fields = [new.fields * "+"]
+#      else
+#        new.fields = [field]
+#      end
+#    end
+#    new.type = :flat
+#    new
+#  end
+#
+#  def to_single
+#    new = {}
+#
+#    if block_given?
+#      through do |k,v|
+#        new[k] = yield v
+#      end
+#    else
+#      case type
+#      when :double
+#        through do |k,v|
+#          new[k] = v.first.first
+#        end
+#      when :flat
+#        through do |k,v|
+#          new[k] = v.first
+#        end
+#      when :single
+#        return self
+#      when :list
+#        through do |k,v|
+#          new[k] = v.nil? ? nil : v.first
+#        end
+#      end
+#    end
+#
+#    self.annotate(new)
+#    new.type = :single
+#    new.fields = [new.fields.first] if new.fields.length > 1
+#    new
+#  end
+#
+#
+#  def to_onehot(boolean = false)
+#    all_values = values.flatten.uniq.collect{|v| v.to_s}.sort
+#    index = TSV.setup({}, :key_field => key_field, :fields => all_values, :type => :list)
+#    index.cast = :to_i unless boolean
+#    through do |key,values|
+#      v = all_values.collect{|_v| values.include?(_v)}
+#      v = v.collect{|_v| _v ? 1 : 0 } unless boolean
+#      index[key] = v
+#    end
+#    index
+#  end
+#
+#  def merge(other)
+#    self.annotate(super(other))
+#  end
+#end
+#