Class: Params

Inherits:
Object
  • Object
show all
Defined in:
lib/seqtrimnext/classes/params.rb

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(path) ⇒ Params

Creates the structure and start the reading of parameter’s file



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# File 'lib/seqtrimnext/classes/params.rb', line 10

def initialize(path)
  @params = {}
  @comments = {}
  # @param_order={}
  @mids = {}
  @ab_adapters={}
  @adapters={}
  @linkers = {}
  @clusters = {}

  @plugin_comments = {}

  read_file(path)
end

Class Method Details

.generate_sample_params ⇒ Object 



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# File 'lib/seqtrimnext/classes/params.rb', line 381

def self.generate_sample_params

  filename = 'sample_params.txt'
  x=1
  while File.exists?(filename)
    filename = "sample_params#{x}.txt"
    x+=1
  end

  f=File.open(filename,'w')
  f.puts "SAMPLE_PARAMS"
  f.close

  puts "Sample params file generated: #{filename}"

end

Instance Method Details

#check_db_param(errors, db_param_name) ⇒ Object

def split_databases(db_param_name)



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# File 'lib/seqtrimnext/classes/params.rb', line 333

def check_db_param(errors,db_param_name)
  if !get_param(db_param_name).empty?
    # expand database paths
    dbs= get_param(db_param_name).gsub('"','').split(/\s+/)
    # puts "ALGO"*20
    # puts "INPUT DATABASES:\n"+dbs.join(',')

    procesed_dbs=[]
    #
    # TODO - chequear aqui que la db no esta vacia y que esta formateada.
    dbs.reverse_each {|db_p|
      db=File.expand_path(db_p)

      if !File.exists?(db)
        path=File.join($FORMATTED_DB_PATH,db_p)
      else
        path=db
      end


      if Dir.glob(path+'*.n*').entries.empty?
        puts "DB file #{path} not formatted"

        if File.writable_real?(path)
          cmd = "makeblastdb -in #{path} -parse_seqids -dbtype nucl"
          system(cmd)
        else
          raise "Can't format database. We don't have write permissions in: #{path}"
        end
      end

      procesed_dbs << path

      if !File.exists?(path)
        raise "DB File #{path} does not exists"
        # exit
      end
    }

    db_paths = '"'+procesed_dbs.join(' ')+'"'

    set_param(db_param_name,db_paths)

    puts "USED DATABASES\n"+db_paths
  end
end

#check_param(errors, param, param_class, default_value = nil, comment = nil) ⇒ Object 



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# File 'lib/seqtrimnext/classes/params.rb', line 398

def check_param(errors,param,param_class,default_value=nil, comment=nil)

  if !exists?(param)
    if default_value.nil? #|| (default_value.is_a?(String) && default_value.empty?)
      errors.push "The param #{param} is required and no default value is available"
    else
      set_param(param,default_value,comment)
    end
  end

  s = get_param(param)


  set_comment(get_plugin,param,comment)

  # check_class=Object.const_get(param_class)
  begin

    case param_class
    when 'Integer'
      r = Integer(s)
    when 'Float'
      r = Float(s)
    when 'String'
      r = String(s)
    when 'DB'
      # it is a string
      r = String(s)
      # and must be a valid db

      r = check_db_param(errors,param)

    when 'PluginList'
      r=String(s)
      r= check_plugin_list_param(errors,param)
    end

  rescue Exception => e
    message="Current value is ##{s}#. "
    if param_class=='DB'
      message += e.message
    end

    errors.push "Param #{param} is not a valid #{param_class}. #{message}"
  end
  # end

end

#check_plugin_list_param(errors, param_name) ⇒ Object 



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# File 'lib/seqtrimnext/classes/params.rb', line 306

def check_plugin_list_param(errors,param_name)
  # get plugin list
  pl_list=get_param(param_name)

  # puts pl_list,param_name
  list=pl_list.split(',')

  list.map!{|e| e.strip}

  # puts "Lista:",list.join(',')


  # always the pluginExtractInserts at the end
  list.delete('PluginExtractInserts')
  list << 'PluginExtractInserts'

  set_param(param_name,list.join(','))
  # if !list.include?('PluginExtractInserts')
  #   raise "PluginExtractInserts do not exists"
  #
  # end



end

#exists?(param_name) ⇒ Boolean

Returns true if exists the parameter and nil if don’t

Returns:

  • (Boolean) 


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# File 'lib/seqtrimnext/classes/params.rb', line 302

def exists?(param_name)
  return !@params[param_name].nil?
end

#get_ab_adapter(adapter) ⇒ Object

Return the ab of param



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# File 'lib/seqtrimnext/classes/params.rb', line 214

def get_ab_adapter(adapter)
  # return @ab_adapters[adapter]
  return get_fasta(@ab_adapters,adapter,"ab_adapter")
end

#get_adapter(adapter) ⇒ Object 



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# File 'lib/seqtrimnext/classes/params.rb', line 219

def get_adapter(adapter)
  # return @adapters[adapter]
  return get_fasta(@adapters,adapter,"adapter")
end

#get_comment(plugin, param) ⇒ Object 



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# File 'lib/seqtrimnext/classes/params.rb', line 251

def get_comment(plugin,param)
  res = nil
  if @plugin_comments[plugin]
    res =@plugin_comments[plugin][param]
  end
  return res
end

#get_fasta(list, name, type) ⇒ Object 



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# File 'lib/seqtrimnext/classes/params.rb', line 190

def get_fasta(list,name,type)
  res = list[name]

  if res.nil?
    $LOG.error("Error. The #{type}: #{name} was not correctly loaded")
    raise "Error. The #{type}: #{name} was not found in loaded #{name}s: #{list.map{|k,v| k}}."
  end

  return res
end

#get_linker(linker) ⇒ Object

Return the linker of param



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# File 'lib/seqtrimnext/classes/params.rb', line 208

def get_linker(linker)
  # return @linkers[linker]
  return get_fasta(@linkers,linker,"linker")
end

#get_mid(mid) ⇒ Object

Return the mid’s size of param



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# File 'lib/seqtrimnext/classes/params.rb', line 202

def get_mid(mid)
  # return @mids[mid]
  return get_fasta(@mids,mid,"mid")
end

#get_param(param) ⇒ Object

Return the parameter’s list in an array



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# File 'lib/seqtrimnext/classes/params.rb', line 185

def get_param(param)
  #$LOG.debug "Get Param:  #{@params[param]}"
  return @params[param]
end

#get_plugin ⇒ Object 



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# File 'lib/seqtrimnext/classes/params.rb', line 225

def get_plugin
  plugin='General'
  # puts caller(2)[1]
  at = caller(2)[1]
  if /^(.+?):(\d+)(?::in `(.*)')?/ =~ at
    file = Regexp.last_match[1]
    line = Regexp.last_match[2].to_i
    method = Regexp.last_match[3]
    plugin=File.basename(file,File.extname(file))

  end
  
end

#load_ab_adapters(path_file) ⇒ Object

Load ab_adapters file



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# File 'lib/seqtrimnext/classes/params.rb', line 99

def load_ab_adapters(path_file)
  @ab_adapters=load_db_fastas(path_file)
  # puts @ab_adapters
end

#load_adapters(path_file) ⇒ Object

load normal adapters



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# File 'lib/seqtrimnext/classes/params.rb', line 105

def load_adapters(path_file)
  @adapters=load_db_fastas(path_file)
end

#load_db_fastas(input_paths) ⇒ Object

end def



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# File 'lib/seqtrimnext/classes/params.rb', line 59

def load_db_fastas(input_paths)

  res={}

  if (!input_paths.nil?) & (input_paths!='')
    # remove quotes
    paths=input_paths.gsub(/\A['"]+|['"]+\Z/, "")

    # split paths by spaces
    # puts "PATHS:"
    # puts paths.split(' ')
    paths.split(' ').each do |path_file|

      if File.exists?(path_file)
        ff = FastaFile.new(path_file)
        ff.each {|n,f|
          res[n]=f
        }

        ff.close
      end
    end

  end

  # puts "LOADED_DB #{paths}:"
  # res.each do |k,v|
  #   puts k
  # end

  return res
end

#load_linkers(path_file) ⇒ Object

Load mid’s file



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# File 'lib/seqtrimnext/classes/params.rb', line 111

def load_linkers(path_file)
  @linkers=load_db_fastas(path_file)
  # puts @linkers
end

#load_mids(path_file) ⇒ Object

Load mid’s file



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# File 'lib/seqtrimnext/classes/params.rb', line 93

def load_mids(path_file)
  @mids=load_db_fastas(path_file)
  # puts @mids
end

#load_repeated_seqs(file_path) ⇒ Object 



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# File 'lib/seqtrimnext/classes/params.rb', line 116

def load_repeated_seqs(file_path)
  @clusters={}

  if File.exists?(file_path)
    # File.open(ARGV[0]).each_line do |line|
    $LOG.debug("Repeated file path:"+file_path)
    File.open(file_path).each_line do |line|
      #puts line,line[0]
      # en ruby19 line[0] da el caracter, no el chr
      #if (line[0]!=62) && (line[0]!=48)
      # if (line[0]!='>'[0]) && (line[0]!='0'[0])

      # line doesn't finish in *
      if (line[0]!='>'[0]) && (!(line =~ /\*$/))

        #puts line
        # puts line,line[0]
        if line =~ />([^\.]+)\.\.\.\s/
          #puts 'ok'
          # puts $1
          @clusters[$1]=1
        end
      end
    end
    $LOG.info("Repeated sequence count: #{@clusters.count}")
  else
    $LOG.error("Clustering file's doesn't exists: #{@clusters.count}")
  end


end

#print_parameters ⇒ Object

Prints the pair name/numeric-value for every parameter



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# File 'lib/seqtrimnext/classes/params.rb', line 177

def print_parameters()
  @params.each do |clave, valor|
    #$LOG.debug  "The Parameter #{clave} have the value " +valor.to_s
    puts "#{clave} = #{valor} "
  end
end

#read_file(path_file) ⇒ Object

Reads param’s file



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# File 'lib/seqtrimnext/classes/params.rb', line 26

def read_file(path_file)

  if path_file && File.exists?(path_file)
    comments= []
    File.open(path_file).each_line do |line|
      line.chomp! # delete end of line

      if !line.empty?
        if !(line =~ /^\s*#/)   # if line is not a comment
          # extract the parameter's name in params[0] and the parameter's value in params[1]
          params = line.split(/\s*=\s*/)

          # store in the hash the pair key/value, in our case will be name/numeric-value ,
          # that are save in params[0] and params[1],  respectively
          if (!params[0].nil?) && (!params[1].nil?)
            set_param(params[0].strip,params[1].strip,comments)
            comments=[]
          end

          #$LOG.debug "read: #{params[1]}"
        else
          comments << line.gsub(/^\s*#/,'')
        end # end if comentario
      end #end if line
    end #end each
    if @params.empty?
      puts "INVALID PARAMETER FILE: #{path_file}. No parameters defined"
      exit
    end

  end
end

#repeated_seq?(name) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/seqtrimnext/classes/params.rb', line 148

def repeated_seq?(name)
  return !@clusters[name].nil?
end

#save_file(path_file) ⇒ Object

Reads param’s file



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# File 'lib/seqtrimnext/classes/params.rb', line 153

def save_file(path_file)

  f=File.open(path_file,'w')
  @plugin_comments.keys.sort.reverse.each do |plugin_name|
    f.puts "#"*50
    f.puts "# " + plugin_name
    f.puts "#"*50
    f.puts ''

    @plugin_comments[plugin_name].keys.each do |param|
      comment=get_comment(plugin_name,param)
      if !comment.nil? && !comment.empty? && comment!=''
        f.puts comment.map{|c| '# '+c if c!=''}
      end
      f.puts ''
      f.puts "#{param} = #{@params[param]}"
      f.puts ''
    end
  end
  f.close

end

#set_comment(plugin, param, comment) ⇒ Object 



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# File 'lib/seqtrimnext/classes/params.rb', line 260

def set_comment(plugin,param,comment)
  if !comment.is_a?(Array) && !comment.nil?
    comment=comment.split("\n").compact.map{|l| l.strip}
  end

  if @plugin_comments[plugin].nil?
    @plugin_comments[plugin]={}
  end

  old_comment=''
  # remove from other plugins
  @plugin_comments.each do |plugin_name,comments|
    if comments.keys.include?(param) && plugin_name!=plugin
      old_comment=comments[param]
      comments.delete(param)
    end
  end

  if comment.nil?
    comment=old_comment
  end

  # @comments[param]=(comment || [''])
  @plugin_comments[plugin][param]=(comment || [''])
  # puts @plugin_comments.keys.to_json

  # remove empty comments

  @plugin_comments.reverse_each do |plugin_name,comments|
    if comments.empty?
      @plugin_comments.delete(plugin_name)
    end
  end

end

#set_mid(param, value) ⇒ Object 



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# File 'lib/seqtrimnext/classes/params.rb', line 297

def set_mid(param,value)
  @mids[param] = value
end

#set_param(param, value, comment = nil) ⇒ Object 



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# File 'lib/seqtrimnext/classes/params.rb', line 239

def set_param(param,value,comment = nil)
  plugin=get_plugin

  @params[param] = value

  if get_comment(plugin,param).nil?
    set_comment(plugin,param,comment)
  end


end