Class: Params
- Inherits:
-
Object
- Object
- Params
- Defined in:
- lib/seqtrimnext/classes/params.rb
Class Method Summary collapse
Instance Method Summary collapse
-
#check_db_param(errors, db_param_name) ⇒ Object
def split_databases(db_param_name).
- #check_param(errors, param, param_class, default_value = nil, comment = nil) ⇒ Object
- #check_plugin_list_param(errors, param_name) ⇒ Object
-
#exists?(param_name) ⇒ Boolean
Returns true if exists the parameter and nil if don’t.
-
#get_ab_adapter(adapter) ⇒ Object
Return the ab of param.
- #get_adapter(adapter) ⇒ Object
- #get_comment(plugin, param) ⇒ Object
- #get_fasta(list, name, type) ⇒ Object
-
#get_linker(linker) ⇒ Object
Return the linker of param.
-
#get_mid(mid) ⇒ Object
Return the mid’s size of param.
-
#get_param(param) ⇒ Object
Return the parameter’s list in an array.
- #get_plugin ⇒ Object
-
#initialize(path) ⇒ Params
constructor
Creates the structure and start the reading of parameter’s file.
-
#load_ab_adapters(path_file) ⇒ Object
Load ab_adapters file.
-
#load_adapters(path_file) ⇒ Object
load normal adapters.
-
#load_db_fastas(input_paths) ⇒ Object
end def.
-
#load_linkers(path_file) ⇒ Object
Load mid’s file.
-
#load_mids(path_file) ⇒ Object
Load mid’s file.
- #load_repeated_seqs(file_path) ⇒ Object
-
#print_parameters ⇒ Object
Prints the pair name/numeric-value for every parameter.
-
#read_file(path_file) ⇒ Object
Reads param’s file.
- #repeated_seq?(name) ⇒ Boolean
-
#save_file(path_file) ⇒ Object
Reads param’s file.
- #set_comment(plugin, param, comment) ⇒ Object
- #set_mid(param, value) ⇒ Object
- #set_param(param, value, comment = nil) ⇒ Object
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 393 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 345 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.(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 410 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 ="Current value is ##{s}#. " if param_class=='DB' += e. end errors.push "Param #{param} is not a valid #{param_class}. #{}" end # end end |
#check_plugin_list_param(errors, param_name) ⇒ Object
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# File 'lib/seqtrimnext/classes/params.rb', line 318 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
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# File 'lib/seqtrimnext/classes/params.rb', line 314 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 226 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 231 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 263 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 202 def get_fasta(list,name,type) res = list[name] if res.nil? $LOG.error("Error. The #{type}: #{name} was not correctly loaded") raise "Error. The #{type}: #{name} was not found in loaded #{name}s: #{list.map{|k,v| k}}." end return res end |
#get_linker(linker) ⇒ Object
Return the linker of param
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# File 'lib/seqtrimnext/classes/params.rb', line 220 def get_linker(linker) # return @linkers[linker] return get_fasta(@linkers,linker,"linker") end |
#get_mid(mid) ⇒ Object
Return the mid’s size of param
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# File 'lib/seqtrimnext/classes/params.rb', line 214 def get_mid(mid) # return @mids[mid] return get_fasta(@mids,mid,"mid") end |
#get_param(param) ⇒ Object
Return the parameter’s list in an array
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# File 'lib/seqtrimnext/classes/params.rb', line 197 def get_param(param) #$LOG.debug "Get Param: #{@params[param]}" return @params[param] end |
#get_plugin ⇒ Object
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# File 'lib/seqtrimnext/classes/params.rb', line 237 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 111 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 117 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 71 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 123 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 105 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 128 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 $LOG.error("Clustering file's doesn't exists: #{@clusters.count}") end end |
#print_parameters ⇒ Object
Prints the pair name/numeric-value for every parameter
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# File 'lib/seqtrimnext/classes/params.rb', line 189 def print_parameters() @params.each do |clave, valor| #$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 line =~ /^\s*([^=]*)\s*=\s*(.*)\s*$/ params=[$1,$2] # 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 $LOG.debug "read: #{params[0]}=#{params[1]}" if !$LOG.nil? 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
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# File 'lib/seqtrimnext/classes/params.rb', line 160 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 165 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 272 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 309 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 251 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 |