lib/seqtrimnext/classes/params.rb in seqtrimnext-2.0.51 vs lib/seqtrimnext/classes/params.rb in seqtrimnext-2.0.52
- old
+ new
@@ -125,11 +125,11 @@
#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
@@ -187,16 +187,16 @@
return @params[param]
end
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
# Return the mid's size of param
def get_mid(mid)
@@ -229,168 +229,154 @@
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))
-
- # puts "CALLER: #{plugin}"
- # puts [file, line, method]
end
end
- def set_param(param,value,comment=nil)
- plugin=get_plugin
+ def set_param(param,value,comment = nil)
+ plugin=get_plugin
- @params[param] = value
+ @params[param] = value
- if get_comment(plugin,param).nil?
- set_comment(plugin,param,comment)
- end
+ if get_comment(plugin,param).nil?
+ set_comment(plugin,param,comment)
+ end
- end
+ end
- # def set_order(plugin,param)
- #
- # if @param_order[plugin].nil?
- # @param_order[plugin]=[]
- # end
- #
- # if !@param_order[plugin].index(param)
- # @param_order[plugin].push param
- # end
- # end
-
-
def get_comment(plugin,param)
- res = nil
- if @plugin_comments[plugin]
- res =@plugin_comments[plugin][param]
- end
- return res
- end
+ res = nil
+ if @plugin_comments[plugin]
+ res =@plugin_comments[plugin][param]
+ end
+ return res
+ end
def set_comment(plugin,param,comment)
- if !comment.is_a?(Array) && !comment.nil?
- comment=comment.split("\n").compact.map{|l| l.strip}
- end
+ 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
+ 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
+ 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
+ if comment.nil?
+ comment=old_comment
+ end
- # @comments[param]=(comment || [''])
- @plugin_comments[plugin][param]=(comment || [''])
- # puts @plugin_comments.keys.to_json
+ # @comments[param]=(comment || [''])
+ @plugin_comments[plugin][param]=(comment || [''])
+ # puts @plugin_comments.keys.to_json
- # remove empty comments
+ # remove empty comments
- @plugin_comments.reverse_each do |plugin_name,comments|
- if comments.empty?
- @plugin_comments.delete(plugin_name)
- end
- end
+ @plugin_comments.reverse_each do |plugin_name,comments|
+ if comments.empty?
+ @plugin_comments.delete(plugin_name)
+ end
+ end
- end
-
+ end
+
def set_mid(param,value)
- @mids[param] = value
- end
- #attr_accessor :h # to accede to the atribute 'h' from out of this class
+ @mids[param] = value
+ end
# Returns true if exists the parameter and nil if don't
def exists?(param_name)
- return !@params[param_name].nil?
- end
-
+ return !@params[param_name].nil?
+ end
+
def check_plugin_list_param(errors,param_name)
- # get plugin list
- pl_list=get_param(param_name)
+ # get plugin list
+ pl_list=get_param(param_name)
- # puts pl_list,param_name
- list=pl_list.split(',')
+ # puts pl_list,param_name
+ list=pl_list.split(',')
- list.map!{|e| e.strip}
+ list.map!{|e| e.strip}
- # puts "Lista:",list.join(',')
+ # puts "Lista:",list.join(',')
- # always the pluginExtractInserts at the end
- list.delete('PluginExtractInserts')
- list << 'PluginExtractInserts'
+ # 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
+ set_param(param_name,list.join(','))
+ # if !list.include?('PluginExtractInserts')
+ # raise "PluginExtractInserts do not exists"
+ #
+ # end
- end
+ end
# def split_databases(db_param_name)
def check_db_param(errors,db_param_name)
- # expand database paths
- dbs= get_param(db_param_name).gsub('"','').split(/\s+/)
- # puts "ALGO"*20
- # puts "INPUT DATABASES:\n"+dbs.join(',')
+ 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)
+ 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 !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 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
+ 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
+ procesed_dbs << path
- if !File.exists?(path)
- raise "DB File #{path} does not exists"
- # exit
- end
- }
+ if !File.exists?(path)
+ raise "DB File #{path} does not exists"
+ # exit
+ end
+ }
- db_paths = '"'+procesed_dbs.join(' ')+'"'
+ db_paths = '"'+procesed_dbs.join(' ')+'"'
- set_param(db_param_name,db_paths)
+ set_param(db_param_name,db_paths)
- puts "USED DATABASES\n"+db_paths
- end
+ puts "USED DATABASES\n"+db_paths
+ end
+ end
def self.generate_sample_params
filename = 'sample_params.txt'