Class: PepXML
- Inherits:
-
Object
- Object
- PepXML
- Defined in:
- lib/protk/pepxml.rb
Overview
require ‘rexml/document’ require ‘rexml/xpath’
Instance Attribute Summary collapse
-
#file_name ⇒ Object
Returns the value of attribute file_name.
Instance Method Summary collapse
-
#extract_db ⇒ Object
Obtain the database name from the given input file.
-
#extract_engine ⇒ Object
Obtain the search engine name from the input file The name of the engine is returned in lowercase and should contain no spaces Names of common engines are searched for and extracted in simplified form if possible.
- #extract_enzyme ⇒ Object
-
#find_runs ⇒ Object
TODO: Make this faster and more memory efficient by using XML::Reader as in the functions above.
-
#initialize(file_name) ⇒ PepXML
constructor
A new instance of PepXML.
- #is_valid_type(type) ⇒ Object
- #type_from_base_name(basename) ⇒ Object
- #type_from_summary_attributes(atts) ⇒ Object
Constructor Details
#initialize(file_name) ⇒ PepXML
Returns a new instance of PepXML.
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# File 'lib/protk/pepxml.rb', line 13 def initialize(file_name) @file_name=file_name XML::Error.set_handler(&XML::Error::QUIET_HANDLER) pepxml_parser=XML::Parser.file("#{file_name}") @pepxml_ns_prefix="xmlns:" @pepxml_ns="xmlns:http://regis-web.systemsbiology.net/pepXML" @pepxml_doc=pepxml_parser.parse if not @pepxml_doc.root.namespaces.default @pepxml_ns_prefix="" @pepxml_ns=nil end end |
Instance Attribute Details
#file_name ⇒ Object
Returns the value of attribute file_name.
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# File 'lib/protk/pepxml.rb', line 11 def file_name @file_name end |
Instance Method Details
#extract_db ⇒ Object
Obtain the database name from the given input file
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# File 'lib/protk/pepxml.rb', line 32 def extract_db() reader = XML::Reader.file(self.file_name) throw "Failed to open xml file #{file_name}" unless reader!=nil while(reader.read) # For pep.xml files # if ( reader.name == "search_database" ) dbnode=reader. dbvalue=dbnode['local_path'] reader.close return dbvalue end # For prot.xml files # if ( reader.name == "protein_summary_header" ) dbnode=reader. dbvalue=dbnode['reference_database'] reader.close return dbvalue end end end |
#extract_engine ⇒ Object
Obtain the search engine name from the input file The name of the engine is returned in lowercase and should contain no spaces Names of common engines are searched for and extracted in simplified form if possible
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# File 'lib/protk/pepxml.rb', line 67 def extract_engine() reader = XML::Reader.file(self.file_name) throw "Failed to open xml file #{file_name}" unless reader!=nil while(reader.read) if ( reader.name == "search_summary" ) dbnode=reader. dbvalue=dbnode['search_engine'] reader.close engine_name=dbvalue.gsub(/ /,"_") engine_name=engine_name.gsub(/\(/,"") engine_name=engine_name.gsub(/\)/,"") engine_name=engine_name.gsub(/\!/,"") return engine_name.downcase end end end |
#extract_enzyme ⇒ Object
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# File 'lib/protk/pepxml.rb', line 86 def extract_enzyme() reader = XML::Reader.file(self.file_name) throw "Failed to open xml file #{file_name}" unless reader!=nil while(reader.read) if ( reader.name == "sample_enzyme" ) dbnode=reader. dbvalue=dbnode['name'] reader.close return dbvalue.downcase end end end |
#find_runs ⇒ Object
TODO: Make this faster and more memory efficient by using XML::Reader as in the functions above
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# File 'lib/protk/pepxml.rb', line 146 def find_runs() run_summaries = @pepxml_doc.find("//#{@pepxml_ns_prefix}msms_run_summary", @pepxml_ns) runs = {} run_summaries.each do |summary| base_name = summary.attributes["base_name"] if not runs.has_key?(base_name) bn = summary.attributes["base_name"] runs[base_name] = {:base_name => summary.attributes["base_name"]} if is_valid_type(type_from_summary_attributes(summary.attributes)) runs[base_name][:type] = type_from_summary_attributes(summary.attributes) elsif is_valid_type(type_from_base_name(bn)) runs[base_name][:type] = type_from_base_name(bn) else runs[base_name][:type] = "mzML" # Same guess as peptide prophet makes end end end runs end |
#is_valid_type(type) ⇒ Object
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# File 'lib/protk/pepxml.rb', line 130 def is_valid_type(type) case type when /^mgf$/i return true when /^mzML$/i return true when /^mzXML$/i return true else return false end end |
#type_from_base_name(basename) ⇒ Object
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# File 'lib/protk/pepxml.rb', line 102 def type_from_base_name(basename) # A common error is for tools to include the extension in the base_name attribute. # We exploit this to guess the type ext_guess="" case basename when /.mgf$/ ext_guess="mgf" when /.mzML$/ ext_guess="mzML" when /.mzXML$/ ext_guess="mzXML" else ext_guess="" end ext_guess end |
#type_from_summary_attributes(atts) ⇒ Object
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# File 'lib/protk/pepxml.rb', line 119 def type_from_summary_attributes(atts) if is_valid_type(atts["raw_data_type"]) return atts["raw_data_type"] end if is_valid_type(atts["raw_data"]) return atts["raw_data"] end return "" end |