protk 1.4.1 → 1.4.2

data/lib/protk/physical_constants.rb

@@ -0,0 +1 @@
+HYDROGEN_MASS=1.00794

data/lib/protk/protein.rb

@@ -1,4 +1,5 @@
 require 'protk/peptide'
+require 'protk/mzidentml_doc'
 
 include LibXML
 
@@ -14,6 +15,21 @@ class Protein
 	attr_accessor :percent_coverage
 	attr_accessor :peptides
 
+	def as_protxml
+		node = XML::Node.new('protein')
+    	node['protein_name']=self.protein_name.to_s
+    	node['n_indistinguishable_proteins']=self.n_indistinguishable_proteins.to_s
+    	node['probability']=self.probability.to_s
+    	node['percent_coverage']=self.percent_coverage.to_s
+    	node['unique_stripped_peptides']=self.peptides.collect {|p| p.sequence }.join("+")
+    	node['total_number_peptides']=self.peptides.length.to_s
+    	self.peptides.each do |peptide|  
+    		node<<peptide.as_protxml
+    	end
+    	node
+	end
+
+
 	class << self
 
 		# <protein_group group_number="1" probability="1.0000">
@@ -46,6 +62,52 @@ class Protein
 			prot.peptides = peptide_nodes.collect { |e| Peptide.from_protxml(e) }
 			prot
 		end
+
+
+		# <ProteinAmbiguityGroup id="PAG_0">
+		# 	<ProteinDetectionHypothesis id="PAG_0_1" dBSequence_ref="JEMP01000193.1_rev_g3500.t1 280755" passThreshold="false">
+		# 		<PeptideHypothesis peptideEvidence_ref="PepEv_1">
+		# 			<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_1_1"/>
+		# 		</PeptideHypothesis>
+		# 		<cvParam cvRef="PSI-MS" accession="MS:1002403" name="group representative"/>
+		# 		<cvParam cvRef="PSI-MS" accession="MS:1002401" name="leading protein"/>
+		# 		<cvParam cvRef="PSI-MS" accession="MS:1001093" name="sequence coverage" value="0.0"/>
+		# 	</ProteinDetectionHypothesis>
+		# 	<cvParam cvRef="PSI-MS" accession="MS:1002470" name="PeptideShaker protein group score" value="0.0"/>
+		# 	<cvParam cvRef="PSI-MS" accession="MS:1002471" name="PeptideShaker protein group confidence" value="0.0"/>
+		# 	<cvParam cvRef="PSI-MS" accession="MS:1002545" name="PeptideShaker protein confidence type" value="Not Validated"/>
+		# 	<cvParam cvRef="PSI-MS" accession="MS:1002415" name="protein group passes threshold" value="false"/>
+		# </ProteinAmbiguityGroup>
+
+
+		# Note:
+		# This is hacked together to work for a specific PeptideShaker output type
+		# Refactor and properly respect cvParams for real conversion
+		#
+		def from_mzid(xmlnode)
+
+			coverage_cvparam=""
+			prot=new()
+			groupnode = xmlnode.parent
+
+			prot.group_number=groupnode.attributes['id'].split("_").last.to_i+1
+			prot.protein_name=MzIdentMLDoc.get_dbsequence(xmlnode,xmlnode.attributes['dBSequence_ref']).attributes['accession']
+			prot.n_indistinguishable_proteins=MzIdentMLDoc.get_proteins_for_group(groupnode).length
+			prot.group_probability=MzIdentMLDoc.get_cvParam(groupnode,"MS:1002470").attributes['value'].to_f
+
+			coverage_node=MzIdentMLDoc.get_cvParam(xmlnode,"MS:1001093")
+
+			prot.percent_coverage=coverage_node.attributes['value'].to_f if coverage_node
+			prot.probability = MzIdentMLDoc.get_protein_probability(xmlnode)
+			# require 'byebug';byebug
+
+			peptide_nodes=MzIdentMLDoc.get_peptides_for_protein(xmlnode)
+
+			prot.peptides = peptide_nodes.collect { |e| Peptide.from_mzid(e) }
+			prot
+		end
+
+
 		private :new
 	end
 
@@ -62,11 +124,12 @@ class Protein
 			if best_peptides[seq].nil?
 				best_peptides[seq]=peptide				
 			else
-				best_peptides[seq]=peptide if peptide.nsp_adjusted_probability > best_peptides[seq].nsp_adjusted_probability
+				best_peptides[seq]=peptide if peptide.probability > best_peptides[seq].probability
 			end
 		end
 
 		best_peptides.values
 	end
 
+
 end

data/lib/protk/protein_group.rb

@@ -0,0 +1,70 @@
+
+require 'protk/peptide'
+require 'protk/protein'
+require 'protk/mzidentml_doc'
+require 'protk/protxml_writer'
+
+include LibXML
+
+
+class ProteinGroup
+
+	attr_accessor :group_number
+	attr_accessor :group_probability
+	attr_accessor :proteins
+
+	class << self
+
+		# <ProteinAmbiguityGroup id="PAG_0">
+		# 	<ProteinDetectionHypothesis id="PAG_0_1" dBSequence_ref="JEMP01000193.1_rev_g3500.t1 280755" passThreshold="false">
+		# 		<PeptideHypothesis peptideEvidence_ref="PepEv_1">
+		# 			<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_1_1"/>
+		# 		</PeptideHypothesis>
+		# 		<cvParam cvRef="PSI-MS" accession="MS:1002403" name="group representative"/>
+		# 		<cvParam cvRef="PSI-MS" accession="MS:1002401" name="leading protein"/>
+		# 		<cvParam cvRef="PSI-MS" accession="MS:1001093" name="sequence coverage" value="0.0"/>
+		# 	</ProteinDetectionHypothesis>
+		# 	<cvParam cvRef="PSI-MS" accession="MS:1002470" name="PeptideShaker protein group score" value="0.0"/>
+		# 	<cvParam cvRef="PSI-MS" accession="MS:1002471" name="PeptideShaker protein group confidence" value="0.0"/>
+		# 	<cvParam cvRef="PSI-MS" accession="MS:1002545" name="PeptideShaker protein confidence type" value="Not Validated"/>
+		# 	<cvParam cvRef="PSI-MS" accession="MS:1002415" name="protein group passes threshold" value="false"/>
+		# </ProteinAmbiguityGroup>
+
+
+		# Note:
+		# This is hacked together to work for a specific PeptideShaker output type
+		# Refactor and properly respect cvParams for real conversion
+		#
+		def from_mzid(groupnode)
+
+			group=new()
+
+			group.group_number=groupnode.attributes['id'].split("_").last.to_i+1
+			group.group_probability=MzIdentMLDoc.get_cvParam(groupnode,"MS:1002470").attributes['value'].to_f
+
+			# require 'byebug';byebug
+
+			protein_nodes=MzIdentMLDoc.get_proteins_for_group(groupnode)
+
+			group.proteins = protein_nodes.collect { |e| Protein.from_mzid(e) }
+			group
+		end
+
+
+		private :new
+	end
+
+	def initialize()
+
+	end
+
+	def as_protxml()
+		node = XML::Node.new('protein_group')
+    	node["group_number"] = self.group_number.to_s
+    	node["group_probability"] = self.group_probability.to_s
+    	self.proteins.each { |prot| node << prot.as_protxml }
+    	node
+	end
+
+
+end

data/lib/protk/protxml_writer.rb

@@ -0,0 +1,27 @@
+include LibXML
+
+class ProtXMLWriter < Object
+
+	PROTXML_NS_PREFIX="protxml"
+	PROTXML_NS="http://regis-web.systemsbiology.net/protXML"
+
+	attr :template_doc
+	attr :protein_summary_node
+
+	def initialize
+		template_path="#{File.dirname(__FILE__)}/data/template_prot.xml"
+		template_parser=XML::Parser.file(template_path)
+		@template_doc=template_parser.parse
+		@protein_summary_node=@template_doc.root
+	end
+
+	def append_protein_group(pg_node)
+		# require 'byebug';byebug
+		@protein_summary_node << pg_node
+	end
+
+	def save(file_path)
+		@template_doc.save(file_path,:indent=>true,:encoding => XML::Encoding::UTF_8)
+	end
+
+end

data/lib/protk/psm.rb

@@ -0,0 +1,222 @@
+
+require 'protk/mzidentml_doc'
+require 'libxml'
+
+include LibXML
+
+
+class String
+  def to_bool
+    return true if self == true || self =~ (/^(true|t|yes|y|1)$/i)
+    return false if self == false || self =~ (/^(false|f|no|n|0)$/i)
+    raise ArgumentError.new("invalid value for Boolean: \"#{self}\"")
+  end
+end
+
+class PeptideEvidence
+	attr_accessor :peptide_prev_aa
+	attr_accessor :peptide_next_aa
+	attr_accessor :protein
+	attr_accessor :protein_descr
+	# attr_accessor :peptide_sequence
+	attr_accessor :is_decoy
+
+# <PeptideEvidence isDecoy="false" pre="K" post="G" start="712"
+#     end="722" peptide_ref="KSPVYKVHFTR"
+#     dBSequence_ref="JEMP01000193.1_rev_g3500.t1" id="PepEv_1" />
+	class << self
+
+		def from_mzid(pe_node)
+			pe = new()
+			pe.peptide_prev_aa=pe_node.attributes['pre']
+			pe.peptide_next_aa=pe_node.attributes['post']
+			pe.is_decoy=pe_node.attributes['isDecoy'].to_bool
+
+			# peptide_ref = pe_node.attributes['peptide_ref']
+			prot_ref = pe_node.attributes['dBSequence_ref']
+			# pep_node = MzIdentMLDoc.find(pe_node,"Peptide[@id=\'#{peptide_ref}\']",true)[0]
+			prot_node = MzIdentMLDoc.find(pe_node,"DBSequence[@id=\'#{prot_ref}\']",true)[0]
+
+
+			# <DBSequence id="JEMP01000193.1_rev_g3500.t1"
+			# accession="JEMP01000193.1_rev_g3500.t1"
+			# searchDatabase_ref="SearchDB_1">
+			#   <cvParam cvRef="PSI-MS" accession="MS:1001088"
+			#   name="protein description" value="280755|283436" />
+			# </DBSequence>
+			pe.protein=prot_node.attributes['accession']
+			pe.protein_descr=MzIdentMLDoc.get_cvParam(prot_node,"MS:1001088")['value']
+
+
+			# pe.peptide_sequence=pep_node
+
+			pe
+		end
+
+
+		private :new
+	end
+
+	def initialize()
+
+	end
+
+#	<alternative_protein protein="lcl|JEMP01000005.1_rev_g4624.t1" 
+# protein_descr="652491|654142" num_tol_term="2" peptide_prev_aa="K" peptide_next_aa="Y"/>
+# We use this only for alternative_proteins
+# The first peptide_evidence item is baked into the attributes of a spectrum_query
+	def as_pepxml()
+		alt_node = XML::Node.new('alternative_protein')
+		alt_node['protein']=self.protein
+		alt_node['protein_descr']=self.protein_descr
+		alt_node['peptide_prev_aa']=self.peptide_prev_aa
+		alt_node['peptide_next_aa']=self.peptide_next_aa
+
+
+		alt_node
+	end
+
+end
+
+# <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8167.00003.00003.2" start_scan="3" end_scan="3" 
+#precursor_neutral_mass="1398.7082" assumed_charge="2" index="2" experiment_label="mr176">
+# <search_result>
+# <search_hit hit_rank="1" peptide="SQVFQLESTFDV" peptide_prev_aa="R" peptide_next_aa="K" protein="tr|Q90853|Q90853_CHICK" 
+# protein_descr="Homeobox protein OS=Gallus gallus GN=GH6 PE=2 SV=1" num_tot_proteins="1" 
+# num_matched_ions="9" tot_num_ions="22" calc_neutral_pep_mass="1380.6557" massdiff="18.053" num_tol_term="1" 
+# num_missed_cleavages="0" is_rejected="0">
+# <search_score name="hyperscore" value="23.9"/>
+# <search_score name="nextscore" value="19.3"/>
+# <search_score name="bscore" value="9.6"/>
+# <search_score name="yscore" value="7.6"/>
+# <search_score name="cscore" value="0"/>
+# <search_score name="zscore" value="0"/>
+# <search_score name="ascore" value="0"/>
+# <search_score name="xscore" value="0"/>
+# <search_score name="expect" value="0.099"/>
+# <analysis_result analysis="peptideprophet">
+# <peptideprophet_result probability="0.9997" all_ntt_prob="(0.0000,0.9997,0.9999)">
+# <search_score_summary>
+# <parameter name="fval" value="2.3571"/>
+# <parameter name="ntt" value="1"/>
+# <parameter name="nmc" value="0"/>
+# <parameter name="massd" value="18.053"/>
+# </search_score_summary>
+# </peptideprophet_result>
+# </analysis_result>
+# </search_hit>
+# </search_result>
+# </spectrum_query>
+
+class PSM
+
+
+	attr_accessor :peptide
+	attr_accessor :calculated_mz
+	attr_accessor :experimental_mz
+	attr_accessor :charge
+
+	attr_accessor :scores
+	attr_accessor :peptide_evidence
+
+	class << self
+
+		# <SpectrumIdentificationResult spectraData_ref="ma201_Vp_1-10.mzML.mgf"
+		# spectrumID="index=3152" id="SIR_1">
+		#   <SpectrumIdentificationItem passThreshold="false"
+		#   rank="1" peptide_ref="KSPVYKVHFTR"
+		#   calculatedMassToCharge="1360.7615466836999"
+		#   experimentalMassToCharge="1362.805053710938"
+		#   chargeState="1" id="SII_1_1">
+		#     <PeptideEvidenceRef peptideEvidence_ref="PepEv_1" />
+		#     <Fragmentation>
+		#       <IonType charge="1" index="1 4">
+		#         <FragmentArray measure_ref="Measure_MZ"
+		#         values="175.2081208 560.3388993" />
+		#         <FragmentArray measure_ref="Measure_Int"
+		#         values="94.0459823608 116.2766723633" />
+		#         <FragmentArray measure_ref="Measure_Error"
+		#         values="0.08916864948798775 0.0449421494880653" />
+		#         <cvParam cvRef="PSI-MS" accession="MS:1001220"
+		#         name="frag: y ion" />
+		#       </IonType>
+		#     </Fragmentation>
+		#     <cvParam cvRef="PSI-MS" accession="MS:1002466"
+		#     name="PeptideShaker PSM score" value="0.0" />
+		#     <cvParam cvRef="PSI-MS" accession="MS:1002467"
+		#     name="PeptideShaker PSM confidence" value="0.0" />
+		#     <cvParam cvRef="PSI-MS" accession="MS:1002052"
+		#     name="MS-GF:SpecEValue" value="1.4757611E-6" />
+		#     <cvParam cvRef="PSI-MS" accession="MS:1001117"
+		#     name="theoretical mass" value="1360.7615466836999" />
+		#     <cvParam cvRef="PSI-MS" accession="MS:1002543"
+		#     name="PeptideShaker PSM confidence type"
+		#     value="Not Validated" />
+		#   </SpectrumIdentificationItem>
+		#   <cvParam cvRef="PSI-MS" accession="MS:1000796"
+		#   name="spectrum title"
+		#   value="Suresh Vp 1 to 10_BAF.3535.3535.1" />
+		#   <cvParam cvRef="PSI-MS" accession="MS:1000894"
+		#   name="retention time" value="6855.00001" unitCvRef="UO"
+		#   unitAccession="UO:0000010" unitName="seconds" />
+		# </SpectrumIdentificationResult>
+
+
+
+		def from_mzid(psm_node)
+			psm = new()
+			psm.peptide = MzIdentMLDoc.get_sequence_for_psm(psm_node)
+			peptide_evidence_nodes = MzIdentMLDoc.get_peptide_evidence_from_psm(psm_node)
+			psm.peptide_evidence = peptide_evidence_nodes.collect { |pe| PeptideEvidence.from_mzid(pe) }
+
+			psm.calculated_mz = psm_node.attributes['calculatedMassToCharge'].to_f
+			psm.experimental_mz = psm_node.attributes['experimentalMassToCharge'].to_f
+			psm.charge = psm_node.attributes['chargeState'].to_i
+
+			psm
+		end
+
+
+		private :new
+	end
+
+	def initialize()
+
+	end
+
+	# <search_hit hit_rank="1" peptide="GGYNQDGGSGGGYQGGGGYSGGGGGYQGGQR" 
+	# peptide_prev_aa="R" peptide_next_aa="N" 
+	# protein="lcl|JEMP01000008.1_fwd_g5144.t1" 
+	# num_tot_proteins="1" 
+	# calc_neutral_pep_mass="2768.11967665812" 
+	# massdiff="0.120361328125" 
+	# protein_descr="4860|5785" 
+	# num_tol_term="2" 
+	# num_missed_cleavages="0">
+
+	# From what I can tell, search_hit is always trivially wrapped in search_result 1:1
+	#
+	def as_pepxml()
+		hit_node = XML::Node.new('search_hit')
+		hit_node['peptide']=self.peptide.to_s
+
+		# require 'byebug';byebug
+		first_evidence = self.peptide_evidence.first
+
+		hit_node['peptide_prev_aa']=first_evidence.peptide_prev_aa
+		hit_node['peptide_next_aa']=first_evidence.peptide_next_aa
+		hit_node['protein']=first_evidence.protein
+		hit_node['protein_descr']=first_evidence.protein_descr
+
+		hit_node['num_tot_proteins']=self.peptide_evidence.length.to_s
+
+		alt_evidence = peptide_evidence.drop(1)
+		alt_evidence.each { |ae| hit_node << ae.as_pepxml }
+
+		result_node = XML::Node.new('search_result')
+		result_node << hit_node
+		result_node
+	end
+
+
+end

data/lib/protk/search_tool.rb

@@ -5,8 +5,7 @@
 # Provides common functionality used by all msms search tools.
 #
 # It allows;
-# 1. Specification of the search database using a simple name ... this class provides the necessary search for the actual file
-# 2. Output files to be specified via a prefix or suffix to be added to the name of the corresponding input file
+# 1. Output files to be specified via a prefix or suffix to be added to the name of the corresponding input file
 # 
 
 require 'optparse'
@@ -21,10 +20,6 @@ class SearchTool < Tool
   def initialize(option_support=[])
     super(option_support)
 
-    # if (option_support.include? :database)
-    #   add_value_option(:database,"sphuman",['-d', '--database dbname', 'Specify the database to use for this search. Can be a named protk database or the path to a fasta file'])        
-    # end
-    
     if ( option_support.include? :enzyme )
       add_value_option(:enzyme,"Trypsin",['--enzyme enz', 'Enzyme'])
     end

data/lib/protk/sniffer.rb

@@ -0,0 +1,35 @@
+
+class Sniffer
+
+	@sniff_lines = 100
+
+	# Return nil if undetectable
+	# Return detected format otherwise
+	def self.sniff_format(filepath)
+		if self.is_mgf_format(filepath)
+			return "mgf"
+		elsif self.is_mzml_format(filepath)
+			return "mzML"
+		end
+		return nil
+	end
+
+
+	def self.is_mzml_format(filepath)
+		lines = File.foreach(filepath).first(@sniff_lines).join("\n")
+		if lines =~ /\<mzML.*http\:\/\/psi\.hupo\.org\/ms\/mzml/
+			return true
+		end
+		return false
+	end
+
+	def self.is_mgf_format(filepath)
+		lines = File.foreach(filepath).first(@sniff_lines).join("\n")
+		if lines =~ /^BEGIN IONS/
+			return true
+		end
+		return false
+	end
+
+
+end