protk 1.4.1 → 1.4.2

data/lib/protk/spectrum_query.rb

@@ -0,0 +1,132 @@
+
+require 'protk/mzidentml_doc'
+require 'protk/psm'
+require 'protk/physical_constants'
+
+include LibXML
+
+
+# <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 SpectrumQuery
+
+
+	attr_accessor :spectrum_title
+	attr_accessor :retention_time
+	# attr_accessor :precursor_neutral_mass
+	# attr_accessor :assumed_charge
+
+	# attr_accessor :index
+	attr_accessor :psms
+
+	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(query_node)
+			query = new()
+			query.spectrum_title = MzIdentMLDoc.get_cvParam(query_node,"MS:1000796")['value'].to_s
+			query.retention_time = MzIdentMLDoc.get_cvParam(query_node,"MS:1000894")['value'].to_f
+			items = MzIdentMLDoc.find(query_node,"SpectrumIdentificationItem")
+			query.psms = items.collect { |item| PSM.from_mzid(item) }
+			query
+		end
+
+
+		private :new
+	end
+
+	def initialize()
+
+	end
+
+# <spectrum_query spectrum="SureshVp1to10_BAF.00833.00833.1" start_scan="833" end_scan="833" 
+# precursor_neutral_mass="1214.5937" assumed_charge="1" index="3222">
+# <search_result>
+
+	def as_pepxml()
+		node = XML::Node.new('spectrum_query')
+		node['spectrum']=self.spectrum_title
+		node['retention_time_sec']=self.retention_time.to_s
+
+
+		# Use the first psm to populate spectrum level values
+		first_psm=self.psms.first
+
+		c=first_psm.charge
+
+		node['precursor_neutral_mass']=(first_psm.experimental_mz*c-c*HYDROGEN_MASS).to_s
+		node['assumed_charge']=c.to_s
+
+
+		self.psms.each do |psm|  
+			node << psm.as_pepxml
+		end
+    	node
+	end
+
+
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: protk
 version: !ruby/object:Gem::Version
-  version: 1.4.1
+  version: 1.4.2
 platform: ruby
 authors:
 - Ira Cooke
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-03-24 00:00:00.000000000 Z
+date: 2015-05-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: open4
@@ -206,6 +206,10 @@ executables:
 - protxml_to_table.rb
 - swissprot_to_table.rb
 - protxml_to_psql.rb
+- mzid_to_protxml.rb
+- mzid_to_pepxml.rb
+- spectrast_create.rb
+- spectrast_filter.rb
 extensions:
 - ext/decoymaker/extconf.rb
 extra_rdoc_files: []
@@ -219,6 +223,8 @@ files:
 - bin/mascot_search.rb
 - bin/mascot_to_pepxml.rb
 - bin/msgfplus_search.rb
+- bin/mzid_to_pepxml.rb
+- bin/mzid_to_protxml.rb
 - bin/omssa_search.rb
 - bin/peptide_prophet.rb
 - bin/pepxml_to_table.rb
@@ -229,6 +235,8 @@ files:
 - bin/protxml_to_table.rb
 - bin/repair_run_summary.rb
 - bin/sixframe.rb
+- bin/spectrast_create.rb
+- bin/spectrast_filter.rb
 - bin/swissprot_to_table.rb
 - bin/tandem_search.rb
 - bin/tandem_to_pepxml.rb
@@ -261,6 +269,8 @@ files:
 - lib/protk/data/tandem_isb_native_defaults.xml
 - lib/protk/data/tandem_params.xml
 - lib/protk/data/taxonomy_template.xml
+- lib/protk/data/template_pep.xml
+- lib/protk/data/template_prot.xml
 - lib/protk/data/unimod.xml
 - lib/protk/data/uniprot_accessions.loc
 - lib/protk/data/uniprot_accessions_table.txt
@@ -274,20 +284,28 @@ files:
 - lib/protk/manage_db_rakefile.rake
 - lib/protk/manage_db_tool.rb
 - lib/protk/mascot_util.rb
+- lib/protk/mzidentml_doc.rb
 - lib/protk/mzml_parser.rb
 - lib/protk/omssa_util.rb
 - lib/protk/openms_defaults.rb
 - lib/protk/peptide.rb
 - lib/protk/pepxml.rb
+- lib/protk/pepxml_writer.rb
+- lib/protk/physical_constants.rb
 - lib/protk/plasmodb.rb
 - lib/protk/prophet_tool.rb
 - lib/protk/protein.rb
+- lib/protk/protein_group.rb
 - lib/protk/protein_to_genome_mapper.rb
 - lib/protk/protxml_to_gff_tool.rb
+- lib/protk/protxml_writer.rb
+- lib/protk/psm.rb
 - lib/protk/randomize.rb
 - lib/protk/search_tool.rb
 - lib/protk/setup_rakefile.rake
 - lib/protk/setup_tool.rb
+- lib/protk/sniffer.rb
+- lib/protk/spectrum_query.rb
 - lib/protk/swissprot_database.rb
 - lib/protk/tandem_search_tool.rb
 - lib/protk/tool.rb