protk 1.4.1 → 1.4.2

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@@ -0,0 +1,132 @@
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+
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+ require 'protk/mzidentml_doc'
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+ require 'protk/psm'
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+ require 'protk/physical_constants'
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+
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+ include LibXML
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+
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+
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+ # <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8167.00003.00003.2" start_scan="3" end_scan="3"
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+ #precursor_neutral_mass="1398.7082" assumed_charge="2" index="2" experiment_label="mr176">
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+ # <search_result>
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+ # <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">
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+ # <search_score name="hyperscore" value="23.9"/>
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+ # <search_score name="nextscore" value="19.3"/>
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+ # <search_score name="bscore" value="9.6"/>
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+ # <search_score name="yscore" value="7.6"/>
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+ # <search_score name="cscore" value="0"/>
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+ # <search_score name="zscore" value="0"/>
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+ # <search_score name="ascore" value="0"/>
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+ # <search_score name="xscore" value="0"/>
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+ # <search_score name="expect" value="0.099"/>
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+ # <analysis_result analysis="peptideprophet">
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+ # <peptideprophet_result probability="0.9997" all_ntt_prob="(0.0000,0.9997,0.9999)">
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+ # <search_score_summary>
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+ # <parameter name="fval" value="2.3571"/>
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+ # <parameter name="ntt" value="1"/>
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+ # <parameter name="nmc" value="0"/>
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+ # <parameter name="massd" value="18.053"/>
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+ # </search_score_summary>
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+ # </peptideprophet_result>
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+ # </analysis_result>
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+ # </search_hit>
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+ # </search_result>
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+ # </spectrum_query>
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+
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+ class SpectrumQuery
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+
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+
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+ attr_accessor :spectrum_title
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+ attr_accessor :retention_time
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+ # attr_accessor :precursor_neutral_mass
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+ # attr_accessor :assumed_charge
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+
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+ # attr_accessor :index
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+ attr_accessor :psms
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+
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+ class << self
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+
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+ # <SpectrumIdentificationResult spectraData_ref="ma201_Vp_1-10.mzML.mgf"
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+ # spectrumID="index=3152" id="SIR_1">
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+ # <SpectrumIdentificationItem passThreshold="false"
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+ # rank="1" peptide_ref="KSPVYKVHFTR"
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+ # calculatedMassToCharge="1360.7615466836999"
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+ # experimentalMassToCharge="1362.805053710938"
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+ # chargeState="1" id="SII_1_1">
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+ # <PeptideEvidenceRef peptideEvidence_ref="PepEv_1" />
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+ # <Fragmentation>
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+ # <IonType charge="1" index="1 4">
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+ # <FragmentArray measure_ref="Measure_MZ"
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+ # values="175.2081208 560.3388993" />
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+ # <FragmentArray measure_ref="Measure_Int"
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+ # values="94.0459823608 116.2766723633" />
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+ # <FragmentArray measure_ref="Measure_Error"
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+ # values="0.08916864948798775 0.0449421494880653" />
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+ # <cvParam cvRef="PSI-MS" accession="MS:1001220"
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+ # name="frag: y ion" />
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+ # </IonType>
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+ # </Fragmentation>
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+ # <cvParam cvRef="PSI-MS" accession="MS:1002466"
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+ # name="PeptideShaker PSM score" value="0.0" />
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+ # <cvParam cvRef="PSI-MS" accession="MS:1002467"
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+ # name="PeptideShaker PSM confidence" value="0.0" />
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+ # <cvParam cvRef="PSI-MS" accession="MS:1002052"
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+ # name="MS-GF:SpecEValue" value="1.4757611E-6" />
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+ # <cvParam cvRef="PSI-MS" accession="MS:1001117"
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+ # name="theoretical mass" value="1360.7615466836999" />
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+ # <cvParam cvRef="PSI-MS" accession="MS:1002543"
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+ # name="PeptideShaker PSM confidence type"
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+ # value="Not Validated" />
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+ # </SpectrumIdentificationItem>
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+ # <cvParam cvRef="PSI-MS" accession="MS:1000796"
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+ # name="spectrum title"
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+ # value="Suresh Vp 1 to 10_BAF.3535.3535.1" />
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+ # <cvParam cvRef="PSI-MS" accession="MS:1000894"
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+ # name="retention time" value="6855.00001" unitCvRef="UO"
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+ # unitAccession="UO:0000010" unitName="seconds" />
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+ # </SpectrumIdentificationResult>
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+
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+ def from_mzid(query_node)
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+ query = new()
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+ query.spectrum_title = MzIdentMLDoc.get_cvParam(query_node,"MS:1000796")['value'].to_s
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+ query.retention_time = MzIdentMLDoc.get_cvParam(query_node,"MS:1000894")['value'].to_f
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+ items = MzIdentMLDoc.find(query_node,"SpectrumIdentificationItem")
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+ query.psms = items.collect { |item| PSM.from_mzid(item) }
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+ query
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+ end
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+
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+
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+ private :new
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+ end
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+
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+ def initialize()
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+
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+ end
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+
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+ # <spectrum_query spectrum="SureshVp1to10_BAF.00833.00833.1" start_scan="833" end_scan="833"
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+ # precursor_neutral_mass="1214.5937" assumed_charge="1" index="3222">
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+ # <search_result>
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+
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+ def as_pepxml()
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+ node = XML::Node.new('spectrum_query')
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+ node['spectrum']=self.spectrum_title
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+ node['retention_time_sec']=self.retention_time.to_s
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+
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+
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+ # Use the first psm to populate spectrum level values
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+ first_psm=self.psms.first
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+
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+ c=first_psm.charge
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+
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+ node['precursor_neutral_mass']=(first_psm.experimental_mz*c-c*HYDROGEN_MASS).to_s
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+ node['assumed_charge']=c.to_s
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+
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+
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+ self.psms.each do |psm|
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+ node << psm.as_pepxml
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+ end
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+ node
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+ end
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+
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+
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+ end
metadata CHANGED
@@ -1,14 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: protk
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  version: !ruby/object:Gem::Version
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- version: 1.4.1
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+ version: 1.4.2
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  platform: ruby
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  authors:
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  - Ira Cooke
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2015-03-24 00:00:00.000000000 Z
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+ date: 2015-05-20 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: open4
@@ -206,6 +206,10 @@ executables:
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  - protxml_to_table.rb
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  - swissprot_to_table.rb
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  - protxml_to_psql.rb
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+ - mzid_to_protxml.rb
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+ - mzid_to_pepxml.rb
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+ - spectrast_create.rb
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+ - spectrast_filter.rb
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  extensions:
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  - ext/decoymaker/extconf.rb
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  extra_rdoc_files: []
@@ -219,6 +223,8 @@ files:
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  - bin/mascot_search.rb
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  - bin/mascot_to_pepxml.rb
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  - bin/msgfplus_search.rb
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+ - bin/mzid_to_pepxml.rb
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+ - bin/mzid_to_protxml.rb
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  - bin/omssa_search.rb
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  - bin/peptide_prophet.rb
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  - bin/pepxml_to_table.rb
@@ -229,6 +235,8 @@ files:
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  - bin/protxml_to_table.rb
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  - bin/repair_run_summary.rb
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  - bin/sixframe.rb
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+ - bin/spectrast_create.rb
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+ - bin/spectrast_filter.rb
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  - bin/swissprot_to_table.rb
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  - bin/tandem_search.rb
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  - bin/tandem_to_pepxml.rb
@@ -261,6 +269,8 @@ files:
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  - lib/protk/data/tandem_isb_native_defaults.xml
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  - lib/protk/data/tandem_params.xml
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  - lib/protk/data/taxonomy_template.xml
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+ - lib/protk/data/template_pep.xml
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+ - lib/protk/data/template_prot.xml
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  - lib/protk/data/unimod.xml
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  - lib/protk/data/uniprot_accessions.loc
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  - lib/protk/data/uniprot_accessions_table.txt
@@ -274,20 +284,28 @@ files:
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  - lib/protk/manage_db_rakefile.rake
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  - lib/protk/manage_db_tool.rb
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  - lib/protk/mascot_util.rb
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+ - lib/protk/mzidentml_doc.rb
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  - lib/protk/mzml_parser.rb
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  - lib/protk/omssa_util.rb
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  - lib/protk/openms_defaults.rb
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  - lib/protk/peptide.rb
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  - lib/protk/pepxml.rb
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+ - lib/protk/pepxml_writer.rb
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+ - lib/protk/physical_constants.rb
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  - lib/protk/plasmodb.rb
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  - lib/protk/prophet_tool.rb
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  - lib/protk/protein.rb
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+ - lib/protk/protein_group.rb
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  - lib/protk/protein_to_genome_mapper.rb
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  - lib/protk/protxml_to_gff_tool.rb
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+ - lib/protk/protxml_writer.rb
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+ - lib/protk/psm.rb
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  - lib/protk/randomize.rb
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  - lib/protk/search_tool.rb
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  - lib/protk/setup_rakefile.rake
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  - lib/protk/setup_tool.rb
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+ - lib/protk/sniffer.rb
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+ - lib/protk/spectrum_query.rb
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  - lib/protk/swissprot_database.rb
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  - lib/protk/tandem_search_tool.rb
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  - lib/protk/tool.rb