protk 1.2.6.pre1 → 1.2.6.pre2

data/bin/protxml_to_table.rb

@@ -19,6 +19,11 @@ include LibXML
 tool=Tool.new([:explicit_output])
 tool.option_parser.banner = "Convert a protXML file to a tab delimited table.\n\nUsage: protxml_to_table.rb [options] file1.protXML"
 
+tool.options.groups=false
+tool.option_parser.on("--groups","Print output by groups rather than for each protein") do 
+	tool.options.groups=true
+end
+
 # tool.options.proteinid_regex=".*?\|.*?\|(.*)"
 # tool.option_parser.on( '--regex rexpr', 'Regex' ) do |regex| 
 #   tool.options.proteinid_regex=regex
@@ -58,8 +63,10 @@ column_headers=[
 	"num_peptides","confidence"
 ]
 
-output_fh.write "#{column_headers.join("\t")}\n"
+groups_column_headers=["group_number","group_probability","members"]
 
+output_fh.write "#{column_headers.join("\t")}\n" unless tool.groups
+output_fh.write "#{groups_column_headers.join("\t")}\n" if tool.groups
 
 protein_groups=protxml_doc.find("//#{protxml_ns_prefix}protein_group", protxml_ns)
 
@@ -67,6 +74,8 @@ protein_groups.each do |protein_group|
 
 	proteins=protein_group.find("./#{protxml_ns_prefix}protein", protxml_ns)
 
+	group_members=[]
+
 	proteins.each do |protein| 
 
 		indis_proteins=protein.find("./#{protxml_ns_prefix}indistinguishable_protein", protxml_ns)
@@ -78,6 +87,8 @@ protein_groups.each do |protein_group|
 			protein_id=protein.attributes['protein_name'].match(/.*?\|.*?\|(.*)/)[1]
 		end
 
+		group_members<<protein.attributes['protein_name']
+
 		column_values=[]
 
 		column_values << protein_group.attributes['group_number']
@@ -91,9 +102,21 @@ protein_groups.each do |protein_group|
 		column_values << protein.attributes['unique_stripped_peptides']
 		column_values << protein.attributes['total_number_peptides']
 		column_values << protein.attributes['confidence']
-		output_fh.write(column_values.join("\t"))
-		output_fh.write("\n")
 
+		unless tool.groups			
+			output_fh.write(column_values.join("\t"))
+			output_fh.write("\n")
+		end
 	end
+
+	group_column_values=[protein_group.attributes['group_number']]
+	group_column_values<<protein_group.attributes['probability']
+	group_column_values<<group_members.join(" ")
+
+	if tool.groups
+		output_fh.write(group_column_values.join("\t"))
+		output_fh.write("\n")
+	end
+
 end
 

data/bin/tandem_search.rb

@@ -22,7 +22,7 @@ genv=Constants.new
 #
 search_tool=SearchTool.new([:background,:glyco,:database,:explicit_output,:over_write,
 :enzyme,:modifications,:mass_tolerance_units,:mass_tolerance,:strict_monoisotopic_mass,
-:missed_cleavages,:carbamidomethyl,:methionine_oxidation
+:missed_cleavages,:cleavage_semi,:carbamidomethyl,:methionine_oxidation
   ])
 search_tool.jobid_prefix="x"
 search_tool.option_parser.banner = "Run an X!Tandem msms search on a set of mzML input files.\n\nUsage: tandem_search.rb [options] file1.mzML file2.mzML ..."

data/lib/protk/constants.rb

@@ -133,7 +133,7 @@ class Constants
   end
 
   def msgfplusjar
-    return "#{self.msgfplus_root}/MSGFPlus.jar"
+    return %x[which MSGFPlus.jar]
   end
 
   def pwiz_root
@@ -236,7 +236,7 @@ class Constants
       @protk_dir=ENV['PROTK_INSTALL_DIR']
     end
 
-    # Protk Defaults
+    # Load Protk Defaults
     #
     default_config_yml = YAML.load_file "#{File.dirname(__FILE__)}/data/default_config.yml"
     throw "Unable to read the config file at #{File.dirname(__FILE__)}/data/default_config.yml" unless default_config_yml!=nil
@@ -251,31 +251,31 @@ class Constants
       @env=default_config_yml
     end
 
-    # Application installation directories. From environment variables
+    protk_tool_dirs=["tpp","omssa","openms","msgfplus","blast","pwiz","tandem"]
+
+    # Construct the PATH variable by prepending our preferred paths
     #
-    protk_roots = [["tpp","xinteract"],["omssa","omssacl"],["blast","blastdbcmd"],["pwiz","msconvert"],["msgfplus",""],["openms","ExecutePipeline"]]
+    protk_paths=[]
 
-    protk_roots.each do |r,binaryname|  
-      env_value = ENV["PROTK_#{r.upcase}_ROOT"]
+    # Add PATHs if PROTK_XXX_ROOT is defined
+    #
+    protk_tool_dirs.each do |tooldir|  
+      env_value = ENV["PROTK_#{tooldir.upcase}_ROOT"]
       if ( env_value!=nil)
-        # "FROMPATH" means detect the root value
-        if env_value=="FROMPATH"
-          bin_path=Pathname.new(%x[which #{binaryname}].chomp)
-          if bin_path.exist?
-            env_value=bin_path.realpath.dirname.to_s
-          else
-            env_value=""
-          end
-        end
-        p "Using #{r} root #{env_value}"
-        @env["#{r}_root"]=env_value
+        protk_paths<<env_value
       end
+      protk_paths<<"#{@protk_dir}/tools/#{tooldir}"
     end
+
+    original_path=ENV['PATH']
+    protk_paths<<original_path
+
+
+    ENV['PATH']=protk_paths.join(":")
+
     
     throw "No data found in config file" unless @env!=nil
     @info_level=default_config_yml['message_level']
-
-
     
   end
 

data/lib/protk/data/default_config.yml

@@ -12,11 +12,4 @@ uniprot_sprot_annotation_database: swissprot_annotation
 uniprot_trembl_annotation_database: trembl_annotation
 galaxy_root: galaxy
 default_mascot_server: www.matrixscience.com
-tpp_root: tools/tpp
-omssa_root: tools/omssa
-openms_root: tools/openms
-msgfplus_root: tools/msgfplus
-blast_root: tools/blast
-pwiz_root: tools/pwiz
-tandem_root: tools/tandem
 log_file: Logs/protk.log

data/lib/protk/search_tool.rb

@@ -100,6 +100,13 @@ class SearchTool < Tool
       end
     end
 
+    if ( option_support.include? :cleavage_semi )
+      @options.cleavage_semi=true
+      @option_parser.on( '--no-cleavage-semi', 'Dont allow up to 1 non tryptic terminus on peptides' ) do  
+        @options.cleavage_semi=false
+      end
+    end
+
     if ( option_support.include? :respect_precursor_charges )
       @options.respect_precursor_charges=false
       @option_parser.on( '-q', '--respect-charges','Dont respect charges in the input file. Instead impute them by trying various options') do 

metadata

@@ -1,8 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: protk
 version: !ruby/object:Gem::Version
-  version: 1.2.6.pre1
-  prerelease: 6
+  version: 1.2.6.pre2
 platform: ruby
 authors:
 - Ira Cooke
@@ -14,151 +13,186 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: ftools
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.0'
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.0.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.0'
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.0.0
 - !ruby/object:Gem::Dependency
   name: open4
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.3.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.3.0
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.4'
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.4.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.4'
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.4.3
 - !ruby/object:Gem::Dependency
   name: rest-client
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.6.7
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.6.7
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.6.7
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.6.7
 - !ruby/object:Gem::Dependency
   name: net-ftp-list
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 3.2.5
+    - - '>='
       - !ruby/object:Gem::Version
         version: 3.2.5
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 3.2.5
+    - - '>='
       - !ruby/object:Gem::Version
         version: 3.2.5
 - !ruby/object:Gem::Dependency
   name: spreadsheet
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.7.4
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.7.4
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.7.4
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.7.4
 - !ruby/object:Gem::Dependency
   name: libxml-ruby
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 2.3.3
+        version: '2.7'
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 2.7.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 2.3.3
+        version: '2.7'
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 2.7.0
 - !ruby/object:Gem::Dependency
   name: mascot-dat
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.3.1
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.3.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.3.1
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.3.1
 - !ruby/object:Gem::Dependency
   name: bio-blastxmlparser
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.1
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.1.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.1
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.1.1
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -166,7 +200,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -211,37 +244,7 @@ extensions:
 - ext/protk/decoymaker/extconf.rb
 extra_rdoc_files: []
 files:
-- lib/protk/bio_sptr_extensions.rb
-- lib/protk/biotools_excel_converter.rb
-- lib/protk/command_runner.rb
-- lib/protk/constants.rb
-- lib/protk/convert_util.rb
-- lib/protk/data/make_uniprot_table.rb
-- lib/protk/eupathdb_gene_information_table.rb
-- lib/protk/fastadb.rb
-- lib/protk/galaxy_stager.rb
-- lib/protk/galaxy_util.rb
-- lib/protk/gapped_aligner.rb
-- lib/protk/manage_db_tool.rb
-- lib/protk/mascot_util.rb
-- lib/protk/omssa_util.rb
-- lib/protk/openms_defaults.rb
-- lib/protk/pepxml.rb
-- lib/protk/plasmodb.rb
-- lib/protk/prophet_tool.rb
-- lib/protk/protein_annotator.rb
-- lib/protk/protxml.rb
-- lib/protk/randomize.rb
-- lib/protk/search_tool.rb
-- lib/protk/setup_tool.rb
-- lib/protk/spreadsheet_extensions.rb
-- lib/protk/swissprot_database.rb
-- lib/protk/tool.rb
-- lib/protk/uniprot_mapper.rb
-- lib/protk/xtandem_defaults.rb
-- lib/protk.rb
-- lib/protk/manage_db_rakefile.rake
-- lib/protk/setup_rakefile.rake
+- README.md
 - bin/add_retention_times.rb
 - bin/annotate_ids.rb
 - bin/asapratio.rb
@@ -256,7 +259,6 @@ files:
 - bin/libra.rb
 - bin/make_decoy.rb
 - bin/manage_db.rb
-- bin/mascot2xml.rb
 - bin/mascot_search.rb
 - bin/mascot_to_pepxml.rb
 - bin/msgfplus_search.rb
@@ -276,20 +278,27 @@ files:
 - bin/uniprot_mapper.rb
 - bin/xls_to_table.rb
 - bin/xpress.rb
-- README.md
-- lib/protk/data/apt-get_packages.yaml
-- lib/protk/data/brew_packages.yaml
-- lib/protk/data/default_config.yml
+- ext/protk/decoymaker/decoymaker.c
+- ext/protk/decoymaker/extconf.rb
+- ext/protk/simplealign/extconf.rb
+- lib/protk.rb
+- lib/protk/bio_sptr_extensions.rb
+- lib/protk/biotools_excel_converter.rb
+- lib/protk/command_runner.rb
+- lib/protk/constants.rb
+- lib/protk/convert_util.rb
 - lib/protk/data/ExecutePipeline.trf
 - lib/protk/data/FeatureFinderCentroided.ini
 - lib/protk/data/FeatureFinderIsotopeWavelet.ini
+- lib/protk/data/apt-get_packages.yaml
+- lib/protk/data/brew_packages.yaml
+- lib/protk/data/default_config.yml
 - lib/protk/data/galaxyenv.sh
-- lib/protk/data/pepxml_mascot_template.xml
+- lib/protk/data/make_uniprot_table.rb
 - lib/protk/data/predefined_db.crap.yaml
 - lib/protk/data/predefined_db.sphuman.yaml
 - lib/protk/data/predefined_db.swissprot_annotation.yaml
 - lib/protk/data/predefined_db.swissprot_fasta_annotation.yaml
-- lib/protk/data/predefined_db.trembl_annotation.yaml
 - lib/protk/data/tandem_params.xml
 - lib/protk/data/taxonomy_template.xml
 - lib/protk/data/unimod.xml
@@ -297,34 +306,53 @@ files:
 - lib/protk/data/uniprot_accessions_table.txt
 - lib/protk/data/uniprot_input_accessions.loc
 - lib/protk/data/yum_packages.yaml
-- ext/protk/decoymaker/decoymaker.c
-- ext/protk/simplealign/simplealign.c
-- ext/protk/decoymaker/extconf.rb
-- ext/protk/simplealign/extconf.rb
+- lib/protk/eupathdb_gene_information_table.rb
+- lib/protk/fastadb.rb
+- lib/protk/galaxy_stager.rb
+- lib/protk/galaxy_util.rb
+- lib/protk/gapped_aligner.rb
+- lib/protk/manage_db_rakefile.rake
+- lib/protk/manage_db_tool.rb
+- lib/protk/mascot_util.rb
+- lib/protk/omssa_util.rb
+- lib/protk/openms_defaults.rb
+- lib/protk/pepxml.rb
+- lib/protk/plasmodb.rb
+- lib/protk/prophet_tool.rb
+- lib/protk/protein_annotator.rb
+- lib/protk/protxml.rb
+- lib/protk/randomize.rb
+- lib/protk/search_tool.rb
+- lib/protk/setup_rakefile.rake
+- lib/protk/setup_tool.rb
+- lib/protk/spreadsheet_extensions.rb
+- lib/protk/swissprot_database.rb
+- lib/protk/tool.rb
+- lib/protk/uniprot_mapper.rb
+- lib/protk/xtandem_defaults.rb
 homepage: http://rubygems.org/gems/protk
 licenses: []
+metadata: {}
 post_install_message: Now run protk_setup.rb to install third party tools and manage_db.rb
   to install databases.
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>'
+  - - '>'
     - !ruby/object:Gem::Version
       version: 1.3.1
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.24
+rubygems_version: 2.2.1
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Proteomics Toolkit
 test_files: []
 has_rdoc: