protk 1.2.6.pre5 → 1.3.0.pre1

data/bin/peptide_prophet.rb

@@ -17,102 +17,34 @@ input_stager = nil
 
 # Setup specific command-line options for this tool. Other options are inherited from ProphetTool
 #
-prophet_tool=ProphetTool.new([:glyco,:explicit_output,:over_write,:maldi,:prefix_suffix])
+prophet_tool=ProphetTool.new([
+  :glyco,
+  :explicit_output,
+  :over_write,
+  :maldi,
+  :prefix,
+  :database])
 prophet_tool.option_parser.banner = "Run PeptideProphet on a set of pep.xml input files.\n\nUsage: peptide_prophet.rb [options] file1.pep.xml file2.pep.xml ..."
-prophet_tool.options.output_suffix="_pproph"
-
-prophet_tool.options.useicat = false
-prophet_tool.option_parser.on( '--useicat',"Use icat information" ) do 
-  prophet_tool.options.useicat = true
-end
-
-prophet_tool.options.nouseicat = false
-prophet_tool.option_parser.on( '--no-useicat',"Do not use icat information" ) do 
-  prophet_tool.options.nouseicat = true
-end
-
-prophet_tool.options.phospho = false
-prophet_tool.option_parser.on( '--phospho',"Use phospho information" ) do 
-  prophet_tool.options.phospho = true
-end
-
-prophet_tool.options.usepi = false
-prophet_tool.option_parser.on( '--usepi',"Use pI information" ) do 
-  prophet_tool.options.usepi = true
-end
-
-prophet_tool.options.usert = false
-prophet_tool.option_parser.on( '--usert',"Use hydrophobicity / RT information" ) do 
-  prophet_tool.options.usert = true
-end
-
-prophet_tool.options.accurate_mass = false
-prophet_tool.option_parser.on( '--accurate-mass',"Use accurate mass binning" ) do 
-  prophet_tool.options.accurate_mass = true
-end
-
-prophet_tool.options.no_ntt = false
-prophet_tool.option_parser.on( '--no-ntt',"Don't use NTT model" ) do 
-  prophet_tool.options.no_ntt = true
-end
-
-prophet_tool.options.no_nmc = false
-prophet_tool.option_parser.on( '--no-nmc',"Don't use NMC model" ) do 
-  prophet_tool.options.no_nmc = true
-end
-
-prophet_tool.options.usegamma = false
-prophet_tool.option_parser.on( '--usegamma',"Use Gamma distribution to model the negatives" ) do 
-  prophet_tool.options.usegamma = true
-end
-
-prophet_tool.options.use_only_expect = false
-prophet_tool.option_parser.on( '--use-only-expect',"Only use Expect Score as the discriminant" ) do 
-  prophet_tool.options.use_only_expect = true
-end
-
-prophet_tool.options.force_fit = false
-prophet_tool.option_parser.on( '--force-fit',"Force fitting of mixture model and bypass checks" ) do 
-  prophet_tool.options.force_fit = true
-end
-
-prophet_tool.options.allow_alt_instruments=false
-prophet_tool.option_parser.on( '--allow-alt-instruments',"Warning instead of exit with error if instrument types between runs is different" ) do 
-  prophet_tool.options.allow_alt_instruments = true
-end
-
-prophet_tool.options.one_ata_time = false
-prophet_tool.option_parser.on( '-F', '--one-ata-time', 'Create a separate pproph output file for each analysis' ) do 
-  prophet_tool.options.one_ata_time = true
-end
-
-prophet_tool.options.decoy_prefix="decoy"
-prophet_tool.option_parser.on( '--decoy-prefix prefix', 'Prefix for decoy sequences') do |prefix|
-  prophet_tool.options.decoy_prefix = prefix
-end 
-
-prophet_tool.options.no_decoys = false
-prophet_tool.option_parser.on( '--no-decoy', 'Don\'t use decoy sequences to pin down the negative distribution') do 
-  prophet_tool.options.no_decoys = true
-end
-
-prophet_tool.options.experiment_label=nil
-prophet_tool.option_parser.on('--experiment-label label','used to commonly label all spectra belonging to one experiment (required by iProphet)') do |label|
-  prophet_tool.options.experiment_label = label
-end  
-
-prophet_tool.options.override_database=nil
-prophet_tool.option_parser.on( '--override-database database', 'Manually specify database') do |database|
-  prophet_tool.options.override_database = database
-end
-
-exit unless prophet_tool.check_options 
-
-if ( ARGV[0].nil? )
-    puts "You must supply an input file"
-    puts prophet_tool.option_parser 
-    exit
-end
+@output_suffix="_pproph"
+prophet_tool.options.database=nil
+
+prophet_tool.add_boolean_option(:useicat,false,['--useicat',"Use icat information"])
+prophet_tool.add_boolean_option(:phospho,false,['--phospho',"Use phospho information"])
+prophet_tool.add_boolean_option(:usepi,false,['--usepi',"Use pI information"])
+prophet_tool.add_boolean_option(:usert,false,['--usert',"Use hydrophobicity / RT information"])
+prophet_tool.add_boolean_option(:accurate_mass,false,['--accurate-mass',"Use accurate mass binning"])
+prophet_tool.add_boolean_option(:no_ntt,false,['--no-ntt',"Don't use NTT model"])
+prophet_tool.add_boolean_option(:no_nmc,false,['--no-nmc',"Don't use NMC model"])
+prophet_tool.add_boolean_option(:usegamma,false,['--usegamma',"Use Gamma distribution to model the negatives"])
+prophet_tool.add_boolean_option(:use_only_expect,false,['--use-only-expect',"Only use Expect Score as the discriminant"])
+prophet_tool.add_boolean_option(:force_fit,false,['--force-fit',"Force fitting of mixture model and bypass checks"])
+prophet_tool.add_boolean_option(:allow_alt_instruments,false,['--allow-alt-instruments',"Warning instead of exit with error if instrument types between runs is different"])
+prophet_tool.add_boolean_option(:one_ata_time,false,['-F', '--one-ata-time', 'Create a separate pproph output file for each analysis'])
+prophet_tool.add_value_option(:decoy_prefix,"decoy",['--decoy-prefix prefix', 'Prefix for decoy sequences'])
+prophet_tool.add_boolean_option(:no_decoys,false,['--no-decoy', 'Don\'t use decoy sequences to pin down the negative distribution'])
+prophet_tool.add_value_option(:experiment_label,nil,['--experiment-label label','used to commonly label all spectra belonging to one experiment (required by iProphet)'])
+
+exit unless prophet_tool.check_options(true)
 
 throw "When --output and -F options are set only one file at a time can be run" if  ( ARGV.length> 1 ) && ( prophet_tool.explicit_output!=nil ) && (prophet_tool.one_ata_time!=nil)
 
@@ -133,10 +65,11 @@ inputs.each {|file_name|
   name=file_name.chomp
   
   engine=prophet_tool.extract_engine(name)
-  if prophet_tool.override_database
-    db_path = prophet_tool.override_database
+  if prophet_tool.database
+    db_path = prophet_tool.database_info.path
   else
     db_path=prophet_tool.extract_db(name)
+    throw "Unable to find database #{db_path} used for searching. Specify database path using -d option" unless File.exist?(db_path)
   end
   
   
@@ -157,10 +90,10 @@ inputs=file_info.collect do |info|
   end
   throw "All files to be analyzed must have been searched with the same database and search engine" unless (info[1][:engine]==engine) && (info[1][:database])
 
-  retname=  "#{prophet_tool.input_base_path(info[0],".pep.xml")}.pep.xml"
-  if ( info[0]=~/\.dat$/)
-    retname=info[0]
-  end
+  retname=  info[0]
+  # if ( info[0]=~/\.dat$/)
+  #   retname=info[0]
+  # end
       
   retname
 
@@ -219,9 +152,7 @@ def generate_command(genv,prophet_tool,inputs,output,database,engine)
   
   if prophet_tool.useicat
     cmd << " -Oi "
-  end
-  
-  if prophet_tool.nouseicat
+  else
     cmd << " -Of"
   end
   
@@ -255,9 +186,7 @@ def run_peptide_prophet(genv,prophet_tool,cmd,output_path,engine)
   if ( !prophet_tool.over_write && Pathname.new(output_path).exist? )
     genv.log("Skipping analysis on existing file #{output_path}",:warn)   
   else
-    jobscript_path="#{output_path}.pbs.sh"
-    job_params={:jobid=>engine, :vmem=>"900mb", :queue => "lowmem"}
-    code=prophet_tool.run(cmd,genv,job_params,jobscript_path)
+    code=prophet_tool.run(cmd,genv)
     throw "Command failed with exit code #{code}" unless code==0
   end
 end
@@ -265,27 +194,23 @@ end
 
 cmd=""
 if ( prophet_tool.one_ata_time )
-  inputs.each { |input|
-    
-    output_file_name="#{prophet_tool.output_prefix}#{input}_#{engine}_interact#{prophet_tool.output_suffix}.pep.xml"
+  
+  inputs.each do |input|
+    output_file_name=Tool.default_output_path(input,".pep.xml",prophet_tool.output_prefix,@output_suffix)
     
     cmd=generate_command(genv,prophet_tool,input,output_file_name,database,engine)
+    run_peptide_prophet(genv,prophet_tool,cmd,output_file_name,engine)        
+  end
 
-    run_peptide_prophet(genv,prophet_tool,cmd,output_file_base_name,engine)
-    
-        
-  }
 else  
+
   if (prophet_tool.explicit_output==nil)
-    output_file_name="#{prophet_tool.output_prefix}#{engine}_interact#{prophet_tool.output_suffix}.pep.xml"
+    output_file_name=Tool.default_output_path(inputs,".pep.xml",prophet_tool.output_prefix,@output_suffix)    
   else
-
     output_file_name=prophet_tool.explicit_output
-
   end
+
   cmd=generate_command(genv,prophet_tool,inputs,output_file_name,database,engine)
-  puts cmd
-  %x['ls']
   run_peptide_prophet(genv,prophet_tool,cmd,output_file_name,engine)
     
 end

data/bin/pepxml_to_table.rb

@@ -19,26 +19,17 @@ include LibXML
 tool=Tool.new([:explicit_output])
 tool.option_parser.banner = "Convert a pepXML file to a tab delimited table.\n\nUsage: pepxml_to_table.rb [options] file1.pep.xml"
 
-exit unless tool.check_options 
-
-if ( ARGV[0].nil? )
-    puts "You must supply an input file"
-    puts tool.option_parser 
-    exit
-end
-
-# Obtain a global environment object
-#genv=Constants.new
+exit unless tool.check_options(true)
 
 input_file=ARGV[0]
 
-output_file="#{input_file}.txt"
-
-output_file = tool.explicit_output if tool.explicit_output!=nil
-
-output_fh=File.new("#{output_file}",'w')
+if tool.explicit_output
+  output_fh=File.new("#{tool.explicit_output}",'w')  
+else
+  output_fh=$stdout
+end
 
-output_fh.write "protein\tpeptide\tassumed_charge\tcalc_neutral_pep_mass\tneutral_mass\tretention_time\tstart_scan\tend_scan\tsearch_engine\tpeptideprophet_prob\tinterprophet_prob\n"
+output_fh.write "protein\tpeptide\tassumed_charge\tcalc_neutral_pep_mass\tneutral_mass\tretention_time\tstart_scan\tend_scan\tsearch_engine\traw_score\tpeptideprophet_prob\tinterprophet_prob\n"
 
 XML::Error.set_handler(&XML::Error::QUIET_HANDLER)
 
@@ -68,18 +59,24 @@ spectrum_queries.each do |query|
   start_scan=query.attributes['start_scan']
   end_scan=query.attributes['end_scan']
 
-  search_engine=""
-  search_score_names=top_search_hit.find("./#{pepxml_ns_prefix}search_score/@name",pepxml_ns).collect {|s| s.to_s}
+  run_summary_node=query.parent
+  # puts run_summary_node
+  search_summary_node=run_summary_node.find("./#{pepxml_ns_prefix}search_summary",pepxml_ns)[0]
+   # puts search_summary_node.attributes.each { |e| puts e }
+  search_engine=search_summary_node.attributes['search_engine']
+
+  # search_engine=""
 
-  search_engine=query.parent.attributes['search_engine']
 
-  # if ( search_score_names.length==2 && search_score_names.grep(/^name.*=.*pvalue/))
-  #   search_engine="omssa" 
-  # elsif ( search_score_names.grep(/^name.*=.*ionscore/))
-  #   search_engine="mascot"
-  # elsif ( search_score_names.grep(/^name.*=.*hyperscore/) )
-  #   search_engine="x!tandem"
-  # end
+  raw_score=""
+  case search_engine
+  when /[Tt]andem/
+    search_score_nodes=top_search_hit.find("./#{pepxml_ns_prefix}search_score[@name=\"expect\"]",[pepxml_ns])
+    raw_score=search_score_nodes[0].attributes['value']
+  when /MS\-GF/
+    search_score_nodes=top_search_hit.find("./#{pepxml_ns_prefix}search_score[@name=\"EValue\"]",[pepxml_ns])
+    raw_score=search_score_nodes[0].attributes['value']    
+  end
 
   
   pp_result=top_search_hit.find("./#{pepxml_ns_prefix}analysis_result/#{pepxml_ns_prefix}peptideprophet_result/@probability",pepxml_ns)
@@ -90,7 +87,7 @@ spectrum_queries.each do |query|
   peptide_prophet_prob=pp_result[0].value if ( pp_result.length>0 )
   interprophet_prob=ip_result[0].value if ( ip_result.length>0)
   
-  output_fh.write "#{protein}\t#{peptide}\t#{assumed_charge}\t#{calc_neutral_pep_mass}\t#{neutral_mass}\t#{retention_time}\t#{start_scan}\t#{end_scan}\t#{search_engine}\t#{peptide_prophet_prob}\t#{interprophet_prob}\n"
+  output_fh.write "#{protein}\t#{peptide}\t#{assumed_charge}\t#{calc_neutral_pep_mass}\t#{neutral_mass}\t#{retention_time}\t#{start_scan}\t#{end_scan}\t#{search_engine}\t#{raw_score}\t#{peptide_prophet_prob}\t#{interprophet_prob}\n"
 
 end
 

data/bin/protein_prophet.rb

@@ -17,98 +17,41 @@ for_galaxy = GalaxyUtil.for_galaxy?
 
 # Setup specific command-line options for this tool. Other options are inherited from ProphetTool
 #
-prophet_tool=ProphetTool.new([:glyco,:explicit_output,:over_write,:prefix_suffix])
+prophet_tool=ProphetTool.new([:glyco,:explicit_output,:over_write,:prefix])
 prophet_tool.option_parser.banner = "Run ProteinProphet on a set of pep.xml input files.\n\nUsage: protein_prophet.rb [options] file1.pep.xml file2.pep.xml ..."
-prophet_tool.options.output_suffix="_protproph"
 
-prophet_tool.options.iproph = false
-prophet_tool.option_parser.on( '--iprophet-input',"Inputs are from iProphet" ) do 
-  prophet_tool.options.iproph = true
-end
-
-prophet_tool.options.nooccam = false
-prophet_tool.option_parser.on( '--no-occam',"Do not attempt to derive the simplest protein list explaining observed peptides" ) do 
-  prophet_tool.options.nooccam = true
-end
-
-prophet_tool.options.groupwts = false
-prophet_tool.option_parser.on( '--group-wts',"Check peptide's total weight (rather than actual weight) in the Protein Group against the threshold" ) do 
-  prophet_tool.options.groupwts = true
-end
-
-prophet_tool.options.normprotlen = false
-prophet_tool.option_parser.on( '--norm-protlen',"Normalize NSP using Protein Length" ) do 
-  prophet_tool.options.normprotlen = true
-end
+@output_suffix="_protproph"
 
-prophet_tool.options.logprobs = false
-prophet_tool.option_parser.on( '--log-prob',"Use the log of probability in the confidence calculations" ) do 
-  prophet_tool.options.logprobs = true
-end
-
-prophet_tool.options.confem = false
-prophet_tool.option_parser.on( '--confem',"Use the EM to compute probability given the confidence" ) do 
-  prophet_tool.options.confem = true
-end
-
-prophet_tool.options.allpeps = false
-prophet_tool.option_parser.on( '--allpeps',"Consider all possible peptides in the database in the confidence model" ) do 
-  prophet_tool.options.allpeps = true
-end
-
-prophet_tool.options.unmapped = false
-prophet_tool.option_parser.on( '--unmapped',"Report results for unmapped proteins" ) do 
-  prophet_tool.options.unmapped = true
-end
-
-prophet_tool.options.instances = false
-prophet_tool.option_parser.on( '--instances',"Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment" ) do 
-  prophet_tool.options.instances = true
-end
-
-prophet_tool.options.delude = false
-prophet_tool.option_parser.on( '--delude',"Do NOT use peptide degeneracy information when assessing proteins" ) do 
-  prophet_tool.options.delude = true
-end
-
-prophet_tool.options.minprob = 0.05
-prophet_tool.option_parser.on( '--minprob mp',"Minimum peptide prophet probability for peptides to be considered" ) do |mp|
-  prophet_tool.options.minprob = mp
-end
-
-prophet_tool.options.minindep = 0
-prophet_tool.option_parser.on( '--minindep mp',"Minimum percentage of independent peptides required for a protein" ) do |mp|
-  prophet_tool.options.minindep = mp
-end
-
-exit unless prophet_tool.check_options 
-
-if ( ARGV[0].nil? )
-    puts "You must supply an input file"
-    puts prophet_tool.option_parser 
-    exit
-end
+prophet_tool.add_boolean_option(:iproph,false,['--iprophet-input',"Inputs are from iProphet"])
+prophet_tool.add_boolean_option(:nooccam,false,['--no-occam',"Do not attempt to derive the simplest protein list explaining observed peptides"])
+prophet_tool.add_boolean_option(:groupwts,false,['--group-wts',"Check peptide's total weight (rather than actual weight) in the Protein Group against the threshold"])
+prophet_tool.add_boolean_option(:normprotlen,false,['--norm-protlen',"Normalize NSP using Protein Length"])
+prophet_tool.add_boolean_option(:logprobs,false,['--log-prob',"Use the log of probability in the confidence calculations"])
+prophet_tool.add_boolean_option(:confem,false,['--confem',"Use the EM to compute probability given the confidence"])
+prophet_tool.add_boolean_option(:allpeps,false,['--allpeps',"Consider all possible peptides in the database in the confidence model"])
+prophet_tool.add_boolean_option(:unmapped,false,['--unmapped',"Report results for unmapped proteins"])
+prophet_tool.add_boolean_option(:instances,false,['--instances',"Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment"])
+prophet_tool.add_boolean_option(:delude,false,['--delude',"Do NOT use peptide degeneracy information when assessing proteins"])
+prophet_tool.add_value_option(:minprob,0.05,['--minprob mp',"Minimum peptide prophet probability for peptides to be considered"])
+prophet_tool.add_value_option(:minindep,0,['--minindep mp',"Minimum percentage of independent peptides required for a protein"])
 
+exit unless prophet_tool.check_options(true)
 
 # Obtain a global environment object
 genv=Constants.new
 
-if ( prophet_tool.explicit_output==nil )
-	output_file="#{prophet_tool.output_prefix}interact#{prophet_tool.output_suffix}.prot.xml"
- else 
-	output_file=prophet_tool.explicit_output 
-end
+inputs = ARGV.collect {|file_name| file_name.chomp }
 
-p output_file
+if ( prophet_tool.explicit_output )
+  output_file=prophet_tool.explicit_output
+else
+  output_file=Tool.default_output_path(inputs,".prot.xml",prophet_tool.output_prefix,@output_suffix)
+end
 
 if ( !Pathname.new(output_file).exist? || prophet_tool.over_write )
 
   cmd="ProteinProphet NOPLOT "
 
-  inputs = ARGV.collect {|file_name| 
-    file_name.chomp
-  }
-
   if for_galaxy
     inputs = inputs.collect {|ip| GalaxyUtil.stage_pepxml(ip) }
   end
@@ -122,10 +65,7 @@ if ( !Pathname.new(output_file).exist? || prophet_tool.over_write )
 
   # Run the analysis
   #
-  jobscript_path="#{output_file}.pbs.sh"
-  job_params={:jobid=>"protproph", :vmem=>"900mb", :queue => "lowmem"}
-  genv.log("Running #{cmd}",:info)
-  code = prophet_tool.run(cmd,genv,job_params,jobscript_path)
+  code = prophet_tool.run(cmd,genv)
   throw "Command failed with exit code #{code}" unless code==0
 else
   genv.log("Protein Prophet output file #{output_file} already exists. Run with -r option to replace",:warn)