protk 1.1.0.pre

data/bin/repair_run_summary.rb

@@ -0,0 +1,113 @@
+#!/usr/bin/env ruby
+#
+# This file is part of protk
+# Created by Ira Cooke 2/12/2011
+#
+# Repairs the msms_run_summary tag in a pepXML document to contain a specified file and datatype
+# This tool should only be used on pepXML files that contain a single msms_run_summary (eg not interprophet results)
+#
+
+
+require 'protk/constants'
+require 'protk/command_runner'
+require 'protk/tool'
+require 'libxml'
+
+include LibXML
+
+# Environment with global constants
+#
+genv=Constants.new
+
+
+# Setup specific command-line options for this tool. Other options are inherited from Tool
+#
+tool=Tool.new()
+tool.option_parser.banner = "Repair msms_run_summary tag in a pepXML file.\n\nUsage: repair_run_summary.rb [options] file1.pepXML"
+
+tool.options.new_base_name=nil
+tool.option_parser.on( '-N', '--base-name mzmlfile', 'Original MSMS spectrum file used for search' ) do |file| 
+  tool.options.new_base_name = file
+end
+
+tool.options.raw_data_type=nil
+tool.option_parser.on( '-R', '--raw-type type', 'Raw data type used for search' ) do |type| 
+  tool.options.raw_data_type = type
+end
+
+tool.options.omssa_ion_tolerance=nil
+tool.option_parser.on('--omssa-itol fitol','Add a fragment ion tolerance parameter to the omssa search summary') do |fitol|
+  tool.options.omssa_ion_tolerance=fitol
+end
+
+tool.option_parser.parse!
+
+pepxml_file=ARGV[0]
+
+# Read the input file
+#
+parser=XML::Parser.file(pepxml_file)
+doc=parser.parse
+
+new_base_name=tool.new_base_name
+raw_data_type=tool.raw_data_type
+
+genv.log("Repairing #{pepxml_file} to #{new_base_name} format #{raw_data_type}",:info)
+
+if ( new_base_name==nil )
+  # Try X!Tandem first 
+  # It would be parameter spectrum,path
+  #
+  spectrum_path = doc.find('//xmlns:msms_run_summary/xmlns:search_summary/xmlns:parameter[@name="spectrum, path"]','xmlns:http://regis-web.systemsbiology.net/pepXML')[0]
+  if ( spectrum_path!=nil)
+    new_base_name=spectrum_path.attributes['value']
+    raw_data_type="mzML" # Always is for X!Tandem
+  end
+end
+
+if ( new_base_name==nil )
+  # Try Mascot 
+  # It would be parameter File path
+  #
+  #<parameter name="FILE" value="dataset_2.dat"/>
+  file_path = doc.find('//xmlns:msms_run_summary/xmlns:search_summary/xmlns:parameter[@name="FILE"]','xmlns:http://regis-web.systemsbiology.net/pepXML')[0]
+  if ( file_path!=nil)
+    
+    run_summary=doc.find('//xmlns:msms_run_summary','xmlns:http://regis-web.systemsbiology.net/pepXML')[0]
+    old_base_name=run_summary.attributes['base_name']
+    base_dir_path=Pathname.new(old_base_name).dirname.to_s
+    
+    new_base_name="#{base_dir_path}/#{file_path.attributes['value']}"
+    raw_data_type="mgf" # Always is for Mascot
+  end
+  
+end
+
+throw "Could not find original spectrum filename in pepXML and none provided" unless new_base_name!=nil
+
+
+run_summary=doc.find('//xmlns:msms_run_summary','xmlns:http://regis-web.systemsbiology.net/pepXML')
+if ( run_summary[0]==nil)
+  # Try without namespace (OMSSA)
+  run_summary=doc.find('//msms_run_summary')
+  
+  if ( tool.options.omssa_ion_tolerance !=nil)
+    search_summary=doc.find('//search_summary')[0]
+    p search_summary
+    pmnode=XML::Node.new('parameter')
+    pmnode["name"]="to"
+    pmnode["value"]=tool.options.omssa_ion_tolerance.to_s
+    search_summary << pmnode
+    
+  end
+  
+  raw_data_type="mgf"
+end
+
+throw "No run summary found" unless run_summary[0]!=nil
+
+run_summary[0].attributes['base_name']=new_base_name
+run_summary[0].attributes['raw_data']=raw_data_type
+
+
+doc.save(pepxml_file)

data/bin/tandem_search.rb

@@ -0,0 +1,292 @@
+#!/usr/bin/env ruby
+#
+# This file is part of protk
+# Created by Ira Cooke 17/12/2010
+#
+# Runs an MS/MS search using the X!Tandem search engine
+#
+
+require 'protk/constants'
+require 'protk/command_runner'
+require 'protk/search_tool'
+require 'protk/xtandem_defaults'
+require 'libxml'
+
+include LibXML
+
+# Environment with global constants
+#
+genv=Constants.new
+
+# Setup specific command-line options for this tool. Other options are inherited from SearchTool
+#
+search_tool=SearchTool.new({:msms_search=>true,:background=>true,:glyco=>true,:database=>true,:explicit_output=>true,:over_write=>true,:msms_search_detailed_options=>true})
+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 ..."
+search_tool.options.output_suffix="_tandem"
+
+tandem_defaults=XTandemDefaults.new.path
+search_tool.options.tandem_params=tandem_defaults
+search_tool.option_parser.on( '-T', '--tandem-params tandem', 'XTandem parameters to use' ) do |parms| 
+  search_tool.options.tandem_params = parms
+end
+
+search_tool.options.no_pepxml=false
+search_tool.option_parser.on( '-P', '--no-pepxml', 'Dont convert to pepXML after running the search') do
+  search_tool.options.no_pepxml=true
+end
+
+search_tool.options.keep_params_files=false
+search_tool.option_parser.on( '-K', '--keep-params-files', 'Keep X!Tandem parameter files' ) do 
+  search_tool.options.keep_params_files = true
+end
+
+search_tool.option_parser.parse!
+
+
+# Set search engine specific parameters on the SearchTool object
+#
+tandem_bin="#{genv.xtandem}"
+
+throw "Could not find X!Tandem executable" unless FileTest.exists?(tandem_bin)
+
+tandem_params=search_tool.tandem_params
+
+case
+when Pathname.new(search_tool.database).exist? # It's an explicitly named db  
+  current_db=Pathname.new(search_tool.database).realpath.to_s
+else
+  current_db=search_tool.current_database :fasta
+end
+
+
+
+
+# Parse options from a parameter file (if provided), or from the default parameter file
+#
+params_parser=XML::Parser.file(tandem_params)
+std_params=params_parser.parse
+
+# Parse taxonomy template file
+#
+taxo_parser=XML::Parser.file(XTandemDefaults.new.taxonomy_path)
+taxo_doc=taxo_parser.parse
+
+# Galaxy changes things like @ to __at__ we need to change it back
+#
+def decode_modification_string(mstring)
+  mstring.gsub!("__at__","@")
+  mstring.gsub!("__oc__","{")
+  mstring.gsub!("__cc__","}")
+  mstring.gsub!("__ob__","[")
+  mstring.gsub!("__cb__","]")
+  mstring
+end
+
+def generate_parameter_doc(std_params,output_path,input_path,taxo_path,current_db,search_tool,genv)
+  
+  
+  # Set the input and output paths 
+  #
+  input_notes=std_params.find('/bioml/note[@type="input" and @label="spectrum, path"]')
+  throw "Exactly one spectrum, path note is required in the parameter file" unless input_notes.length==1
+  input_notes[0].content=input_path
+
+  output_notes=std_params.find('/bioml/note[@type="input" and @label="output, path"]')
+  throw "Exactly one output, path note is required in the parameter file" unless output_notes.length==1
+  output_notes[0].content=output_path
+  
+  # Set the path to the scoring algorithm default params. We use one from ISB
+  #
+  scoring_notes=std_params.find('/bioml/note[@type="input" and @label="list path, default parameters"]')
+  throw "Exactly one list path, default parameters note is required in the parameter file" unless scoring_notes.length==1
+  scoring_notes[0].content="#{genv.tpp_root}/bin/isb_default_input_kscore.xml"
+
+  # Taxonomy and Database
+  #  
+  db_notes=std_params.find('/bioml/note[@type="input" and @label="protein, taxon"]')
+  throw "Exactly one protein, taxon note is required in the parameter file" unless db_notes.length==1
+  db_notes[0].content=search_tool.database.downcase
+
+  taxo_notes=std_params.find('/bioml/note[@type="input" and @label="list path, taxonomy information"]')
+  throw "Exactly one list path, taxonomy information note is required in the parameter file" unless taxo_notes.length==1
+  taxo_notes[0].content=taxo_path
+
+  fragment_tol = search_tool.fragment_tol
+  
+  fmass=std_params.find('/bioml/note[@type="input" and @label="spectrum, fragment monoisotopic mass error"]')
+  p fmass
+  throw "Exactly one spectrum, fragment monoisotopic mass error note is required in the parameter file" unless fmass.length==1
+  fmass[0].content=fragment_tol.to_s
+  
+  precursor_tol = search_tool.precursor_tol
+  ptol_plus=precursor_tol*0.5
+  ptol_minus=precursor_tol*0.5
+
+  # Precursor mass matching 
+  #
+  pmass_minus=std_params.find('/bioml/note[@type="input" and @label="spectrum, parent monoisotopic mass error minus"]')
+  throw "Exactly one spectrum, parent monoisotopic mass error minus note is required in the parameter file" unless pmass_minus.length==1
+  pmass_minus[0].content=ptol_minus.to_s
+
+  pmass_plus=std_params.find('/bioml/note[@type="input" and @label="spectrum, parent monoisotopic mass error plus"]')
+  throw "Exactly one spectrum, parent monoisotopic mass error plus note is required in the parameter file" unless pmass_plus.length==1
+  pmass_plus[0].content=ptol_plus.to_s
+
+  pmass_err_units=std_params.find('/bioml/note[@type="input" and @label="spectrum, parent monoisotopic mass error units"]')
+  throw "Exactly one spectrum, parent monoisotopic mass error units note is required in the parameter file. Got #{pmass_err_units.length}" unless pmass_err_units.length==1
+  
+  
+  pmass_err_units[0].content=search_tool.precursor_tolu
+
+  if search_tool.strict_monoisotopic_mass
+    isotopic_error=std_params.find('/bioml/note[@type="input" and @label="spectrum, parent monoisotopic mass isotope error"]')
+    throw "Exactly one spectrum, parent monoisotopic mass isotope error is required in the parameter file" unless isotopic_error.length==1
+    isotopic_error[0].content="no"
+  end
+  
+  
+  # Fixed and Variable Modifications
+  #
+  unless search_tool.carbamidomethyl 
+    mods=std_params.find('/bioml/note[@type="input" and @id="carbamidomethyl-fixed"]')
+    mods.each{ |node| node.remove!}
+  end
+  
+  unless search_tool.glyco
+    mods=std_params.find('/bioml/note[@type="input" and @id="glyco-variable"]')
+    mods.each{ |node| node.remove!}    
+  end
+  
+  unless search_tool.methionine_oxidation
+    mods=std_params.find('/bioml/note[@type="input" and @id="methionine-oxidation-variable"]')
+    mods.each{ |node| node.remove!}        
+  end  
+  
+  var_mods = search_tool.var_mods.split(",").collect { |mod| mod.lstrip.rstrip }.reject {|e| e.empty? }
+  var_mods=var_mods.collect {|mod| decode_modification_string(mod) }
+  fix_mods = search_tool.fix_mods.split(",").collect { |mod| mod.lstrip.rstrip }.reject { |e| e.empty? }
+  fix_mods=fix_mods.collect {|mod| decode_modification_string(mod)}
+  
+  root_bioml_node=std_params.find('/bioml')[0]
+  
+  mod_id=1
+  var_mods.each do |vm|
+
+    mod_type="potential modification mass"
+    mod_type = "potential modification motif" if ( vm=~/[\[\]\(\)\{\}\!]/ )      
+    mod_id_label = "custom-variable-mod-#{mod_id.to_s}"
+    mod_id=mod_id+1
+    mnode=XML::Node.new('node')
+    mnode["id"]=mod_id_label
+    mnode["type"]="input"
+    mnode["label"]="residue, #{mod_type}"
+    mnode.content=vm
+    
+    root_bioml_node << mnode
+  end
+  
+  mod_id=1
+  fix_mods.each do |fm|
+    mod_type="modification mass"
+    mod_type = "modification motif" if ( fm=~/[\[\]\(\)\{\}\!]/ )      
+    mod_id_label = "custom-fixed-mod-#{mod_id.to_s}"
+    mod_id=mod_id+1
+    mnode=XML::Node.new('node')
+    mnode["id"]=mod_id_label
+    mnode["type"]="input"
+    mnode["label"]="residue, #{mod_type}"
+    mnode.content=fm
+    
+    root_bioml_node << mnode
+  end
+
+  #p root_bioml_node
+  std_params
+  
+end
+
+def generate_taxonomy_doc(taxo_doc,current_db,search_tool)
+
+  taxon_label=taxo_doc.find('/bioml/taxon')
+  throw "Exactly one taxon label is required in the taxonomy_template file" unless taxon_label.length==1
+  taxon_label[0].attributes['label']=search_tool.database.downcase
+
+  db_file=taxo_doc.find('/bioml/taxon/file')
+  throw "Exactly one database file is required in the taxonomy_template file" unless db_file.length==1
+  db_file[0].attributes['URL']=current_db
+
+  taxo_doc
+end
+
+# Run the search engine on each input file
+#
+ARGV.each do |filename|
+
+  input_path=Pathname.new(filename.chomp).realpath.to_s
+  output_path="#{search_tool.output_base_path(filename.chomp)}.tandem"
+
+  if ( search_tool.explicit_output==nil )
+    pepxml_path="#{output_path.match(/(.*)\.tandem$/)[1]}.pep.xml"
+  else
+    pepxml_path=search_tool.explicit_output
+  end
+  
+  output_exists=false
+  if ( !search_tool.no_pepxml && Pathname.new(pepxml_path).exist?)
+    output_exists=true
+  end
+  
+  if ( search_tool.no_pepxml && Pathname.new(output_path).exist? )
+    output_exists=true
+  end
+    
+  # Only proceed if the output file is not present or we have opted to over-write it
+  #
+  if ( search_tool.over_write || !output_exists )
+
+    # Create the taxonomy file in the same directory as the params file
+    # 
+    taxo_path="#{search_tool.input_base_path(filename.chomp)}.taxonomy.xml"
+    mod_taxo_doc=generate_taxonomy_doc(taxo_doc,current_db,search_tool)
+    mod_taxo_doc.save(taxo_path)
+
+    # Modify the default XML document to contain search specific details and save it so it can be used in the search
+    #    
+    mod_params=generate_parameter_doc(std_params,output_path,input_path,taxo_path,current_db,search_tool,genv)
+    params_path="#{search_tool.input_base_path(filename.chomp)}.tandem.params"
+    mod_params.save(params_path)
+
+    # The basic command
+    #
+    cmd= "#{tandem_bin} #{params_path}"
+
+    # pepXML conversion and repair
+    #
+    unless search_tool.no_pepxml
+      repair_script="#{File.dirname(__FILE__)}/repair_run_summary.rb"      
+      cmd << "; #{genv.tandem2xml} #{output_path} #{pepxml_path}; #{repair_script} #{pepxml_path}; rm #{output_path}"
+    end
+
+    # Add a cleanup command unless the user wants to keep params files
+    #
+    unless search_tool.keep_params_files 
+      cmd << "; rm #{params_path}; rm #{taxo_path}"
+    end
+
+    # In case the user specified background running we need to create a jobscript path
+    #
+    jobscript_path="#{output_path}.pbs.sh"
+ 
+    # Run the search
+    #
+    job_params= {:jobid => search_tool.jobid_from_filename(filename)}
+    job_params[:queue]="lowmem"
+    job_params[:vmem]="900mb"
+    code = search_tool.run(cmd,genv,job_params,jobscript_path)
+    throw "Command failed with exit code #{code}" unless code==0
+  else
+    genv.log("Skipping search on existing file #{output_path}",:warn)        
+  end
+
+end

data/bin/template_search.rb

@@ -0,0 +1,144 @@
+#!/usr/bin/env ruby
+#
+# This file is part of protk
+# Created by Ira Cooke 14/12/2010
+#
+# Runs an MS/MS search using the MSGFPlus search engine
+#
+require 'protk/search_tool'
+
+
+# Setup specific command-line options for this tool. Other options are inherited from SearchTool
+#
+search_tool=SearchTool.new({:msms_search=>true,:background=>false,:glyco=>true,:database=>true,:explicit_output=>true,:over_write=>true,:msms_search_detailed_options=>true})
+search_tool.option_parser.banner = "Run an msms search on a set of msms spectrum input files.\n\nUsage: template_search.rb [options] file1.mzML file2.mzML ..."
+search_tool.options.output_suffix="_template"
+
+search_tool.options.custom_option="default"
+search_tool.option_parser.on('--custom-opt value','Custom option relevant to this tool only (Default default)') do |val|
+  search_tool.options.custom_option=val
+end
+  
+search_tool.option_parser.parse!
+
+# Set search engine specific parameters on the SearchTool object
+#
+msgf_bin="#{genv.msgf_bin}/MSGFPlus.jar"
+
+case 
+when Pathname.new(search_tool.database).exist? # It's an explicitly named db
+  current_db=Pathname.new(search_tool.database).realpath.to_s
+else
+  current_db=search_tool.current_database :fasta
+end
+
+fragment_tol = search_tool.fragment_tol
+precursor_tol = search_tool.precursor_tol
+
+
+throw "When --output is set only one file at a time can be run" if  ( ARGV.length> 1 ) && ( search_tool.explicit_output!=nil ) 
+
+# Run the search engine on each input file
+#
+ARGV.each do |filename|
+
+  if ( search_tool.explicit_output!=nil)
+    output_path=search_tool.explicit_output
+  else
+    output_path="#{search_tool.output_base_path(filename.chomp)}.mzid"
+  end
+  
+  # (*.mzML, *.mzXML, *.mgf, *.ms2, *.pkl or *_dta.txt)
+  # Get the input file extension
+  ext = Pathname.new(filename).extname
+
+
+
+  input_path="#{search_tool.input_base_path(filename.chomp)}#{ext}"
+
+  # Only proceed if the output file is not present or we have opted to over-write it
+  #
+  if ( search_tool.over_write || !Pathname.new(output_path).exist? )
+  
+    # The basic command
+    #
+    cmd= "java -Xmx#{search_tool.java_mem} -jar #{msgf_bin} -d #{current_db} -s #{input_path} -o #{output_path} "
+
+    #Missed cleavages
+    #
+    throw "Maximum value for missed cleavages is 2" if ( search_tool.missed_cleavages > 2)
+    cmd << " -ntt #{search_tool.missed_cleavages}"
+
+    # Precursor tolerance
+    #
+    cmd << " -t #{search_tool.precursor_tol}#{search_tool.precursor_tolu}"
+    
+    # Instrument type
+    #
+    cmd << " -inst 2"
+    
+#    cmd << " -m 4"
+
+    cmd << " -addFeatures 1"
+
+    # Enzyme
+    #
+  #    if ( search_tool.enzyme!="Trypsin")
+  #      cmd << " -e #{search_tool.enzyme}"
+  #    end
+
+  mods_path="#{search_tool.input_base_path(filename.chomp)}.msgfplus_mods.txt"
+  mods_file=File.open(mods_path,'w+')
+
+    # Variable Modifications
+    #
+    if ( search_tool.var_mods !="" && !search_tool.var_mods =~/None/) # Checking for none is to cope with galaxy input
+      var_mods = search_tool.var_mods.split(",").collect { |mod| mod.lstrip.rstrip }.reject {|e| e.empty? }.join(",")
+      if ( var_mods !="" )
+        cmd << " -mv #{var_mods}"
+      end
+    else 
+      # Add options related to peptide modifications
+      #
+      if ( search_tool.glyco )
+        cmd << " -mv 119 "
+      end
+    end
+
+  # Fixed modifications
+  #
+    if ( search_tool.fix_mods !="" && !search_tool.fix_mods=~/None/)
+      fix_mods = search_tool.fix_mods.split(",").collect { |mod| mod.lstrip.rstrip }.reject { |e| e.empty? }.join(",")
+      if ( fix_mods !="")
+        cmd << " -mf #{fix_mods}"    
+      end
+    else
+      if ( search_tool.has_modifications )
+        cmd << " -mf "
+        if ( search_tool.carbamidomethyl )
+          cmd<<"3 "
+        end
+
+        if ( search_tool.methionine_oxidation )
+          cmd<<"1 "
+        end
+
+      end
+    end
+    
+    # Up to here we've formulated the omssa command. The rest is cleanup
+    p "Running:#{cmd}"
+    
+    # Run the search
+    #
+    job_params= {:jobid => search_tool.jobid_from_filename(filename) }
+    job_params[:queue]="lowmem"
+    job_params[:vmem]="900mb"    
+    search_tool.run(cmd,genv,job_params)
+
+
+  else
+    genv.log("Skipping search on existing file #{output_path}",:warn)       
+  end
+
+end

data/bin/unimod_to_loc.rb

@@ -0,0 +1,118 @@
+#!/usr/bin/env ruby
+#
+# This file is part of MSLIMS
+# Created by Ira Cooke 12/4/2010
+#
+# Reads a unimod xml file (eg from a Mascot installation) and produces a loc file with names of allowable chemical modifications
+#
+
+require 'libxml'
+
+include LibXML
+
+unimod_file=ARGV[0]
+
+unimod_file=XML::Parser.file(unimod_file)
+unimod_doc=unimod_file.parse
+
+
+all_mods=[]
+
+umd = unimod_doc.find('//umod:unimod/umod:modifications/umod:mod')
+
+umd.each { |mod| 
+  
+  # Special Cases
+  #
+  title=mod.attributes['title']
+  if ( title=="Oxidation" || title=="Phospho" || title=="Sulfo")
+    if ( title=="Oxidation")
+      all_mods.push("Oxidation (HW)")
+      all_mods.push("Oxidation (M)")
+    end
+    
+    if ( title=="Phospho")
+      all_mods.push("Phospho (ST)")
+      all_mods.push("Phospho (Y)")      
+    end
+    
+    if ( title=="Sulfo")
+      all_mods.push("Sulfo (S)")
+      all_mods.push("Sulfo (T)")      
+      all_mods.push("Sulfo (Y)")      
+    end
+    
+  else
+  
+    # Deal with the anywhere sites which can be concatenated
+    #
+    if ( mod.attributes['title'] !~ /^iTRAQ/ && mod.attributes['title'] !~ /^mTRAQ/ )
+      anywhere_sites = mod.find('./umod:specificity[@hidden="0" and @position="Anywhere"]')
+      if ( anywhere_sites.length>0 )
+
+        sites=[]
+
+        anywhere_sites.each { |s| 
+          sites.push("#{s.attributes['site']}")
+        }
+        sites.sort!
+        specificity="("
+        sites.each { |s| specificity<<s }
+        specificity<<")"
+
+        all_mods.push("#{mod.attributes['title']} #{specificity}")
+         
+      end    
+    
+    else
+      anywhere_sites = mod.find('./umod:specificity[@hidden="0" and @position="Anywhere"]')
+      anywhere_sites.each { |s| 
+        all_mods.push("#{mod.attributes['title']} (#{s.attributes['site']})")    
+      }
+    end
+
+    specifics=mod.find('./umod:specificity[@hidden="0" and @position!="Anywhere"]')
+    if ( specifics.length > 0 )
+      specifics.each { |specific_mod|
+
+        specificity=specific_mod.attributes['site']
+        if ( specific_mod.attributes['position'] =~ /^Protein/)
+          specificity=specific_mod.attributes['position']
+        end
+
+        if ( (specific_mod.attributes['position'] =~ /Any N-term/) && (specific_mod.attributes['site'] =~ /^[CQEM]$/) )
+          specificity="N-term #{specific_mod.attributes['site']}"
+        end
+
+        if ( (specific_mod.attributes['position'] =~ /Any C-term/) && (specific_mod.attributes['site'] =~ /^[M]$/) )
+          specificity="C-term #{specific_mod.attributes['site']}"
+        end
+
+        all_mods.push("#{mod.attributes['title']} (#{specificity})")
+        
+      }
+      
+    end
+    
+  end
+  
+}
+
+
+all_mods=all_mods.sort {|a,b| a.downcase <=> b.downcase}
+
+loc_output=File.new("mascot_mods.loc",'w')
+
+loc_output << "#This file lists the names of chemical modifications acceptable for proteomics search engines\n"
+loc_output << "#\n"
+loc_output << "#So, unimod_names.loc could look something like this:\n"
+loc_output << "#\n"
+
+all_mods.each { |am| 
+  key = am.downcase.gsub(" ","").gsub("\(","\_").gsub("\)","\_").gsub("\:","\_").gsub("\-\>","\_")
+  loc_output << "#{am}\t#{key}\t#{am}\t#{key}\n"
+}
+
+loc_output.close
+
+