protk 1.2.6.pre5 → 1.3.0.pre1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 876bb41de9b07d9a9b08132e2d44439e6de0c990
-  data.tar.gz: 799b9dd4c2a8c3720e315a7ade0085a7f54f31f9
+  metadata.gz: 5aa7ddfc73e97717cd296b99ad7796420af4af80
+  data.tar.gz: 8872996c6ff14306573ca698736dac00e34c43fa
 SHA512:
-  metadata.gz: db8bf6c295925c649431ce25eccf10c55a15c4146f827d9ed9f55ad95f8ad50f3fc7aed04cf6d9a78d5311244e4ba7fd6e8954f068b50385f852a9b729c1e017
-  data.tar.gz: 312cd4aefc3380cd2311c41d0dac8dacf40d4f58a404fb6c86ed67e9454895f877ad7a465c55c8d3a721fd10e4a78b709975be3c530ed87502f9da4adbcfa35f
+  metadata.gz: 8b9162aaf5c6ee9c54e0f089e2499b47735eb12c325e35564b7b312d0553e5b09e7ea37114effd033b2b36f4646ad3080124cb31399288d5aac849fd8df894b8
+  data.tar.gz: 7f65f321c1f5909af31a059e843a96a8ea9c9522dac6423abad2d6987d733e766907630cb8a5a31b616cc26830d6e66219106fd66a239e1d19f69eabb6a90e26

data/README.md

@@ -7,20 +7,44 @@
 ***
 ## What is it?
 
-Protk is a wrapper for various proteomics tools. It aims to present a consistent interface to a wide variety of tools and provides support for managing protein databases. 
+Protk is a suite of tools for proteomics. It aims to present a simple and consistent command-line interface across otherwise disparate third party tools.  The following analysis tasks are currently supported; 
+
+- Tandem MS search with X!Tandem, Mascot, OMSSA and MS-GF+
+- Peptide and Protein inference with Peptide Prophet, iProphet and Protein Prophet
+- Conversion of pepXML or protXML to tabulular format
 
 
 ## Installation
  
-The easiest intallation method is to use rubygems.  You might need to install the libxml2 package on your system first (eg libxml-dev on Ubuntu)
+Protk is a ruby gem and requires ruby 2.0 or higher with support for libxml2. To avoid installation problems we recommend using [rvm](https://rvm.io) to install ruby.
 
 ``` shell
     gem install protk
 ```
 
-## Configuration
 
-By default protk will install tools and databases into `.protk` in your home directory.  If this is not desirable you can change the protk root default by setting the environment variable `PROTK_INSTALL_DIR`. You can also avoid using a `.protk` directory altogether (see below)
+
+## Usage
+
+Protk consists of a suite of small ruby programs.  After installing the protk rubygem the following should be available for running in your shell.  Help can be obtained on using any program by typing its name without any arguments.  Note than many protk programs require third party tools to be installed, see [Configuration](#user-content-configuration) below for instructions on installing these.
+
+- `tandem_search.rb` Run an X!Tandem search. Requires [X!Tandem](http://www.thegpm.org/TANDEM/)
+- `mascot_search.rb` Run a Mascot search. Requires a [Mascot](http://www.matrixscience.com/server.html) server
+- `msgfplus_search.rb` Run an MS-GF+ search. Requires [MS-GF+](https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355)
+- `omssa_search.rb` Run an OMSSA search. Requires [OMSSA](ftp://ftp.ncbi.nih.gov/pub/lewisg/omssa/CURRENT/)
+- `peptide_prophet.rb` Perform peptide inference based on search engine scores. Requires the [TPP](http://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/)
+- `interprophet.rb` Perform peptide inference across multiple search engines. Requires the [TPP](http://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/)
+- `protein_prophet.rb` Perform protein inference. Requires the [TPP](http://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/)
+- `mascot_to_pepxml.rb` Convert raw mascot dat files to pepXML. Requires the [TPP](http://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/)
+- `tandem_to_pepxml.rb` Convert raw X!Tandem outputs to pepXML. Requires the [TPP](http://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/)
+- `pepxml_to_table.rb` Convert pepXML to tabular format
+- `protxml_to_table.rb` Convert protXML to tabular format
+- `make_decoy.rb` Generate semi-random decoy sequences
+- `sixframe.rb` Generate six-frame translations of DNA sequences
+- `protk_setup.rb` Install third party dependencies
+- `manage_db.rb` Manage protein databases
+
+## Configuration
 
 Protk includes a setup tool to install various third party proteomics tools such as the TPP, OMSSA, MS-GF+, Proteowizard.  If this tool is used it installs everything under `.protk/tools`.  To perform such an installation use;
 
@@ -28,16 +52,12 @@ Protk includes a setup tool to install various third party proteomics tools such
     protk_setup.rb tpp omssa blast msgfplus pwiz
 ```
 
-Alternatively, these tools may already be present on your system, or you may prefer to install them yourself.  In that case simply ensure that all executables are included in your `$PATH`. Those executables will be used as a fallback if nothing is available under the `.protk` installation directory.
-
-
-Instead off using protk_setup.rb all it might be preferable to only install some of the protk tool dependencies.  'all' is just an alias for the following full target list, any of which can be omitted with the consequence that tools depending on that component will not be available.
-
+By default protk will install tools and databases into `.protk` in your home directory.  If this is not desirable you can change the protk root default by setting the environment variable `PROTK_INSTALL_DIR`. If you prefer to install the tools yourself protk will find them provided they are included in your `$PATH`. Those executables will be used as a fallback if nothing is available under the `.protk` installation directory.
 
 
 ## Sequence databases
 
-After running the setup.sh script you should run manage_db.rb to install specific sequence databases for use by the search engines. Protk comes with several predefined database configurations. For example, to install a database consisting of human entries from Swissprot plus known contaminants use the following commands;
+Protk also includes a script called manage_db.rb to install specific sequence databases for use by the search engines if desired. Databases installed via manage_db.rb can be invoked using a shorthand name rather than a full path to a fasta file, and Protk also provides some automation for database upgrades. Protk comes with several predefined database configurations. For example, to install a database consisting of human entries from Swissprot plus known contaminants use the following commands;
 
 ```sh
 manage_db.rb add --predefined crap
@@ -52,54 +72,73 @@ You should now be able to run database searches, specifying this database by usi
 manage_db.rb add --ftp-source 'ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/reldate.txt' --include-filters '/OS=Homo\ssapiens/' --id-regex 'sp\|.*\|(.*?)\s' --add-decoys --make-blast-index --archive-old sphuman
 ```
 
-## Annotation databases
+## Galaxy Integration
 
-The manage_db.rb script also deals with annotation databases.  Actually at this stage the only useful annotation database it has support for is the Swissprot Uniprot database which contains detailed information on protein entries.  The following commands download and index this database.
+Many protk tools have equivalent galaxy wrappers available on the [galaxy toolshed](http://toolshed.g2.bx.psu.edu/) .  In order for these tools to work you will also need to make sure that protk, as well as the necessary third party dependencies are available to galaxy during tool execution. If you install protk using the default system ruby (without rvm) this will probably just work, however you will lose the ability to run specific versions of tools against specific versions of protk.  The recommended method of installing protk for use with galaxy is as follows;
 
-```sh
-manage_db.rb add --predefined swissprot_annotation
-manage_db.rb update swissprot_annotation
-```
+1. Ensure you have a working install of galaxy. 
+
+	[Full instructions](https://wiki.galaxyproject.org/Admin/GetGalaxy) are available on the official Galaxy project wiki page.  We assume you have galaxy installed in a directory called galaxy-dist.
+
+2. Install rvm if you haven't allready.  See [here](https://rvm.io/) for more information.
+
+	```bash
+		curl -sSL https://get.rvm.io | bash -s stable
+	```
+
+3. Install a compatible version of ruby using rvm. Ruby 2.0 or higher is required
+
+	```bash
+		rvm install 2.1
+	```
 
-Once this step is complete you should be able to use annotation tools such as the uniprot_annotation.rb tool
+4.  Install protk in an isolated gemset using rvm.
 
-## Galaxy integration
+	This sets up an isolated environment where only a specific version of protk is available.  We name the environment according to the protk version (1.2.6 in this example).
 
-Although all the protk tools can be run directly from the command-line a nicer way to run them (and visualise outputs) is to use the galaxy web application.
+	```bash
+		rvm 2.1
+		rvm gemset create protk1.2.6
+		rvm use 2.1@protk1.2.6
+		gem install protk -v 1.2.6
+	```
 
-The preferred method for use of protk with galaxy is to install via the [galaxy toolshed](http://toolshed.g2.bx.psu.edu).  You can find protk tools under the Proteomics heading.  You will still need to install and setup galaxy itself (step 1 below) and you should familiarise yourself with the admin functions of galaxy including tool installation.  Lots of instructions on this are available on the [toolshed wiki](http://wiki.galaxyproject.org/Tool%20Shed).  One final note is that although protk based tools are configured to automatically install their dependencies via the toolshed you should take careful note of the system packages that must be installed before proceeding.  In addition it is also a good idea to install low-level tools (eg the galaxy_protk repository) before installing dependent tools (eg TPP Prophets).
+5. Configure Galaxy's tool dependency directory.
 
-1. Check out and install the latest stable galaxy [see the official galaxy wiki for more detailed setup instructions](http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy,"galaxy wiki")
+	Create a directory for galaxy tool dependencies. This must be outside the galaxy-dist directory. I usually create a directory called tool_dependencies alongside galaxy-dist.
+	Open the file `universe_wsgi.ini` in the galaxy-dist directory and set the configuration option `tool_dependency_dir` to point to the directory you just created, eg;
 
-    ```sh
-    hg clone https://bitbucket.org/galaxy/galaxy-dist 
-    cd galaxy-dist
-    sh run.sh
-    ```
+	```
+		tool_dependency_dir = ../tool_dependencies
+	```
 
+6.  Create a tool dependency that sets up protk in the environment created by rvm
 
-2. Make the protk tools available to galaxy. (Legacy. This step is not needed when installing via the toolshed)
+	In this example we create the environment for protk `1.2.6` as this was the version installed in step 4 above.
 
-    - Create a directory for galaxy tool dependencies. It's best if this directory is outside the galaxy-dist directory. I usually create a directory called `tool_depends` alongside `galaxy-dist`.
-    - Open the file `universe_wsgi.ini` in the `galaxy-dist` directory and set the configuration option `tool_dependency_dir` to point to the directory you just created
-    - Create a protkgem directory inside `<tool_dependency_dir>`. 
+	```bash
+		cd <tool_dependency_dir>
+		mkdir protk
+		cd protk
+		mkdir 1.2.6
+		ln -s 1.2.6 default
+		echo `rvm env --path 2.1@protk1.2.6` > 1.2.6/env.sh
+	```
 
-        ```sh
-        cd <tool_dependency_dir>
-        mkdir protkgem
-		cd protkgem
-        mkdir rvm193
-        ln -s rvm193 default
-        cd default
-        ln -s ~/.protk/galaxy/env.sh env.sh
-        ```
+7. Keep things up to date
 
-3. After installing the protk wrapper tools from the toolshed it will be necessary to tell those tools about databases you have installed. Use the manage_db.rb tool to do this.  In particular the manage_db.rb tool has a -G option to automatically tell galaxy about the location of its databases.  To use this though you will need to tell protk about the location of your galaxy install.  To do this
-    - Create a file named `config.yml` inside your .protk directory
-    - Add the line `galaxy_root: /home/galaxy/galaxy-dist` to config.yml substituting the actual path to the root directory of your galaxy installation
+	When new versions of galaxy tools are released they may change the version of protk that is required.  Check the release notes on the tool to see what is needed.  For example, if upgrading to version 1.2.7 you would do the following;
 
-        ```sh 
-        echo 'galaxy_root: /home/galaxy/galaxy-dist' > ~/.protk/config.yml
-        ```
+	```bash
+		rvm 2.1
+		rvm gemset create protk1.2.7
+		rvm use 2.1@protk1.2.7
+		gem install protk -v 1.2.7
+		cd <tool_dependency_dir>/protk/
+		mkdir 1.2.7
+		rvmenv=`rvm env --path 2.1@protk1.2.7`
+		echo ". $rvmenv" > 1.2.7/env.sh
+		ln -s 1.2.7 default
+	```
 
 

data/bin/add_retention_times.rb

@@ -17,14 +17,14 @@ include LibXML
 #
 genv=Constants.new
 
-tool=Tool.new([:over_write])
+tool=Tool.new([:over_write,:explicit_output])
 tool.option_parser.banner = "Look up retention times in a raw file and \
 add them to a pepxml file.\n\nUsage: add_retention_times.rb [options] file1.pep.xml file2.mgf"
 
 exit unless tool.check_options 
 
 if ( ARGV[0].nil? || ARGV[1].nil? )
-    puts "You must supply an input file"
+    puts "You must supply an input pepxml file and an input mgf file"
     puts tool.option_parser 
     exit
 end
@@ -51,8 +51,6 @@ if not pepxml_doc.root.namespaces.default
   pepxml_ns=nil
 end
 
-
-
 queries=pepxml_doc.find("//#{pepxml_ns_prefix}spectrum_query", pepxml_ns)
 
 queries.each do |query|
@@ -86,4 +84,10 @@ queries.each do |query|
 	end
 end
 
-pepxml_doc.save(pepxml_file)
+if tool.explicit_output.nil? 
+	pepxml_doc.save(pepxml_file)	
+else
+	pepxml_doc.save(tool.explicit_output)
+end
+
+

data/bin/augustus_to_proteindb.rb

@@ -10,20 +10,16 @@ require 'protk/tool'
 require 'bio'
 
 tool=Tool.new([:explicit_output])
-tool.option_parser.banner = "Create a protein database from Augustus gene prediction output that is suitable for later processing by proteogenomics tools.\n\nUsage: augustus_to_proteindb.rb [options] augustus.gff3"
+tool.option_parser.banner = "Create a protein database from Augustus gene prediction \
+output that is suitable for later processing by proteogenomics tools.\
+\n\nUsage: augustus_to_proteindb.rb [options] augustus.gff3"
 
-tool.options.add_transcript_info=false
-tool.option_parser.on( '--info', 'Include CDS coordinates' ) do  
-  tool.options.add_transcript_info=true
-end
+tool.add_value_option(:explicit_output,nil,['-o', '--output out', 'An explicitly named output file. \
+  The default is to write to standard output'])
+tool.add_boolean_option(:add_transcript_info,false,['--info','Include CDS Coordinates'])
 
-exit unless tool.check_options 
 
-if ( ARGV[0].nil? )
-    puts "You must supply an input file"
-    puts tool.option_parser 
-    exit
-end
+exit unless tool.check_options(true)
 
 inname=ARGV.shift
 

data/bin/interprophet.rb

@@ -16,65 +16,49 @@ for_galaxy = GalaxyUtil.for_galaxy?
 
 # Setup specific command-line options for this tool. Other options are inherited from ProphetTool
 #
-prophet_tool=ProphetTool.new([:explicit_output,:over_write,:prefix_suffix])
-prophet_tool.option_parser.banner = "Run InterProphet on a set of pep.xml input files.\n\nUsage: interprophet.rb [options] file1.pep.xml file2.pep.xml ..."
-prophet_tool.options.output_suffix="_iproph"
-
-
-prophet_tool.options.no_nss=""
-prophet_tool.option_parser.on( '--no-nss', 'Don\'t use NSS (Number of Sibling Searches) in Model' ) do 
-  prophet_tool.options.no_nss="NONSS"
-end
+prophet_tool=ProphetTool.new([
+  :explicit_output,
+  :over_write,
+  :prefix])
 
-prophet_tool.options.no_nrs=""
-prophet_tool.option_parser.on('--no-nrs', 'Don\'t use NRS (Number of Replicate Spectra) in Model' ) do
-  prophet_tool.options.no_nrs="NONRS"
-end
-
-prophet_tool.options.no_nse=""
-prophet_tool.option_parser.on('--no-nse', 'Don\'t use NSE (Number of Sibling Experiments) in Model' ) do
-  prophet_tool.options.no_nse="NONSE"
-end
+prophet_tool.option_parser.banner = "Run InterProphet on a set of pep.xml input files.\n\nUsage: interprophet.rb [options] file1.pep.xml file2.pep.xml ..."
+@output_suffix="_iproph"
 
-prophet_tool.options.no_nsi=""
-prophet_tool.option_parser.on("--no-nsi",'Don\'t use NSE (Number of Sibling Ions) in Model' ) do
-  prophet_tool.options.no_nsi="NONSI"
-end
 
-prophet_tool.options.no_nsm=""
-prophet_tool.option_parser.on("--no-nsm",'Don\'t use NSE (Number of Sibling Modifications) in Model' ) do
-  prophet_tool.options.no_nsm="NONSM"
-end
+prophet_tool.add_boolean_option(:no_nss,false,['--no-nss', 'Don\'t use NSS (Number of Sibling Searches) in Model'])
+prophet_tool.add_boolean_option(:no_nrs,false,['--no-nrs', 'Don\'t use NRS (Number of Replicate Spectra) in Model'])
+prophet_tool.add_boolean_option(:no_nse,false,['--no-nse', 'Don\'t use NSE (Number of Sibling Experiments) in Model'])
+prophet_tool.add_boolean_option(:no_nsi,false,["--no-nsi",'Don\'t use NSE (Number of Sibling Ions) in Model'])
+prophet_tool.add_boolean_option(:no_nsm,false,["--no-nsm",'Don\'t use NSE (Number of Sibling Modifications) in Model'])
+prophet_tool.add_value_option(:min_prob,"",["--minprob mp","Minimum probability cutoff "])
 
-prophet_tool.options.min_prob=""
-prophet_tool.option_parser.on("--minprob mp","Minimum probability cutoff ") do |mp|
-  prophet_tool.options.min_prob=mp
-end
+exit unless prophet_tool.check_options(true)
 
-exit unless prophet_tool.check_options
-if ( ARGV[0].nil? )
-    puts "You must supply an input file"
-    puts prophet_tool.option_parser 
-    exit
-end
 
 # Obtain a global environment object
 genv=Constants.new
 
+inputs = ARGV.collect {|file_name| 
+  file_name.chomp
+}
+
 if ( prophet_tool.explicit_output != nil )
-    output_file=prophet_tool.explicit_output
+  output_file=prophet_tool.explicit_output
 else
-  output_file="#{prophet_tool.output_prefix}interact#{prophet_tool.output_suffix}.pep.xml"
+  output_file=Tool.default_output_path(inputs[0],".pep.xml",prophet_tool.output_prefix,@output_suffix)
 end
 
 if ( !Pathname.new(output_file).exist? || prophet_tool.over_write )
 
-  cmd="InterProphetParser #{prophet_tool.options.no_nss} #{prophet_tool.options.no_nrs} #{prophet_tool.options.no_nse} #{prophet_tool.options.no_nsi} #{prophet_tool.options.no_nsm}"
-  cmd << " MINPROB=#{prophet_tool.min_prob}" if ( prophet_tool.min_prob !="" )
+  cmd="InterProphetParser "
 
-  inputs = ARGV.collect {|file_name| 
-    file_name.chomp
-  }
+  cmd<<"NONSS " if prophet_tool.options.no_nss
+  cmd<<"NONRS " if prophet_tool.options.no_nrs
+  cmd<<"NONSE " if prophet_tool.options.no_nse
+  cmd<<"NONSI " if prophet_tool.options.no_nsi
+  cmd<<"NONSM " if prophet_tool.options.no_nsm
+
+  cmd << " MINPROB=#{prophet_tool.min_prob}" if ( prophet_tool.min_prob !="" )
 
   if for_galaxy
     inputs = inputs.collect {|ip| GalaxyUtil.stage_pepxml(ip) }
@@ -86,9 +70,7 @@ if ( !Pathname.new(output_file).exist? || prophet_tool.over_write )
 
   # Run the analysis
   #
-  jobscript_path="#{output_file}.pbs.sh"
-  job_params={:jobid=>"iprophet", :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
     
 else

data/bin/make_decoy.rb

@@ -22,40 +22,13 @@ include LibXML
 tool=Tool.new([:explicit_output])
 tool.option_parser.banner = "Create a decoy database from real protein sequences.\n\nUsage: make_decoy.rb [options] realdb.fasta"
 
-tool.options.db_length=0
-tool.option_parser.on('-L len','--db-length len','Number of sequences to generate') do |len|
-  tool.options.db_length=len.to_i
-end
-
-tool.options.prefix_string="decoy_"
-tool.option_parser.on('-P str','--prefix-string str','String to prepend to sequence ids') do |str|
-  tool.options.prefix_string=str
-end
-
-tool.options.reverse_only=false
-tool.option_parser.on('--reverse-only','Just reverse sequences. Dont try to randomize') do 
-  tool.options.reverse_only=true
-end
-
-tool.options.id_regex=".*?\\|(.*?)[ \\|]"
-tool.option_parser.on('--id-regex regex','Regex for finding IDs. If reverse-only is used then this will be used to find ids and prepend with the decoy string. Default .*?\\|(.*?)[ \\|]') do regex
-  tool.options.id_regex=regex
-end
-
-tool.options.append=false
-tool.option_parser.on('-A','--append','Append input sequences to the generated database') do 
-  tool.options.append=true
-end
-
-
-exit unless tool.check_options 
-
-if ( ARGV[0].nil? )
-    puts "You must supply an input file"
-    puts tool.option_parser 
-    exit
-end
+tool.add_value_option(:db_length,0,['-L len','--db-length len','Number of sequences to generate'])
+tool.add_value_option(:prefix_string,"decoy_",['-P str','--prefix-string str','String to prepend to sequence ids'])
+tool.add_boolean_option(:reverse_only,false,['--reverse-only','Just reverse sequences. Dont try to randomize. Ignores -L'])
+tool.add_value_option(:id_regex,".*?\\|(.*?)[ \\|]",['--id-regex regex','Regex for finding IDs. If reverse-only is used then this will be used to find ids and prepend with the decoy string. Default .*?\\|(.*?)[ \\|]'])
+tool.add_boolean_option(:append,false,['-A','--append','Append input sequences to the generated database'])
 
+exit unless tool.check_options(true,[:explicit_output])
 
 input_file=ARGV[0]
 
@@ -63,11 +36,9 @@ input_file=ARGV[0]
 db_length=tool.db_length
 if ( db_length==0) #If no db length was specified use the number of entries in the input file
   db_length=Bio::FastaFormat.open(input_file).count
-  p "Found #{db_length} entries in input file"
+  puts "Found #{db_length} entries in input file"
 end
 
-output_file="decoy_#{input_file}"
-
 output_file = tool.explicit_output if tool.explicit_output!=nil
 
 genv=Constants.new()
@@ -79,7 +50,8 @@ if (tool.reverse_only)
 	Bio::FastaFormat.open(input_file).each do |seq| 
 		id=nil
 		begin
-			id=seq.definition.scan(/#{id_regex}/)[0][0]
+			# require 'debugger';debugger
+			id=seq.definition.chomp.scan(/#{tool.id_regex}/)[0][0]
 			revdef=seq.definition.sub(id,"#{tool.prefix_string}#{id}")
 			decoys_out.write ">#{revdef}\n#{seq.aaseq}\n"
 		rescue
@@ -91,17 +63,13 @@ else
 	Randomize.make_decoys input_file, db_length, decoys_tmp_file, tool.prefix_string
 end
 
-cmd = "cat #{input_file} #{decoys_tmp_file} >> #{output_file}; rm #{decoys_tmp_file}" if ( tool.append ) 
-
-# Randomize.make_decoys raw_db_filename, db_length, decoys_filename, decoy_prefix
-#   cmd = "cat #{raw_db_filename} #{decoys_filename} >> #{decoy_db_filename}; rm #{decoys_filename}"
+if ( tool.append )
+	cmd ="awk 'FNR==1{print \"\"}1' #{input_file} #{decoys_tmp_file} > #{output_file};"
+	cmd << "rm #{decoys_tmp_file}"
+else
+	cmd = "mv #{decoys_tmp_file} #{output_file}"
+end
 
-p cmd
-# Run the conversion
-#
-job_params= {:jobid => tool.jobid_from_filename(input_file) }
-job_params[:queue]="lowmem"
-job_params[:vmem]="900mb"    
-tool.run(cmd,genv,job_params)
+tool.run(cmd,genv)
 
 

data/bin/mascot_search.rb

@@ -21,7 +21,7 @@ def login(mascot_cgi,username,password)
     authdict[:action]="login"
     authdict[:savecookie]="1"
 
-    p "Logging in to #{mascot_cgi}/login.pl"
+    $genv.log("Logging in to #{mascot_cgi}/login.pl",:info)
 
     response = RestClient.post "#{mascot_cgi}/login.pl", authdict
 
@@ -40,7 +40,7 @@ def download_datfile(mascot_cgi,results_date,results_file,explicit_output,openur
         output_path="#{results_file}"
     end
 
-    puts "Writing output to #{output_path}"
+    $genv.log("Writing output to #{output_path}",:info)
 
     require 'open-uri'
     open("#{output_path}", 'wb') do |file|
@@ -58,6 +58,29 @@ def search_params_dictionary(search_tool,input_file)
     var_mods=""  if var_mods=="None"
     fix_mods="" if fix_mods=="None"
 
+    shorthand_varmods=[]
+    shorthand_fixmods=[]
+
+    shorthand_varmods << ['Oxidation (M)'] if search_tool.methionine_oxidation
+    shorthand_varmods << ['Acetyl (Protein N-term)'] if search_tool.acetyl_nterm
+    shorthand_varmods << ['Deamidated (NQ)'] if search_tool.glyco
+
+    shorthand_fixmods << ['Carbamidomethyl (C)'] if search_tool.carbamidomethyl
+
+    if var_mods.length>0
+        var_mods=[var_mods,"#{shorthand_varmods.join(",")}"].join(",") 
+    else
+        var_mods=shorthand_varmods.join(",")
+    end
+
+
+    if fix_mods.length>0
+        fix_mods=[fix_mods,"#{shorthand_fixmods.join(",")}"].join(",")
+    else
+        fix_mods=shorthand_fixmods.join(",")
+    end
+
+
     postdict={}
     postdict[:SEARCH]="MIS" 
     postdict[:CHARGE]=search_tool.allowed_charges
@@ -90,74 +113,36 @@ $genv=Constants.new
 
 # Setup specific command-line options for this tool. Other options are inherited from SearchTool
 #
-search_tool=SearchTool.new([:explicit_output,:over_write,:database,:enzyme,
-    :modifications,:instrument,:mass_tolerance,
-    :mass_tolerance_units,:precursor_search_type,:missed_cleavages])
-
-search_tool.jobid_prefix="o"
+search_tool=SearchTool.new([
+    :explicit_output,
+    :over_write,
+    :database,
+    :enzyme,
+    :modifications,
+    :methionine_oxidation,
+    :carbamidomethyl,
+    :glyco,
+    :acetyl_nterm,
+    :instrument,
+    :mass_tolerance,
+    :mass_tolerance_units,
+    :precursor_search_type,
+    :missed_cleavages])
 
 search_tool.option_parser.banner = "Run a Mascot msms search on a set of mgf input files.\n\nUsage: mascot_search.rb [options] msmsfile.mgf"
 search_tool.options.output_suffix="_mascot"
 
-search_tool.options.mascot_server="#{$genv.default_mascot_server}/mascot/cgi"
+search_tool.add_value_option(:mascot_server,"#{$genv.default_mascot_server}/mascot/cgi",['-S', '--server url', 'The url to the cgi directory of the mascot server'])
+search_tool.add_value_option(:allowed_charges,"1+,2+,3+",['--allowed-charges ac', 'Allowed precursor ion charges.'])
+search_tool.add_value_option(:email,"",['--email em', 'User email.'])
+search_tool.add_value_option(:username,"",['--username un', 'Username.'])
+search_tool.add_value_option(:httpproxy,nil,['--proxy url', 'The url to a proxy server'])
+search_tool.add_value_option(:mascot_password,"",['--password psswd', 'Password to use when Mascot security is enabled'])
+search_tool.add_boolean_option(:use_security,false,['--use-security', 'When Mascot security is enabled this is required'])
+search_tool.add_value_option(:download_only,nil,['--download-only path', 'Specify a relative path to an existing results file on the server for download eg(20131113/F227185.dat)'])
+search_tool.add_value_option(:timeout,200,['--timeout seconds', 'Timeout for sending data file to mascot in seconds'])
 
-search_tool.options.allowed_charges="1+,2+,3+"
-search_tool.option_parser.on(  '--allowed-charges ac', 'Allowed precursor ion charges. Default=1+,2+,3+' ) do |ac|
- search_tool.options.allowed_charges = ac
-end     
-
-search_tool.options.email=""
-search_tool.option_parser.on('--email em', 'User email.') do |em|
-    search_tool.options.email = em
-end
-
-search_tool.options.username=""
-search_tool.option_parser.on('--username un', 'Username.') do |un|
-    search_tool.options.username = un
-end
-
-search_tool.options.mascot_server="www.matrixscience.com"
-search_tool.option_parser.on( '-S', '--server url', 'The url to the cgi directory of the mascot server' ) do |url| 
-    search_tool.options.mascot_server=url
-end
-
-search_tool.options.mascot_server=""
-search_tool.option_parser.on('--username un', 'Username.') do |un|
-    search_tool.options.username = un
-end
-
-search_tool.options.httpproxy=nil
-search_tool.option_parser.on( '--proxy url', 'The url to a proxy server' ) do |urll| 
-    search_tool.options.httpproxy=urll
-end
-
-search_tool.options.mascot_password=""
-search_tool.option_parser.on( '--password psswd', 'Password to use when Mascot security is enabled' ) do |psswd| 
-    search_tool.options.mascot_password=psswd
-end
-
-search_tool.options.use_security=FALSE
-search_tool.option_parser.on( '--use-security', 'When Mascot security is enabled this is required' ) do  
-    search_tool.options.use_security=TRUE
-end
-
-search_tool.options.export_format="mascotdat"
-search_tool.option_parser.on( '--export format', 'Save results in a specified format. Only mascotdat is currently supported' ) do |format| 
-    search_tool.options.export_format=format
-end
-
-search_tool.options.download_only=nil
-search_tool.option_parser.on( '--download-only path', 'Specify a path to an existing results file for download eg(20131113/F227185.dat)' ) do |path| 
-    search_tool.options.download_only=path
-end
-
-
-search_tool.options.timeout=200
-search_tool.option_parser.on( '--timeout seconds', 'Timeout for sending data file to mascot in seconds' ) do |seconds| 
-    search_tool.options.timeout=seconds.to_i
-end
-
-exit unless search_tool.check_options 
+exit unless search_tool.check_options
 
 if ( ARGV[0].nil? && search_tool.download_only.nil?)
     puts "You must supply an input file"
@@ -214,19 +199,20 @@ else
         puts error_result[0]
         $genv.log("Mascot search failed with response #{search_response}",:warn)
         throw "Mascot search failed with response #{search_response}"
-    elsif (search_tool.export_format=="mascotdat")
+    else (search_tool.export_format=="mascotdat")
         # Search for the location of the mascot data file in the response
         results=/master_results_?2?\.pl\?file=\.*\/data\/(.*)\/(.+\.dat)/.match(search_response)
         results_date=results[1]
         results_file=results[2]
 
         download_datfile mascot_cgi, results_date, results_file,search_tool.explicit_output,openurlcookie
-    else
-        results=/master_results_?2?\.pl\?file=(\.*\/data\/.*\/.+\.dat)/.match(search_response)
-        results_file = results[1]
-        export_results mascot_cgi,cookie,results_file,search_tool.export_format, openurlcookie
-    #    export_results mascot_cgi,cookie,results_file,search_tool.export_format
     end
+    # else
+    #     results=/master_results_?2?\.pl\?file=(\.*\/data\/.*\/.+\.dat)/.match(search_response)
+    #     results_file = results[1]
+    #     export_results mascot_cgi,cookie,results_file,search_tool.export_format, openurlcookie
+    # #    export_results mascot_cgi,cookie,results_file,search_tool.export_format
+    # end
 end