protk 1.2.6.pre2 → 1.2.6.pre3

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -1,3 +1,6 @@
+
+[![Build Status](https://travis-ci.org/iracooke/protk.png?branch=master)](https://travis-ci.org/iracooke/protk)
+
 # protk ( Proteomics toolkit )
 
 
@@ -6,15 +9,6 @@
 
 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. 
 
-***
-
-## Table of Contents
-
-* [Protk](#what-is-it?)
-    * [Installation](#installation)
-    * [Configuration](#configuration)
-
-
 
 ## Installation
  

data/bin/interprophet.rb

@@ -10,6 +10,8 @@
 require 'protk/constants'
 require 'protk/command_runner'
 require 'protk/prophet_tool'
+require 'protk/galaxy_util'
+
 
 # Setup specific command-line options for this tool. Other options are inherited from ProphetTool
 #
@@ -70,7 +72,11 @@ if ( !Pathname.new(output_file).exist? || prophet_tool.over_write )
   cmd << " MINPROB=#{prophet_tool.min_prob}" if ( prophet_tool.min_prob !="" )
 
   inputs = ARGV.collect {|file_name| 
-    file_name.chomp
+    input_name=file_name.chomp
+    unless input_name !~/pep\.xml$/
+        input_name = GalaxyStager.new(input_name, :extension => ".pep.xml").staged_path
+    end
+    input_name
   }
 
   cmd << " #{inputs.join(" ")} #{output_file}"

data/bin/msgfplus_search.rb

@@ -238,7 +238,7 @@ ARGV.each do |filename|
       #if search_tool.explicit_output
       cmd << ";ruby -pi.bak -e \"gsub('post=\\\"?','post=\\\"X')\" #{mzid_output_path}"
       cmd << ";ruby -pi.bak -e \"gsub('pre=\\\"?','pre=\\\"X')\" #{mzid_output_path}"
-      cmd << "; #{genv.idconvert} #{mzid_output_path} --pepXML -o #{Pathname.new(mzid_output_path).dirname}" 
+      cmd << ";idconvert #{mzid_output_path} --pepXML -o #{Pathname.new(mzid_output_path).dirname}" 
       #Then copy the pepxml to the final output path
       cmd << "; mv #{mzid_output_path.chomp('.mzid')}.pepXML #{output_path}"
     end

data/bin/peptide_prophet.rb

@@ -10,6 +10,9 @@
 require 'protk/constants'
 require 'protk/command_runner'
 require 'protk/prophet_tool'
+require 'protk/galaxy_util'
+
+galaxy_util = GalaxyUtil.new
 
 # Setup specific command-line options for this tool. Other options are inherited from ProphetTool
 #
@@ -116,6 +119,11 @@ throw "When --output and -F options are set only one file at a time can be run"
 genv=Constants.new
 
 
+inputs=ARGV.collect { |file_name| file_name.chomp}
+if galaxy_util.for_galaxy? 
+  inputs = inputs.collect {|ip| galaxy_util.stage_pepxml(ip) }
+end
+
 # Interrogate all the input files to obtain the database and search engine from them
 #
 genv.log("Determining search engine and database used to create input files ...",:info)

data/bin/sixframe.rb

@@ -31,6 +31,16 @@ end
 tool=Tool.new([:explicit_output])
 tool.option_parser.banner = "Create a sixframe translation of a genome.\n\nUsage: sixframe.rb [options] genome.fasta"
 
+tool.options.print_coords=false
+tool.option_parser.on( '--coords', 'Write genomic coordinates in the fasta header' ) do 
+  tool.options.print_coords=true
+end
+
+tool.options.keep_header=true
+tool.option_parser.on( '--strip-header', 'Dont write sequence definition' ) do 
+  tool.options.keep_header=false
+end
+
 exit unless tool.check_options 
 
 if ( ARGV[0].nil? )
@@ -86,12 +96,20 @@ file.each do |entry|
         ncbi_scaffold_id = entry.entry_id.gsub('|','_').gsub(' ','_')
         ncbi_accession = "lcl|#{ncbi_scaffold_id}_frame_#{frame}_orf_#{oi}"
 
-#        check_coords(entry.naseq,orf,frame,position_start,position_end)
+        defline=">#{ncbi_accession}"
+
+        if tool.print_coords
+          defline << " #{position_start}|#{position_end}"
+        end
+
+        if tool.keep_header
+          defline << " #{entry.definition}"
+        end
 
         # Output in fasta format
         # start and end positions are always relative to the forward strand
 
-        outfile.write(">#{ncbi_accession} #{position_start}|#{position_end}\n#{orf}\n")
+        outfile.write("#{defline}\n#{orf}\n")
 
       end
       position += orf.length*3+3

data/lib/protk/constants.rb

@@ -145,10 +145,6 @@ class Constants
     end    
   end
 
-  def idconvert
-    return "#{self.pwiz_root}/idconvert"
-  end
-
   def msconvert
     return "#{self.pwiz_root}/msconvert"
   end
@@ -206,7 +202,7 @@ class Constants
   end
 
   def makeblastdb
-    return "#{self.blast_root}/bin/makeblastdb"
+    return "makeblastdb"
   end
 
   def searchblastdb

data/lib/protk/galaxy_util.rb

@@ -6,12 +6,20 @@ require 'fileutils'
 
 class GalaxyUtil
 
-  def self.for_galaxy?
-    for_galaxy = ARGV[0] == "--galaxy"
-    ARGV.shift if for_galaxy
-    return for_galaxy
+  attr_accessor :for_galaxy
+  attr_accessor :stagers
+
+  def initialize()
+    @for_galaxy= ARGV[0]=="--galaxy"
+    ARGV.shift if @for_galaxy    
+    @stagers=[]
   end
 
+  def stage_pepxml(input_pepxml_path)
+    stager = GalaxyStager.new(input_pepxml_path, :extension => ".pep.xml")
+    @stagers << stager
+    stager.staged_path
+  end
 
   def self.stage_protxml(input_protxml_path)
     # This method takes in the path to a protxml created in Galaxy,
@@ -43,4 +51,7 @@ class GalaxyUtil
     protxml_path
   end
 
+
+
+
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: protk
 version: !ruby/object:Gem::Version
-  version: 1.2.6.pre2
+  version: 1.2.6.pre3
 platform: ruby
 authors:
 - Ira Cooke