protk 1.2.3 → 1.2.4

data/bin/annotate_ids.rb

@@ -15,7 +15,7 @@ require 'protk/protein_annotator'
 
 # Setup specific command-line options for this tool. Other options are inherited from Tool
 #
-id_tool=ProphetTool.new([:explicit_output,:over_write])
+id_tool=ProphetTool.new([:explicit_output,:over_write,:prefix_suffix])
 id_tool.option_parser.banner = "Run ID annotation on a prot.xml input file.\n\nUsage: annotate_ids.rb [options] file1.prot.xml"
 id_tool.options.output_prefix="annotated_"
 

data/bin/correct_omssa_retention_times.rb

@@ -17,7 +17,7 @@ require 'protk/omssa_util'
 #
 genv=Constants.new
 
-tool=Tool.new 
+tool=Tool.new([:over_write])
 tool.option_parser.banner = "Correct retention times on a pepxml file produced by omssa using information from an mgf file.\n\nUsage: correct_omssa_retention_times.rb [options] file1.pep.xml file2.mgf"
 tool.option_parser.parse!
 

data/bin/file_convert.rb

@@ -14,6 +14,7 @@ require 'libxml'
 
 include LibXML
 
+# Regex for cleaning mgf sed -i.bak 's/\(PEPMASS=[0-9]*.[0-9]*\)[ \t]*[0-9]*/\1/g'
 
 # Read the input file and search for an instance of the charge state cvParam inside a precursor tag. Return true if one is found. False otherwise
 #

data/bin/interprophet.rb

@@ -13,7 +13,7 @@ require 'protk/prophet_tool'
 
 # Setup specific command-line options for this tool. Other options are inherited from ProphetTool
 #
-prophet_tool=ProphetTool.new([:explicit_output])
+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"
 
@@ -67,7 +67,7 @@ end
 if ( !Pathname.new(output_file).exist? || prophet_tool.over_write )
 
   cmd="#{genv.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=#{min_prob}" if ( prophet_tool.options.min_prob !="" )
+  cmd << " MINPROB=#{prophet_tool.min_prob}" if ( prophet_tool.min_prob !="" )
 
   inputs = ARGV.collect {|file_name| 
     file_name.chomp

data/bin/msgfplus_search.rb

@@ -231,11 +231,11 @@ ARGV.each do |filename|
     
     # As a final part of the command we convert to pepxml
     if search_tool.no_pepxml
+      cmd << "; cp #{mzid_output_path} #{output_path}"
+    elsif search_tool.explicit_output
       cmd << "; #{genv.idconvert} #{mzid_output_path} --pepXML -o #{Pathname.new(mzid_output_path).dirname}" 
       #Then copy the pepxml to the final output path
       cmd << "; cp #{mzid_output_path.chomp('.mzid')}.pepXML #{output_path}"
-    elsif search_tool.explicit_output
-      cmd << "; cp #{mzid_output_path} #{output_path}"
     end
       
 

data/bin/peptide_prophet.rb

@@ -13,7 +13,7 @@ require 'protk/prophet_tool'
 
 # Setup specific command-line options for this tool. Other options are inherited from ProphetTool
 #
-prophet_tool=ProphetTool.new([:glyco,:explicit_output,:maldi])
+prophet_tool=ProphetTool.new([:glyco,:explicit_output,:over_write,:maldi,:prefix_suffix])
 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"
 
@@ -256,7 +256,8 @@ else
 
   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

@@ -71,13 +71,15 @@ spectrum_queries.each do |query|
   search_engine=""
   search_score_names=top_search_hit.find("./#{pepxml_ns_prefix}search_score/@name",pepxml_ns).collect {|s| s.to_s}
 
-  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
+  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
 
   
   pp_result=top_search_hit.find("./#{pepxml_ns_prefix}analysis_result/#{pepxml_ns_prefix}peptideprophet_result/@probability",pepxml_ns)

data/bin/protein_prophet.rb

@@ -26,7 +26,7 @@ end
 
 # Setup specific command-line options for this tool. Other options are inherited from ProphetTool
 #
-prophet_tool=ProphetTool.new([:glyco,:explicit_output])
+prophet_tool=ProphetTool.new([:glyco,:explicit_output,:over_write,:prefix_suffix])
 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"
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: protk
 version: !ruby/object:Gem::Version
-  version: 1.2.3
+  version: 1.2.4
   prerelease: 
 platform: ruby
 authors: