protk 1.2.3 → 1.2.4
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- data/bin/annotate_ids.rb +1 -1
- data/bin/correct_omssa_retention_times.rb +1 -1
- data/bin/file_convert.rb +1 -0
- data/bin/interprophet.rb +2 -2
- data/bin/msgfplus_search.rb +2 -2
- data/bin/peptide_prophet.rb +3 -2
- data/bin/pepxml_to_table.rb +9 -7
- data/bin/protein_prophet.rb +1 -1
- metadata +1 -1
data/bin/annotate_ids.rb
CHANGED
@@ -15,7 +15,7 @@ require 'protk/protein_annotator'
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# Setup specific command-line options for this tool. Other options are inherited from Tool
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#
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18
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-
id_tool=ProphetTool.new([:explicit_output,:over_write])
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18
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+
id_tool=ProphetTool.new([:explicit_output,:over_write,:prefix_suffix])
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id_tool.option_parser.banner = "Run ID annotation on a prot.xml input file.\n\nUsage: annotate_ids.rb [options] file1.prot.xml"
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id_tool.options.output_prefix="annotated_"
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@@ -17,7 +17,7 @@ require 'protk/omssa_util'
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#
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genv=Constants.new
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-
tool=Tool.new
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+
tool=Tool.new([:over_write])
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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"
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tool.option_parser.parse!
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data/bin/file_convert.rb
CHANGED
@@ -14,6 +14,7 @@ require 'libxml'
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include LibXML
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+
# Regex for cleaning mgf sed -i.bak 's/\(PEPMASS=[0-9]*.[0-9]*\)[ \t]*[0-9]*/\1/g'
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# 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
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#
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data/bin/interprophet.rb
CHANGED
@@ -13,7 +13,7 @@ require 'protk/prophet_tool'
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# Setup specific command-line options for this tool. Other options are inherited from ProphetTool
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#
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-
prophet_tool=ProphetTool.new([:explicit_output])
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+
prophet_tool=ProphetTool.new([:explicit_output,:over_write,:prefix_suffix])
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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 ..."
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prophet_tool.options.output_suffix="_iproph"
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@@ -67,7 +67,7 @@ end
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if ( !Pathname.new(output_file).exist? || prophet_tool.over_write )
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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}"
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-
cmd << " MINPROB=#{min_prob}" if ( prophet_tool.
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+
cmd << " MINPROB=#{prophet_tool.min_prob}" if ( prophet_tool.min_prob !="" )
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inputs = ARGV.collect {|file_name|
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file_name.chomp
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data/bin/msgfplus_search.rb
CHANGED
@@ -231,11 +231,11 @@ ARGV.each do |filename|
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# As a final part of the command we convert to pepxml
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if search_tool.no_pepxml
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+
cmd << "; cp #{mzid_output_path} #{output_path}"
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+
elsif search_tool.explicit_output
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cmd << "; #{genv.idconvert} #{mzid_output_path} --pepXML -o #{Pathname.new(mzid_output_path).dirname}"
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#Then copy the pepxml to the final output path
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cmd << "; cp #{mzid_output_path.chomp('.mzid')}.pepXML #{output_path}"
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-
elsif search_tool.explicit_output
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-
cmd << "; cp #{mzid_output_path} #{output_path}"
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end
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data/bin/peptide_prophet.rb
CHANGED
@@ -13,7 +13,7 @@ require 'protk/prophet_tool'
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# Setup specific command-line options for this tool. Other options are inherited from ProphetTool
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#
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-
prophet_tool=ProphetTool.new([:glyco,:explicit_output,:maldi])
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+
prophet_tool=ProphetTool.new([:glyco,:explicit_output,:over_write,:maldi,:prefix_suffix])
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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 ..."
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prophet_tool.options.output_suffix="_pproph"
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@@ -256,7 +256,8 @@ else
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end
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cmd=generate_command(genv,prophet_tool,inputs,output_file_name,database,engine)
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-
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+
puts cmd
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+
%x['ls']
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run_peptide_prophet(genv,prophet_tool,cmd,output_file_name,engine)
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end
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data/bin/pepxml_to_table.rb
CHANGED
@@ -71,13 +71,15 @@ spectrum_queries.each do |query|
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search_engine=""
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search_score_names=top_search_hit.find("./#{pepxml_ns_prefix}search_score/@name",pepxml_ns).collect {|s| s.to_s}
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-
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-
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-
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-
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-
elsif ( search_score_names.grep(/^name.*=.*
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-
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-
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+
search_engine=query.parent.attributes['search_engine']
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+
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+
# if ( search_score_names.length==2 && search_score_names.grep(/^name.*=.*pvalue/))
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+
# search_engine="omssa"
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+
# elsif ( search_score_names.grep(/^name.*=.*ionscore/))
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+
# search_engine="mascot"
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+
# elsif ( search_score_names.grep(/^name.*=.*hyperscore/) )
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+
# search_engine="x!tandem"
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+
# end
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pp_result=top_search_hit.find("./#{pepxml_ns_prefix}analysis_result/#{pepxml_ns_prefix}peptideprophet_result/@probability",pepxml_ns)
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data/bin/protein_prophet.rb
CHANGED
@@ -26,7 +26,7 @@ end
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# Setup specific command-line options for this tool. Other options are inherited from ProphetTool
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#
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-
prophet_tool=ProphetTool.new([:glyco,:explicit_output])
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+
prophet_tool=ProphetTool.new([:glyco,:explicit_output,:over_write,:prefix_suffix])
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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 ..."
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prophet_tool.options.output_suffix="_protproph"
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