protk 1.3.1.pre2 → 1.3.1.pre3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 888f8ebff75c2c33497c9bf4f7aeec182311b7e3
-  data.tar.gz: 4102a91afbee688babe093df8a53b84b097ba0c3
+  metadata.gz: 7d5d14d3a6fdd45c7ac3be6f122a9a30dd5e3823
+  data.tar.gz: c77c6b6a83386426ad8a727866f0c0ca8a0c42b5
 SHA512:
-  metadata.gz: 3e67189a07c6ac237a4def19ad90043ab8919d5492fd43b67cfa5fc3285819b2fd62671375283c5d9dd05618c746603ba829c70225b140b3a52ccba9fafb24f8
-  data.tar.gz: 354a9eb2499d3f8b194ccdef82f06692672435a0e47b5b49197b9f1fba2c27181275d38c98fe6f644750b554b4b1601b873f6a51a0318853b86b17d7783f2e57
+  metadata.gz: 62ddf0c0d8b42a12a34a0f81b866b823a85af7a8cb7908ea6080604fcc64e9fb8c3ad24eb3f7aa8ef6ffc8333d004d778e563fab4e152d054a2dca266c9d0287
+  data.tar.gz: 19bfc66be4caace10de8c4c602a9ff9ed9d397db2f836b60351350ecade6abf9f046de53b2b717ac1a49e483f470a15337cecb27f6b654b8bd9b51d09bb65c62

data/bin/protxml_to_psql.rb

@@ -301,7 +301,7 @@ def lookup_spectra_from_files(file_list,matched_spectra)
 	total_spectra=0
 
 	file_list.each do |file|
-		mzml_parser = MzMLParser.new(file)
+		mzml_parser = MzMLParser.new(find_file(file))
 
 		spec = mzml_parser.next_spectrum
 
@@ -334,7 +334,22 @@ def lookup_spectra_from_files(file_list,matched_spectra)
 
 end
 
-# Setup specific command-line options for this tool. Other options are inherited from ProphetTool
+def find_file(path)
+	if File.exists? path
+		return path
+	else # Search in search paths
+		filename = Pathname.new(path).basename.to_s
+		$search_paths.each do |sp|  
+			pth = File.join(sp,filename)
+			if File.exists? pth
+				return pth				
+			end
+		end
+	end
+	return nil
+end
+
+# Setup specific command-line options for this tool. Other options are inherited
 #
 tool=Tool.new([:explicit_output,:over_write])
 tool.option_parser.banner = "Convert a protXML file to a sqlite database.\n\nUsage: protxml_to_psql.rb [options] file1.protXML"
@@ -347,6 +362,7 @@ exit unless tool.check_options(true,[:explicit_output])
 
 input_file=ARGV.shift
 
+$search_paths = [Pathname.new(input_file).dirname.to_s,Pathname.new(".").realpath.to_s]
 
 if File.exists? tool.explicit_output
 	throw "Cant overwrite existing db #{tool.explicit_output}" unless tool.over_write
@@ -386,7 +402,7 @@ matched_spectra=[]
 headers_with_inputs.each do |header|  
 	pepxml_files = header.attributes['source_files'].split(",")
 	pepxml_files.each do |pepxml_file|
-		matched_spectra.concat insert_psms_from_file(pepxml_file)
+		matched_spectra.concat insert_psms_from_file(find_file(pepxml_file))
 	end
 end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: protk
 version: !ruby/object:Gem::Version
-  version: 1.3.1.pre2
+  version: 1.3.1.pre3
 platform: ruby
 authors:
 - Ira Cooke
@@ -216,38 +216,7 @@ extensions:
 - ext/decoymaker/extconf.rb
 extra_rdoc_files: []
 files:
-- lib/protk/bio_gff3_extensions.rb
-- lib/protk/bio_sptr_extensions.rb
-- lib/protk/command_runner.rb
-- lib/protk/constants.rb
-- lib/protk/convert_util.rb
-- lib/protk/data/make_uniprot_table.rb
-- lib/protk/fastadb.rb
-- lib/protk/galaxy_stager.rb
-- lib/protk/galaxy_util.rb
-- lib/protk/gffdb.rb
-- lib/protk/manage_db_tool.rb
-- lib/protk/mascot_util.rb
-- lib/protk/mzml_parser.rb
-- lib/protk/omssa_util.rb
-- lib/protk/openms_defaults.rb
-- lib/protk/peptide.rb
-- lib/protk/pepxml.rb
-- lib/protk/plasmodb.rb
-- lib/protk/prophet_tool.rb
-- lib/protk/protein.rb
-- lib/protk/protein_to_genome_mapper.rb
-- lib/protk/protxml_to_gff_tool.rb
-- lib/protk/randomize.rb
-- lib/protk/search_tool.rb
-- lib/protk/setup_tool.rb
-- lib/protk/swissprot_database.rb
-- lib/protk/tandem_search_tool.rb
-- lib/protk/tool.rb
-- lib/protk/uniprot_mapper.rb
-- lib/protk.rb
-- lib/protk/manage_db_rakefile.rake
-- lib/protk/setup_rakefile.rake
+- README.md
 - bin/add_retention_times.rb
 - bin/augustus_to_proteindb.rb
 - bin/interprophet.rb
@@ -271,14 +240,22 @@ files:
 - bin/tandem_to_pepxml.rb
 - bin/unimod_to_loc.rb
 - bin/uniprot_mapper.rb
-- README.md
-- lib/protk/data/apt-get_packages.yaml
-- lib/protk/data/brew_packages.yaml
-- lib/protk/data/default_config.yml
+- ext/decoymaker/decoymaker.c
+- ext/decoymaker/extconf.rb
+- lib/protk.rb
+- lib/protk/bio_gff3_extensions.rb
+- lib/protk/bio_sptr_extensions.rb
+- lib/protk/command_runner.rb
+- lib/protk/constants.rb
+- lib/protk/convert_util.rb
 - lib/protk/data/ExecutePipeline.trf
 - lib/protk/data/FeatureFinderCentroided.ini
 - lib/protk/data/FeatureFinderIsotopeWavelet.ini
+- lib/protk/data/apt-get_packages.yaml
+- lib/protk/data/brew_packages.yaml
+- lib/protk/data/default_config.yml
 - lib/protk/data/galaxyenv.sh
+- lib/protk/data/make_uniprot_table.rb
 - lib/protk/data/predefined_db.crap.yaml
 - lib/protk/data/predefined_db.sphuman.yaml
 - lib/protk/data/predefined_db.swissprot_annotation.yaml
@@ -293,8 +270,31 @@ files:
 - lib/protk/data/uniprot_accessions_table.txt
 - lib/protk/data/uniprot_input_accessions.loc
 - lib/protk/data/yum_packages.yaml
-- ext/decoymaker/decoymaker.c
-- ext/decoymaker/extconf.rb
+- lib/protk/fastadb.rb
+- lib/protk/galaxy_stager.rb
+- lib/protk/galaxy_util.rb
+- lib/protk/gffdb.rb
+- lib/protk/manage_db_rakefile.rake
+- lib/protk/manage_db_tool.rb
+- lib/protk/mascot_util.rb
+- lib/protk/mzml_parser.rb
+- lib/protk/omssa_util.rb
+- lib/protk/openms_defaults.rb
+- lib/protk/peptide.rb
+- lib/protk/pepxml.rb
+- lib/protk/plasmodb.rb
+- lib/protk/prophet_tool.rb
+- lib/protk/protein.rb
+- lib/protk/protein_to_genome_mapper.rb
+- lib/protk/protxml_to_gff_tool.rb
+- lib/protk/randomize.rb
+- lib/protk/search_tool.rb
+- lib/protk/setup_rakefile.rake
+- lib/protk/setup_tool.rb
+- lib/protk/swissprot_database.rb
+- lib/protk/tandem_search_tool.rb
+- lib/protk/tool.rb
+- lib/protk/uniprot_mapper.rb
 homepage: http://rubygems.org/gems/protk
 licenses:
 - LGPL-2.1
@@ -315,8 +315,9 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: 1.3.1
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.14
+rubygems_version: 2.2.1
 signing_key: 
 specification_version: 4
 summary: Proteomics Toolkit
 test_files: []
+has_rdoc: