protk 1.2.0 → 1.2.1

data/lib/protk/manage_db_rakefile.rake

@@ -192,6 +192,14 @@ def archive_fasta_file(filename)
   end
 end
 
+def cleanup_file(filename)
+  if  (File.exist? filename  )
+    archive_filename="#{filename}.tmp"
+    p "Cleaning up #{filename}"
+    FileUtils.mv(filename,archive_filename,:force=>true)
+  end
+end
+
 #####################
 # Source Files      #
 #####################
@@ -308,7 +316,9 @@ file raw_db_filename => [source_files,dbspec_file].flatten do
   if ( format == "fasta" && source_filters.length > 0 ) # We can perform concat and filter for fasta only
 
     archive_fasta_file(raw_db_filename) if dbspec[:archive_old]
-  
+
+    cleanup_file(raw_db_filename)
+
     output_fh=File.open(raw_db_filename, "w")
 
     id_regexes=dbspec[:id_regexes]
@@ -360,6 +370,9 @@ file raw_db_filename => [source_files,dbspec_file].flatten do
   else # Other formats just copy a file across ... must be a single source
 
     throw "Only a single source file is permitted for formats other than fasta" unless source_files.length == 1
+
+    cleanup_file(raw_db_filename)
+
     
     sh "cp #{source_files[0]} #{raw_db_filename}" do |ok,res|
       if ! ok 
@@ -379,6 +392,7 @@ file decoy_db_filename => raw_db_filename do
 
   archive_fasta_file(decoy_db_filename) if dbspec[:archive_old]
 
+  cleanup_file(decoy_db_filename)
 
   decoys_filename = "#{dbdir}/decoys_only.fasta"
   decoy_prefix=dbspec[:decoy_prefix]
@@ -450,7 +464,7 @@ if dbspec[:make_blast_index]
   blast_index_files=["#{db_filename}.phr"]
   blast_index_files.each do |indfile|
     file indfile => db_filename do
-      cmd="cd #{dbdir}; #{$genv.makeblastdb} -in #{db_filename} -parse_seqids -dbtype prot"
+      cmd="cd #{dbdir}; #{$genv.makeblastdb} -in #{db_filename} -parse_seqids -dbtype prot -max_file_sz 20000000000"
       p "Creating blast index"
       sh %{ #{cmd} }
     end
@@ -476,18 +490,18 @@ if dbspec[:make_msgf_index]
 end
 
 if format=="dat" && dbspec[:is_annotation_db]
-  dat_index_files=FileList.new(["config.dat","id_AC.index","key_ID.key"].collect {|file| "#{dbdir}/#{file}"}  )
+  dat_index_file= "#{dbdir}/id_AC.index"
+
+  cleanup_file dat_index_file #Regenerate indexes every time
   
-  dat_index_files.each do |indexfile|
-    file indexfile => db_filename do
-      puts "Indexing annotation database"
-      dbclass=Bio::SPTR
-      parser = Bio::FlatFileIndex::Indexer::Parser.new(dbclass, nil, nil)
-      Bio::FlatFileIndex::Indexer::makeindexFlat(dbdir, parser, {}, db_filename)
-    end
+  file dat_index_file => db_filename do
+    puts "Indexing annotation database"
+    dbclass=Bio::SPTR
+    parser = Bio::FlatFileIndex::Indexer::Parser.new(dbclass, nil, nil)
+    Bio::FlatFileIndex::Indexer::makeindexFlat(dbdir, parser, {}, db_filename)
   end
   
-  task dbname => dat_index_files
+  task dbname => dat_index_file
   
 end
 

data/lib/protk/omssa_util.rb

@@ -15,7 +15,7 @@ class OMSSAUtil
     pepxml_doc=parser.parse
     rt_table=MascotUtil.index_mgf_times(mgf_file)
     
-    p "Retention time table #{rt_table}"
+ #   p "Retention time table #{rt_table}"
     
 #    queries=pepxml_doc.find('//x:spectrum_query','x:http://regis-web.systemsbiology.net/pepXML')
     queries=pepxml_doc.find('//spectrum_query')    

data/lib/protk/setup_rakefile.rake

@@ -141,7 +141,7 @@ tpp_url = "https://dl.dropbox.com/u/226794/TPP-4.6.1.tgz"
 tpp_download_file = download_task tpp_url, tpp_packagefile
 
 # Build
-file tpp_installed_file => [:perl_locallib,@build_dir,tpp_download_file] do
+file tpp_installed_file => [@build_dir,tpp_download_file] do
 	sh %{cp #{@download_dir}/#{tpp_packagefile} #{@build_dir}}
 	sh %{eval $(perl -I#{perl_dir}/lib/perl5 -Mlocal::lib=#{perl_dir});cpanm --local-lib=#{env.protk_dir}/perl5 XML::Parser}
 	sh %{eval $(perl -I#{perl_dir}/lib/perl5 -Mlocal::lib=#{perl_dir});cpanm --local-lib=#{env.protk_dir}/perl5 CGI --force}
@@ -303,7 +303,7 @@ def platform_cmake_args
 	''
 end
 
-openms_version="1.9.0"
+openms_version="1.10.0"
 openms_packagefile="OpenMS-#{openms_version}.tar.gz"
 openms_url="https://dl.dropbox.com/u/226794/#{openms_packagefile}"
 openms_installed_file="#{env.featurefinderisotopewavelet}"
@@ -322,6 +322,43 @@ end
 
 task :openms => openms_installed_file
 
+#
+# X!Tandem
+#
+
+def tandem_platform
+	if RbConfig::CONFIG['host_os'] =~ /darwin/ 
+		return 'osx-intel'
+	end
+	'linux'
+end
+
+tandem_version="13-02-01-1"
+tandem_packagefile="tandem-#{tandem_platform}-#{tandem_version}.zip"
+tandem_url="ftp://ftp.thegpm.org/projects/tandem/source/#{tandem_packagefile}"
+tandem_installed_file="#{env.gpmxtandem}"
+
+download_task tandem_url, tandem_packagefile
+
+file tandem_installed_file => [@build_dir,"#{@download_dir}/#{tandem_packagefile}"] do 
+	sh %{cp #{@download_dir}/#{tandem_packagefile} #{@build_dir}}
+    sh %{cd #{@build_dir}; unzip #{tandem_packagefile}}
+    sh %{mkdir -p #{env.tandem_root}}
+    tandem_dirname = "#{tandem_packagefile.chomp('.zip')}"
+
+    if ( tandem_platform=="linux") #Must compile
+    	tandem_src_dir = "#{@build_dir}/#{tandem_dirname}/#{tandem_dirname}/src/"
+    	sh %{cd #{tandem_src_dir}; make}
+    	sh %{cd #{@build_dir}; cp -r ./#{tandem_dirname}/#{tandem_dirname}/bin  #{env.tandem_root}/}
+    else
+    	sh %{cd #{@build_dir}; cp -r ./#{tandem_packagefile.chomp('.zip')}/* #{env.tandem_root}/}
+    	sh %{chmod u+x #{env.gpmtandem}}
+    end
+
+end
+
+task :tandem => tandem_installed_file
+
 #
 # Galaxy Environment
 #

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: protk
 version: !ruby/object:Gem::Version
-  version: 1.2.0
+  version: 1.2.1
   prerelease: 
 platform: ruby
 authors:
@@ -170,15 +170,20 @@ executables:
 - toppas_pipeline.rb
 - gffmerge.rb
 - sixframe.rb
+- uniprot_annotation.rb
 extensions:
 - ext/protk/extconf.rb
 extra_rdoc_files: []
 files:
+- lib/convert_util.rb
+- lib/pepxml.rb
+- lib/protk/big_search_tool.rb
 - lib/protk/bio_sptr_extensions.rb
 - lib/protk/biotools_excel_converter.rb
 - lib/protk/command_runner.rb
 - lib/protk/constants.rb
 - lib/protk/convert_util.rb
+- lib/protk/data/make_uniprot_table.rb
 - lib/protk/eupathdb_gene_information_table.rb
 - lib/protk/fastadb.rb
 - lib/protk/galaxy_stager.rb
@@ -201,6 +206,7 @@ files:
 - lib/protk/uniprot_mapper.rb
 - lib/protk/xtandem_defaults.rb
 - lib/protk.rb
+- lib/protk/big_search_rakefile.rake
 - lib/protk/manage_db_rakefile.rake
 - lib/protk/setup_rakefile.rake
 - bin/annotate_ids.rb
@@ -226,8 +232,10 @@ files:
 - bin/repair_run_summary.rb
 - bin/sixframe.rb
 - bin/tandem_search.rb
+- bin/template_search.rb
 - bin/toppas_pipeline.rb
 - bin/unimod_to_loc.rb
+- bin/uniprot_annotation.rb
 - bin/uniprot_mapper.rb
 - bin/xls_to_table.rb
 - bin/xpress.rb
@@ -243,9 +251,13 @@ files:
 - lib/protk/data/predefined_db.sphuman.yaml
 - lib/protk/data/predefined_db.swissprot_annotation.yaml
 - lib/protk/data/predefined_db.swissprot_fasta_annotation.yaml
+- lib/protk/data/predefined_db.trembl_annotation.yaml
 - lib/protk/data/tandem_params.xml
 - lib/protk/data/taxonomy_template.xml
 - lib/protk/data/unimod.xml
+- lib/protk/data/uniprot_accessions.loc
+- lib/protk/data/uniprot_accessions_table.txt
+- lib/protk/data/uniprot_input_accessions.loc
 - lib/protk/data/yum_packages.yaml
 - ext/protk/protk.c
 - ext/protk/extconf.rb