protk 1.2.6.pre4 → 1.2.6.pre5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 459bfa1d39a6c8b11d6b04f4c2c30a0b85115f30
+  metadata.gz: 876bb41de9b07d9a9b08132e2d44439e6de0c990
+  data.tar.gz: 799b9dd4c2a8c3720e315a7ade0085a7f54f31f9
 SHA512:
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+  metadata.gz: db8bf6c295925c649431ce25eccf10c55a15c4146f827d9ed9f55ad95f8ad50f3fc7aed04cf6d9a78d5311244e4ba7fd6e8954f068b50385f852a9b729c1e017
+  data.tar.gz: 312cd4aefc3380cd2311c41d0dac8dacf40d4f58a404fb6c86ed67e9454895f877ad7a465c55c8d3a721fd10e4a78b709975be3c530ed87502f9da4adbcfa35f

data/bin/augustus_to_proteindb.rb

@@ -104,6 +104,12 @@ def cds_to_header_text(coding_sequence,transcript_id)
   "#{istart}|#{iend}"
 end
 
+# Scaffold identifiers cant contain pipes
+#
+def sanitize_scaffold_idstring(raw_scaffold_string)
+  raw_scaffold_string.split("|")[0]
+end
+
 def sequence_fasta_header(transcript_line,coding_sequences,scaffold)
 
   tmatch=transcript_line.match(/transcript\t(\d+)\t(\d+).*?([-\+]{1}).*?ID=(.*?);/)
@@ -114,7 +120,7 @@ def sequence_fasta_header(transcript_line,coding_sequences,scaffold)
   tstrand = "rev" if tmatch[3]=="-"
 
   tid=tmatch[4]
-  header=">lcl|#{scaffold}_#{tstrand}_#{tid} #{tstart}|#{tend}"
+  header=">lcl|#{sanitize_scaffold_idstring(scaffold)}_#{tstrand}_#{tid} #{tstart}|#{tend}"
   if $add_transcript_info
     coding_sequences.each { |coding_sequence| header << " #{cds_to_header_text(coding_sequence,tid)}" }
   end

data/bin/interprophet.rb

@@ -69,7 +69,7 @@ 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="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=#{prophet_tool.min_prob}" if ( prophet_tool.min_prob !="" )
 
   inputs = ARGV.collect {|file_name| 

data/bin/mascot_to_pepxml.rb

@@ -61,7 +61,7 @@ ARGV.each do |file_name|
   else  #Mascot2XML doesn't support explicitly named output files so we move the file to an appropriate output filename after finishing
     new_basename="#{this_dir}/#{MascotUtil.input_basename(name)}_mascot2xml"
     cmd="cp #{name} #{new_basename}.dat"
-    cmd << "; #{genv.mascot2xml} #{new_basename}.dat -D#{current_db} -E#{tool.enzyme}"
+    cmd << "; Mascot2XML #{new_basename}.dat -D#{current_db} -E#{tool.enzyme}"
     cmd << " -shortid" if tool.shortid
     cmd << "; mv #{new_basename}.pep.xml #{tool.explicit_output}; rm #{new_basename}.dat"
     repair_script="#{File.dirname(__FILE__)}/repair_run_summary.rb"     

data/bin/omssa_search.rb

@@ -82,7 +82,7 @@ case
 when Pathname.new(search_tool.database).exist? # It's an explicitly named db
   current_db=Pathname.new(search_tool.database).realpath.to_s
   if(not FileTest.exists?("#{current_db}.phr"))
-    make_blastdb_cmd << "#{genv.makeblastdb} -dbtype prot -parse_seqids -in #{current_db}; "
+    make_blastdb_cmd << "makeblastdb -dbtype prot -parse_seqids -in #{current_db}; "
   end
 else
   current_db=search_tool.current_database :fasta
@@ -121,7 +121,7 @@ ARGV.each do |filename|
   
     # The basic command
     #
-    cmd = "#{make_blastdb_cmd} #{genv.omssacl} -nt #{search_tool.nthreads} -d #{current_db} -fm #{input_path} -op #{output_path} -w"
+    cmd = "#{make_blastdb_cmd} omssacl -nt #{search_tool.nthreads} -d #{current_db} -fm #{input_path} -op #{output_path} -w"
 
     #Missed cleavages
     #

data/bin/peptide_prophet.rb

@@ -170,6 +170,9 @@ def generate_command(genv,prophet_tool,inputs,output,database,engine)
   
   cmd="xinteract -N#{output}  -l7 -eT -D'#{database}' "
 
+  # Do not produce png plots
+  cmd << " -Ot "
+
   if prophet_tool.glyco 
     cmd << " -Og "
   end

data/bin/protein_prophet.rb

@@ -103,7 +103,7 @@ p output_file
 
 if ( !Pathname.new(output_file).exist? || prophet_tool.over_write )
 
-  cmd="ProteinProphet "
+  cmd="ProteinProphet NOPLOT "
 
   inputs = ARGV.collect {|file_name| 
     file_name.chomp
@@ -131,11 +131,11 @@ else
   genv.log("Protein Prophet output file #{output_file} already exists. Run with -r option to replace",:warn)   
 end
 
-if for_galaxy
+# if for_galaxy
   # Restore references to peptide prophet xml so downstream tools like 
   # libra can find it.
-  input_stager.restore_references("protein_prophet_results.prot.xml")
-end
+  # input_stager.restore_references("protein_prophet_results.prot.xml")
+# end
 
 
 

data/bin/tandem_search.rb

@@ -108,9 +108,7 @@ end
 
 # Set search engine specific parameters on the SearchTool object
 #
-tandem_bin="#{genv.xtandem}"
-
-throw "Could not find X!Tandem executable" unless FileTest.exists?(tandem_bin)
+tandem_bin="tandem"
 
 tandem_params=search_tool.tandem_params
 
@@ -432,7 +430,7 @@ ARGV.each do |filename|
     #
     unless search_tool.no_pepxml
       repair_script="#{File.dirname(__FILE__)}/repair_run_summary.rb"
-      cmd << "; #{genv.tandem2xml} #{output_path} #{pepxml_path}; #{repair_script} #{pepxml_path}"
+      cmd << "; Tandem2XML #{output_path} #{pepxml_path}; #{repair_script} #{pepxml_path}"
       if search_tool.tandem_output 
         cmd << "; cp #{output_path} #{search_tool.tandem_output}"
       else

data/lib/protk/constants.rb

@@ -91,7 +91,7 @@ class Constants
   end
   
   def blast_root
-      "#{@protk_dir}/blast"   
+      "#{@protk_dir}/tools/blast"   
   end
   
   def log_file

data/lib/protk/fastadb.rb

@@ -10,8 +10,8 @@ class FastaDB
   def initialize(blast_database_file_path)
     env = Constants.new
     @database = blast_database_file_path
-    @makedbcmd = env.makeblastdb
-    @searchdbcmd = env.searchblastdb
+    @makedbcmd = "makeblastdb"
+    @searchdbcmd = "blastdbcmd"
   end
 
   def self.create(blast_database_file_path,input_fasta_filepath,type='nucl')

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: protk
 version: !ruby/object:Gem::Version
-  version: 1.2.6.pre4
+  version: 1.2.6.pre5
 platform: ruby
 authors:
 - Ira Cooke