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[jalview.git] / forester / ruby / evoruby / lib / evo / tool / hmmscan_summary.rb

diff --git a/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb b/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb
index 82b2782..db82d4a 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb
@@ -8,11 +8,13 @@
 #
 # last modified: 121003
 
+require 'set'
+
 require 'lib/evo/util/constants'
 require 'lib/evo/util/util'
 require 'lib/evo/util/command_line_arguments'
 require 'lib/evo/io/parser/hmmscan_parser'
-require 'lib/evo/io/parser/uniprot_parser'
+require 'lib/evo/io/web/uniprotkb'
 
 module Evoruby
 
@@ -21,7 +23,7 @@ module Evoruby
     PRG_NAME       = "hsp"
     PRG_VERSION    = "2.000"
     PRG_DESC       = "hmmscan summary"
-    PRG_DATE       = "2012.10.19"
+    PRG_DATE       = "2012.10.23"
     COPYRIGHT      = "2012 Christian M Zmasek"
     CONTACT        = "phylosoft@gmail.com"
     WWW            = "www.phylosoft.org"
@@ -46,6 +48,8 @@ module Evoruby
 
     def run
 
+
+
       Util.print_program_information( PRG_NAME,
         PRG_VERSION,
         PRG_DESC,
@@ -79,7 +83,7 @@ module Evoruby
       allowed_opts.push( IGNORE_DUF_OPTION )
       allowed_opts.push( PARSE_OUT_DESCRIPITION_OPTION )
       allowed_opts.push( HMM_FOR_PROTEIN_OUTPUT )
-       allowed_opts.push( UNIPROT )
+      allowed_opts.push( UNIPROT )
 
       disallowed = cla.validate_allowed_options_as_str( allowed_opts )
       if ( disallowed.length > 0 )
@@ -132,11 +136,11 @@ module Evoruby
           Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
         end
       end
-      
+
       uniprot = ""
-       if ( cla.is_option_set?( UNIPROT ) )
+      if ( cla.is_option_set?( UNIPROT ) )
         begin
-           uniprot = cla.get_option_value( UNIPROT )
+          uniprot = cla.get_option_value( UNIPROT )
         rescue ArgumentError => e
           Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
         end
@@ -175,15 +179,15 @@ module Evoruby
       else
         puts( "column delimiter     : " + column_delimiter )
       end
-      if fs_e_value_threshold >= 0.0 
+      if fs_e_value_threshold >= 0.0
         puts( "E-value threshold   : " + fs_e_value_threshold.to_s )
       else
         puts( "E-value threshold   : no threshold" )
       end
-      if !hmm_for_protein_output.empty? 
+      if !hmm_for_protein_output.empty?
         puts( "HMM for proteins    : " + hmm_for_protein_output )
       end
-      if !uniprot.empty? 
+      if !uniprot.empty?
         puts( "Uniprot             : " + uniprot )
       end
       puts()
@@ -198,7 +202,7 @@ module Evoruby
           fs_e_value_threshold,
           hmm_for_protein_output,
           uniprot )
-      rescue ArgumentError, IOError => e
+      rescue IOError => e
         Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
       end
       domain_counts = get_domain_counts()
@@ -227,17 +231,15 @@ module Evoruby
         fs_e_value_threshold,
         hmm_for_protein_output,
         uniprot )
+
+
+
       Util.check_file_for_readability( inpath )
       Util.check_file_for_writability( outpath )
 
       hmmscan_parser = HmmscanParser.new( inpath )
       results = hmmscan_parser.parse
-      
-      uniprot_entries = nil
-      if !uniprot.empty? 
-        uniprot_entries = read_uniprot( results, uniprot  )
-      end
-      
+
       outfile = File.open( outpath, "a" )
 
       query     = ""
@@ -249,7 +251,7 @@ module Evoruby
 
       hmmscan_results_per_protein = []
 
-      
+
 
       prev_query = ""
 
@@ -285,7 +287,8 @@ module Evoruby
               process_hmmscan_results_per_protein( hmmscan_results_per_protein,
                 fs_e_value_threshold,
                 hmm_for_protein_output,
-                i_e_value_threshold )
+                i_e_value_threshold,
+                true )
             end
             hmmscan_results_per_protein.clear
           end
@@ -300,30 +303,28 @@ module Evoruby
           end
         end
       end
-      if !hmm_for_protein_output.empty?
-        if !hmmscan_results_per_protein.empty?
-          process_hmmscan_results_per_protein( hmmscan_results_per_protein,
-            fs_e_value_threshold,
-            hmm_for_protein_output,
-            i_e_value_threshold )
-        end
+      if !hmm_for_protein_output.empty? && !hmmscan_results_per_protein.empty?
+        process_hmmscan_results_per_protein( hmmscan_results_per_protein,
+          fs_e_value_threshold,
+          hmm_for_protein_output,
+          i_e_value_threshold,
+          true )
       end
+
       outfile.flush()
       outfile.close()
 
     end # def parse
 
-    
-     def read_uniprot( hmmscan_results, uniprot  )  
-        ids = []
-         hmmscan_results.each do | r |
-           ids << r.query
-         end 
-         uniprot_parser = UniprotParser.new uniprot
-         uniprot_entries = uniprot_parser.parse ids 
-         uniprot_entries
-      end
-    
+    def process_id( id )
+      if  id =~ /(sp|tr)\|\S+\|(\S+)/
+        id = $2
+      end
+      id
+    end
+
+
+
     def count_model( model )
       if ( @domain_counts.has_key?( model ) )
         count = @domain_counts[ model ].to_i
@@ -337,7 +338,8 @@ module Evoruby
     def process_hmmscan_results_per_protein( hmmscan_results_per_protein,
         fs_e_value_threshold,
         hmm_for_protein_output,
-        i_e_value_threshold )
+        i_e_value_threshold,
+        uniprotkb )
 
       dc = 0
       # filter according to i-Evalue threshold
@@ -383,7 +385,34 @@ module Evoruby
         s << r.model + " "
       end
       s << "\t"
+      e = UniprotKB::get_entry_by_id( process_id( own.query ) )
+      # if e != nil && e.de != nil
+      #   e.de.each do |i|
+      #
+      #   end
+      # else
+      #   s << "-"
+      # end
+      s << "\t"
+      if e != nil && e.dr != nil
+        e.dr.each do | dr |
+          if dr != nil
+            if dr =~ /PDB;\s+([A-Z0-9]{4});/
+              s << $1
+
+            end
+          end
+        end
+      else
+        s << "-"
+      end
+      s << "\t"
+
 
+
+
+
+      s << "\t"
       overview = make_overview( hmmscan_results_per_protein_filtered, hmm_for_protein_output )
 
       s << overview   + "\t"