X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fevoruby%2Flib%2Fevo%2Ftool%2Fhmmscan_summary.rb;h=bb32da53ffc2b38470d5347f45c2ea97ca9d5935;hb=2f17bcaa7c1b364b5dd8ba7109dea5e5c0575b1e;hp=485da20e4bda1400b1b27ccccef9c5dcfd643170;hpb=9e45dc6637c155a7f44931798e79fa2976256a98;p=jalview.git

diff --git a/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb b/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb
index 485da20..bb32da5 100644
--- a/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb
@@ -6,7 +6,6 @@
 #
 # $Id: hmmscan_parser.rb,v 1.5 2010/12/13 19:00:11 cmzmasek Exp $
 #
-# last modified: 121003
 
 require 'set'
 
@@ -21,14 +20,15 @@ module Evoruby
   class HmmscanSummary
 
     PRG_NAME       = "hsp"
-    PRG_VERSION    = "2.000"
+    PRG_VERSION    = "2.001"
     PRG_DESC       = "hmmscan summary"
-    PRG_DATE       = "2012.10.23"
-    COPYRIGHT      = "2012 Christian M Zmasek"
-    CONTACT        = "phylosoft@gmail.com"
-    WWW            = "www.phylosoft.org"
+    PRG_DATE       = "2013.10.23"
+    COPYRIGHT      = "2013 Christian M Zmasek"
+    CONTACT        = "phyloxml@gmail.com"
+    WWW            = "https://sites.google.com/site/cmzmasek/home/software/forester"
 
     DELIMITER_OPTION              = "d"
+    SPECIES_OPTION                = "s"
     I_E_VALUE_THRESHOLD_OPTION    = "ie"
     FS_E_VALUE_THRESHOLD_OPTION   = "pe"
     HMM_FOR_PROTEIN_OUTPUT        = "m"
@@ -48,16 +48,14 @@ module Evoruby
 
     def run
 
-
-
-      Util.print_program_information( PRG_NAME,
-        PRG_VERSION,
-        PRG_DESC,
-        PRG_DATE,
-        COPYRIGHT,
-        CONTACT,
-        WWW,
-        STDOUT )
+   #   Util.print_program_information( PRG_NAME,
+   #     PRG_VERSION,
+   #     PRG_DESC,
+   #     PRG_DATE,
+   #     COPYRIGHT,
+   #     CONTACT,
+   #     WWW,
+   #     STDOUT )
 
       begin
         cla = CommandLineArguments.new( ARGV )
@@ -66,7 +64,7 @@ module Evoruby
       end
 
       if ( cla.is_option_set?( HELP_OPTION_1 ) ||
-            cla.is_option_set?( HELP_OPTION_2 ) )
+           cla.is_option_set?( HELP_OPTION_2 ) )
         print_help
         exit( 0 )
       end
@@ -84,6 +82,7 @@ module Evoruby
       allowed_opts.push( PARSE_OUT_DESCRIPITION_OPTION )
       allowed_opts.push( HMM_FOR_PROTEIN_OUTPUT )
       allowed_opts.push( UNIPROT )
+      allowed_opts.push( SPECIES_OPTION )
 
       disallowed = cla.validate_allowed_options_as_str( allowed_opts )
       if ( disallowed.length > 0 )
@@ -116,6 +115,8 @@ module Evoruby
         end
       end
 
+
+
       fs_e_value_threshold = -1.0
       if ( cla.is_option_set?( FS_E_VALUE_THRESHOLD_OPTION ) )
         begin
@@ -146,6 +147,15 @@ module Evoruby
         end
       end
 
+      species = "HUMAN"
+      if ( cla.is_option_set?( SPECIES_OPTION ) )
+        begin
+          species = cla.get_option_value( SPECIES_OPTION )
+        rescue ArgumentError => e
+          Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+        end
+      end
+
       ignore_dufs = false
       if ( cla.is_option_set?( IGNORE_DUF_OPTION ) )
         ignore_dufs = true
@@ -156,41 +166,42 @@ module Evoruby
         parse_descriptions = true
       end
 
-      puts()
-      puts( "hmmpfam outputfile  : " + inpath )
-      puts( "outputfile          : " + outpath )
-      if ( i_e_value_threshold >= 0.0 )
-        puts( "i-E-value threshold : " + i_e_value_threshold.to_s )
-      else
-        puts( "i-E-value threshold : no threshold" )
-      end
-      if ( parse_descriptions )
-        puts( "parse descriptions  : true" )
-      else
-        puts( "parse descriptions  : false" )
-      end
-      if ( ignore_dufs )
-        puts( "ignore DUFs         : true" )
-      else
-        puts( "ignore DUFs         : false" )
-      end
-      if ( column_delimiter == "\t" )
-        puts( "column delimiter    : TAB" )
-      else
-        puts( "column delimiter     : " + column_delimiter )
-      end
-      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?
-        puts( "HMM for proteins    : " + hmm_for_protein_output )
-      end
-      if !uniprot.empty?
-        puts( "Uniprot             : " + uniprot )
-      end
-      puts()
+#      puts()
+#      puts( "hmmpfam outputfile  : " + inpath )
+#      puts( "outputfile          : " + outpath )
+#      puts( "species             : " + species )
+#      if ( i_e_value_threshold >= 0.0 )
+#        puts( "i-E-value threshold : " + i_e_value_threshold.to_s )
+#      else
+#        puts( "i-E-value threshold : no threshold" )
+#      end
+#      if ( parse_descriptions )
+#        puts( "parse descriptions  : true" )
+#      else
+#        puts( "parse descriptions  : false" )
+#      end
+#      if ( ignore_dufs )
+#        puts( "ignore DUFs         : true" )
+#      else
+#        puts( "ignore DUFs         : false" )
+#      end
+#      if ( column_delimiter == "\t" )
+#        puts( "column delimiter    : TAB" )
+#      else
+#        puts( "column delimiter     : " + column_delimiter )
+#      end
+#      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?
+#        puts( "HMM for proteins    : " + hmm_for_protein_output )
+#      end
+#      if !uniprot.empty?
+#        puts( "Uniprot             : " + uniprot )
+#      end
+#      puts()
 
       begin
         parse( inpath,
@@ -201,21 +212,21 @@ module Evoruby
           parse_descriptions,
           fs_e_value_threshold,
           hmm_for_protein_output,
-          uniprot )
+          uniprot,
+          species )
       rescue IOError => e
         Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
       end
       domain_counts = get_domain_counts()
 
-
-      puts
-      puts( "domain counts (considering potential i-E-value threshold and ignoring of DUFs):" )
-      puts( "(number of different domains: " + domain_counts.length.to_s + ")" )
-      puts
-      puts( Util.draw_histogram( domain_counts, "#" ) )
-      puts
-      Util.print_message( PRG_NAME, 'OK' )
-      puts
+#      puts
+#      puts( "domain counts (considering potential i-E-value threshold and ignoring of DUFs):" )
+#      puts( "(number of different domains: " + domain_counts.length.to_s + ")" )
+#      puts
+#      puts( Util.draw_histogram( domain_counts, "#" ) )
+#      puts
+#      Util.print_message( PRG_NAME, 'OK' )
+#      puts 
 
     end # def run
 
@@ -230,9 +241,8 @@ module Evoruby
         get_descriptions,
         fs_e_value_threshold,
         hmm_for_protein_output,
-        uniprot )
-
-
+        uniprot,
+        species )
 
       Util.check_file_for_readability( inpath )
       Util.check_file_for_writability( outpath )
@@ -251,8 +261,6 @@ module Evoruby
 
       hmmscan_results_per_protein = []
 
-
-
       prev_query = ""
 
       results.each do | r |
@@ -263,21 +271,21 @@ module Evoruby
         env_to    = r.env_to
 
         if ( ( i_e_value_threshold < 0.0 ) || ( i_e_value <= i_e_value_threshold ) ) &&
-            ( !ignore_dufs || ( model !~ /^DUF\d+/ ) )
+           ( !ignore_dufs || ( model !~ /^DUF\d+/ ) )
           count_model( model )
           outfile.print( query +
-              column_delimiter )
+             column_delimiter )
           if ( get_descriptions )
             outfile.print( desc +
-                column_delimiter )
+               column_delimiter )
           end
           outfile.print( model +
-              column_delimiter +
-              env_from.to_s +
-              column_delimiter +
-              env_to.to_s +
-              column_delimiter +
-              i_e_value.to_s )
+             column_delimiter +
+             env_from.to_s +
+             column_delimiter +
+             env_to.to_s +
+             column_delimiter +
+             i_e_value.to_s )
           outfile.print( Constants::LINE_DELIMITER )
         end
 
@@ -288,7 +296,8 @@ module Evoruby
                 fs_e_value_threshold,
                 hmm_for_protein_output,
                 i_e_value_threshold,
-                true )
+                uniprot,
+                species )
             end
             hmmscan_results_per_protein.clear
           end
@@ -303,17 +312,18 @@ module Evoruby
           end
         end
       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 )
+          uniprot,
+          species )
       end
 
       outfile.flush()
       outfile.close()
-
     end # def parse
 
     def process_id( id )
@@ -323,8 +333,6 @@ module Evoruby
       id
     end
 
-
-
     def count_model( model )
       if ( @domain_counts.has_key?( model ) )
         count = @domain_counts[ model ].to_i
@@ -339,7 +347,8 @@ module Evoruby
         fs_e_value_threshold,
         hmm_for_protein_output,
         i_e_value_threshold,
-        uniprotkb )
+        uniprotkb,
+        species )
 
       dc = 0
       # filter according to i-Evalue threshold
@@ -347,12 +356,14 @@ module Evoruby
       hmmscan_results_per_protein_filtered = []
 
       hmmscan_results_per_protein.each do | r |
+
+
         if r.model == hmm_for_protein_output
-          if r.fs_e_value > fs_e_value_threshold
+          if fs_e_value_threshold > 0.0 && r.fs_e_value > fs_e_value_threshold
             return
           end
         end
-        if r.i_e_value <= i_e_value_threshold
+        if i_e_value_threshold <= 0 || r.i_e_value <= i_e_value_threshold
           hmmscan_results_per_protein_filtered << r
           if r.model == hmm_for_protein_output
             dc += 1
@@ -376,7 +387,7 @@ module Evoruby
 
       s = ""
       s << own.query + "\t"
-      s << "HUMAN" + "\t"
+      s << species + "\t"
       s << own.fs_e_value.to_s + "\t"
       s << own.qlen.to_s + "\t"
       s << dc.to_s + "\t"
@@ -385,11 +396,14 @@ module Evoruby
         s << r.model + " "
       end
       s << "\t"
-      e = UniprotKB::get_entry_by_id( process_id( own.query ) )
 
-      if e != nil
-        s << uniprot_annotation( e )
-        s << "\uniprot_annotationt"
+      if !uniprotkb.empty?
+        #e = UniprotKB::get_entry_by_id( process_id( own.query ) )
+
+        #if e != nil
+        #  s << uniprot_annotation( e )
+        # # s << "\uniprot_annotationt"
+        #end
       end
 
       overview = make_overview( hmmscan_results_per_protein_filtered, hmm_for_protein_output )
@@ -485,7 +499,6 @@ module Evoruby
     end
 
 
-
     def print_help()
       puts( "Usage:" )
       puts()
@@ -497,6 +510,7 @@ module Evoruby
       puts( "           -" + IGNORE_DUF_OPTION  + ": ignore DUFs" )
       puts( "           -" + FS_E_VALUE_THRESHOLD_OPTION  + ": E-value threshold for full protein sequences, only for protein summary" )
       puts( "           -" + HMM_FOR_PROTEIN_OUTPUT + ": HMM for protein summary" )
+      puts( "           -" + SPECIES_OPTION + ": species for protein summary" )
       puts()
     end