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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 55ba7a4..08de9c1 100644 (file)
--- 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'
 
@@ -14,19 +13,18 @@ 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/web/uniprotkb'
 
 module Evoruby
 
   class HmmscanSummary
 
     PRG_NAME       = "hsp"
-    PRG_VERSION    = "2.000"
+    PRG_VERSION    = "2.002"
     PRG_DESC       = "hmmscan summary"
-    PRG_DATE       = "2012.10.23"
-    COPYRIGHT      = "2012 Christian M Zmasek"
-    CONTACT        = "phylosoft@gmail.com"
-    WWW            = "www.phylosoft.org"
+    PRG_DATE       = "130319"
+    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"
@@ -35,7 +33,6 @@ module Evoruby
     HMM_FOR_PROTEIN_OUTPUT        = "m"
     IGNORE_DUF_OPTION             = "i"
     PARSE_OUT_DESCRIPITION_OPTION = "a"
-    UNIPROT                       = "u"
     HELP_OPTION_1                 = "help"
     HELP_OPTION_2                 = "h"
 
@@ -49,8 +46,6 @@ module Evoruby
 
     def run
 
-
-
       Util.print_program_information( PRG_NAME,
         PRG_VERSION,
         PRG_DESC,
@@ -84,7 +79,6 @@ 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( SPECIES_OPTION )
 
       disallowed = cla.validate_allowed_options_as_str( allowed_opts )
@@ -118,8 +112,6 @@ module Evoruby
         end
       end
 
-
-
       fs_e_value_threshold = -1.0
       if ( cla.is_option_set?( FS_E_VALUE_THRESHOLD_OPTION ) )
         begin
@@ -141,15 +133,6 @@ module Evoruby
         end
       end
 
-      uniprot = ""
-      if ( cla.is_option_set?( UNIPROT ) )
-        begin
-          uniprot = cla.get_option_value( UNIPROT )
-        rescue ArgumentError => e
-          Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
-        end
-      end
-
       species = "HUMAN"
       if ( cla.is_option_set?( SPECIES_OPTION ) )
         begin
@@ -201,9 +184,6 @@ module Evoruby
       if !hmm_for_protein_output.empty?
         puts( "HMM for proteins    : " + hmm_for_protein_output )
       end
-      if !uniprot.empty?
-        puts( "Uniprot             : " + uniprot )
-      end
       puts()
 
       begin
@@ -215,14 +195,12 @@ module Evoruby
           parse_descriptions,
           fs_e_value_threshold,
           hmm_for_protein_output,
-          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 + ")" )
@@ -245,11 +223,8 @@ module Evoruby
         get_descriptions,
         fs_e_value_threshold,
         hmm_for_protein_output,
-        uniprot,
         species )
 
-
-
       Util.check_file_for_readability( inpath )
       Util.check_file_for_writability( outpath )
 
@@ -267,8 +242,6 @@ module Evoruby
 
       hmmscan_results_per_protein = []
 
-
-
       prev_query = ""
 
       results.each do | r |
@@ -304,7 +277,6 @@ module Evoruby
                 fs_e_value_threshold,
                 hmm_for_protein_output,
                 i_e_value_threshold,
-                false,
                 species )
             end
             hmmscan_results_per_protein.clear
@@ -326,13 +298,11 @@ module Evoruby
           fs_e_value_threshold,
           hmm_for_protein_output,
           i_e_value_threshold,
-          false,
           species )
       end
 
       outfile.flush()
       outfile.close()
-
     end # def parse
 
     def process_id( id )
@@ -342,8 +312,6 @@ module Evoruby
       id
     end
 
-
-
     def count_model( model )
       if ( @domain_counts.has_key?( model ) )
         count = @domain_counts[ model ].to_i
@@ -358,7 +326,6 @@ module Evoruby
         fs_e_value_threshold,
         hmm_for_protein_output,
         i_e_value_threshold,
-        uniprotkb,
         species )
 
       dc = 0
@@ -369,13 +336,12 @@ module Evoruby
       hmmscan_results_per_protein.each do | r |
 
 
-
         if r.model == hmm_for_protein_output
-          if i_e_value_threshold >= 0.0 && 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 i_e_value_threshold < 0 || 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
@@ -409,13 +375,6 @@ module Evoruby
       end
       s << "\t"
 
-      #e = UniprotKB::get_entry_by_id( process_id( own.query ) )
-
-      #if e != nil
-      #  s << uniprot_annotation( e )
-      # # s << "\uniprot_annotationt"
-      #end
-
       overview = make_overview( hmmscan_results_per_protein_filtered, hmm_for_protein_output )
 
       s << overview  + "\t"
@@ -424,7 +383,6 @@ module Evoruby
 
       prev_r = nil
       hmmscan_results_per_protein_filtered.each do | r |
-
         if  prev_r != nil
           s << make_interdomain_sequence( r.env_from - prev_r.env_to - 1 )
         else
@@ -438,23 +396,10 @@ module Evoruby
         s << "]"
         prev_r = r
       end
-      s << make_interdomain_sequence( own.qlen - prev_r.env_from, false )
+      s << make_interdomain_sequence( own.qlen - prev_r.env_to, false )
       puts s
     end
 
-    def uniprot_annotation( e )
-      s = ""
-      pdb_ids = e.get_pdb_ids
-      if !pdb_ids.empty?
-        pdb_ids.each do | pdb |
-          s << pdb << ", "
-        end
-      else
-        s << "-"
-      end
-      s
-    end
-
     def calc_linkers(  hmmscan_results_per_protein_filtered, hmm_for_protein_output )
       linkers = ""
       prev_r = nil
@@ -509,7 +454,6 @@ module Evoruby
     end
 
 
-
     def print_help()
       puts( "Usage:" )
       puts()
@@ -521,6 +465,7 @@ 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