inprogress

[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 a443ca2..3b29968 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'
 
@@ -21,12 +20,12 @@ 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"
@@ -49,8 +48,6 @@ module Evoruby
 
     def run
 
-
-
       Util.print_program_information( PRG_NAME,
         PRG_VERSION,
         PRG_DESC,
@@ -67,7 +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
@@ -118,7 +115,7 @@ module Evoruby
         end
       end
 
-      
+
 
       fs_e_value_threshold = -1.0
       if ( cla.is_option_set?( FS_E_VALUE_THRESHOLD_OPTION ) )
@@ -151,7 +148,7 @@ module Evoruby
       end
 
       species = "HUMAN"
-       if ( cla.is_option_set?( SPECIES_OPTION ) )
+      if ( cla.is_option_set?( SPECIES_OPTION ) )
         begin
           species = cla.get_option_value( SPECIES_OPTION )
         rescue ArgumentError => e
@@ -222,7 +219,6 @@ module Evoruby
       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 + ")" )
@@ -248,8 +244,6 @@ module Evoruby
         uniprot,
         species )
 
-
-
       Util.check_file_for_readability( inpath )
       Util.check_file_for_writability( outpath )
 
@@ -267,8 +261,6 @@ module Evoruby
 
       hmmscan_results_per_protein = []
 
-
-
       prev_query = ""
 
       results.each do | r |
@@ -279,21 +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
 
@@ -320,17 +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 )
@@ -340,8 +333,6 @@ module Evoruby
       id
     end
 
-
-
     def count_model( model )
       if ( @domain_counts.has_key?( model ) )
         count = @domain_counts[ model ].to_i
@@ -357,7 +348,7 @@ module Evoruby
         hmm_for_protein_output,
         i_e_value_threshold,
         uniprotkb,
-        species      )
+        species )
 
       dc = 0
       # filter according to i-Evalue threshold
@@ -365,12 +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 i_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
@@ -403,11 +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 )
@@ -503,7 +499,6 @@ module Evoruby
     end
 
 
-
     def print_help()
       puts( "Usage:" )
       puts()
@@ -515,6 +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