in progress

diff --git a/forester/ruby/evoruby/lib/evo/io/parser/uniprot_parser.rb b/forester/ruby/evoruby/lib/evo/io/parser/uniprot_parser.rb
index 28a5730..ec2b9f0 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/io/parser/uniprot_parser.rb
+++ b/forester/ruby/evoruby/lib/evo/io/parser/uniprot_parser.rb
@@ -37,9 +37,11 @@ module Evoruby
       dr = []
       read = false
       File.open( @file ).each do | line |
-        if line.index ID == 0
+        if line.index( ID ) == 0
+          puts line 
           ids.each do | id |
-            if line.index id == 0
+            puts " " + id
+            if line.index( id ) == 0
               read = true
               break
             end
@@ -51,7 +53,7 @@ module Evoruby
             e = UniprotEntry.new
             e.de = de
             e.dr = dr
-            entries << e
+            entries[ id ] = e
             de = []
             dr = []
           else

diff --git a/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb b/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb
index 82b2782..e6ba67d 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb
@@ -21,7 +21,7 @@ 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"
@@ -79,7 +79,7 @@ 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 )
@@ -305,7 +305,8 @@ 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, 
+             uniprot_entries )
         end
       end
       outfile.flush()
@@ -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,
+         uniprot_entries      )
 
       dc = 0
       # filter according to i-Evalue threshold
@@ -383,7 +385,8 @@ module Evoruby
         s << r.model + " "
       end
       s << "\t"
-
+     s <<  uniprot_entries[  own.query ]
+       s << "\t"
       overview = make_overview( hmmscan_results_per_protein_filtered, hmm_for_protein_output )
 
       s << overview   + "\t"