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 db82d4a..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'
 
@@ -21,14 +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"
@@ -48,8 +48,6 @@ module Evoruby
 
     def run
 
-
-
       Util.print_program_information( PRG_NAME,
         PRG_VERSION,
         PRG_DESC,
@@ -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
@@ -159,6 +169,7 @@ module Evoruby
       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
@@ -201,13 +212,13 @@ 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 + ")" )
@@ -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 |
@@ -288,7 +296,8 @@ module Evoruby
                 fs_e_value_threshold,
                 hmm_for_protein_output,
                 i_e_value_threshold,
-                true )
+                false,
+                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 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
@@ -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"
@@ -385,37 +396,19 @@ 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"
-
-
 
+      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
 
-      s << "\t"
       overview = make_overview( hmmscan_results_per_protein_filtered, hmm_for_protein_output )
 
-      s << overview   + "\t"
+      s << overview  + "\t"
 
       s << calc_linkers(  hmmscan_results_per_protein_filtered, hmm_for_protein_output )  + "\t"
 
@@ -439,6 +432,18 @@ module Evoruby
       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 = ""
@@ -494,7 +499,6 @@ module Evoruby
     end
 
 
-
     def print_help()
       puts( "Usage:" )
       puts()
@@ -506,6 +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