add parameter to clean Name,product,dbxref,product attributes. Append…

bin/agat_sp_manage_functional_annotation.pl

@@ -22,6 +22,10 @@
 my $opt_reffile;
 my $opt_output;
 my $opt_BlastFile;
+my $opt_CleanNameAttribute; # Should we remove the Name attribute value if already exists - bolean
+my $opt_CleanProductAttribute; # Should we remove the product attribute value if already exists - bolean
+my $opt_CleanOntology_termAttribute; # Should we remove the Ontology_term attribute value if already exists - bolean
+my $opt_CleanDbxrefAttribute; # Should we remove the Dbxref attribute value if already exists - bolean
 my $opt_InterproFile;
 my $opt_name = undef;
 my $opt_nameU;
@@ -77,6 +81,10 @@
 GetOptions(
  'f|ref|reffile|gff|gff3=s' => \$opt_reffile,
  'b|blast=s'                => \$opt_BlastFile,
+ 'clean_name!'              => \$opt_CleanNameAttribute,
+ 'clean_product!'           => \$opt_CleanProductAttribute,
+ 'clean_dbxref!'            => \$opt_CleanDbxrefAttribute,
+ 'clean_ontology!'          => \$opt_CleanOntology_termAttribute,
  'd|db=s'                   => \$opt_dataBase,
  'be|blast_evalue=f'        => \$opt_blastEvalue,
  'pe=i'                     => \$opt_pe,
@@ -298,20 +306,16 @@
     foreach my $id_level1 (keys %{$hash_omniscient ->{'level1'}{$primary_tag_level1}}) {
       my $feature_level1 = $hash_omniscient->{'level1'}{$primary_tag_level1}{$id_level1};
 
-      # Clean NAME attribute
-      if ($feature_level1->has_tag('Name')) {
-        $feature_level1->remove_tag('Name');
-      }
-
-      #Manage Name if option setting
+      #Manage Name 
+      clean_attribute($feature_level1, "Name"); # Clean NAME attribute
       if ( $opt_BlastFile ) {
 
         if (exists ($geneNameBlast{$id_level1})) {
           my @list_names = @{$geneNameBlast{$id_level1}};
-          create_or_replace_tag($feature_level1, 'Name', \@list_names);
+          create_or_append_tag($feature_level1, 'Name', \@list_names);
           $nbNamedGene++;
 
-          # Keep track of ducplicated gene names <= Find another way
+          # Keep track of duplicated gene names <= Find another way
           foreach my $name (@list_names){
 
             if (exists ($geneNameGiven{$name})) {
@@ -335,16 +339,12 @@
 
             my $level2_ID = lc($feature_level2->_tag_value('ID'));
 
-            # Clean NAME attribute
-            if ($feature_level2->has_tag('Name')) {
-              $feature_level2->remove_tag('Name');
-            }
-
-            # Manage Name if option set
+            # Manage Name 
+            clean_attribute($feature_level2, "Name"); # Clean NAME attribute
             if ($opt_BlastFile) {
               # add gene Name
               if (exists ($mRNANameBlast{$level2_ID})) {
-                create_or_replace_tag($feature_level2, 'Name', $mRNANameBlast{$level2_ID});
+                create_or_append_tag($feature_level2, 'Name', $mRNANameBlast{$level2_ID});
                 add_attribute_to_cds($hash_omniscient, $level2_ID, 'Name', $mRNANameBlast{$level2_ID});
               }
 
@@ -370,13 +370,14 @@
               my $productData = printProductFunct($level2_ID);
 
               #add product attribute
+              clean_attribute($feature_level2, "product"); # Clean product attribute
               if ($productData ne "") {
                 add_attribute_to_cds($hash_omniscient, $level2_ID, 'product', $productData);
                 if ($feature_level2->has_tag('pseudo')) {
                   create_or_replace_tag($feature_level2, 'Note', "product:$productData");
                 }
                 else {
-                  create_or_replace_tag($feature_level2, 'product', $productData);
+                  create_or_append_tag($feature_level2, 'product', $productData);
                 }
               }
               else {
@@ -385,7 +386,7 @@
                   create_or_replace_tag($feature_level2, 'Note', "product:hypothetical protein");
                 }
                 else {
-                  create_or_replace_tag($feature_level2, 'product', "hypothetical protein");
+                  create_or_append_tag($feature_level2, 'product', "hypothetical protein");
                 }
               } #Case where the protein is not known
             }
@@ -651,12 +652,39 @@
                 ####
                  ##
 
+# remove the attribute provided
+sub clean_attribute {
+  my ($feature, $tag) = @_;
+
+  if ($opt_CleanNameAttribute and $tag eq "Name"){
+    if ($feature->has_tag('Name')) {
+      $feature->remove_tag('Name');
+    }
+  }
+  if ($opt_CleanProductAttribute and $tag eq "product"){
+    if ($feature->has_tag('product')) {
+      $feature->remove_tag('product');
+    }
+  }
+  if ($opt_CleanDbxrefAttribute and $tag eq "Dbxref"){
+    if ($feature->has_tag('Dbxref')) {
+      $feature->remove_tag('Dbxref');
+    }
+  }
+  if ($opt_CleanOntology_termAttribute and $tag eq "Ontology_term"){
+    if ($feature->has_tag('Ontology_term')) {
+      $feature->remove_tag('Ontology_term');
+    }
+  }
+}
+
 sub add_attribute_to_cds {
   my ($hash_omniscient, $level2_ID, $tag, $value) = @_;
 
   if($opt_populate_cds){
     if ( exists_keys ($hash_omniscient, ('level3', 'cds', lc($level2_ID)) ) ) {
       foreach my $feature_level3 ( @{$hash_omniscient->{'level3'}{'cds'}{lc($level2_ID)}}) {
+        clean_attribute($feature_level3, $tag);
         $feature_level3->add_tag_value($tag, $value);
       }
     }
@@ -730,6 +758,7 @@ sub addFunctions {
       my $data_list;
 
       if (lc($function_type) eq "go") {
+        clean_attribute($feature, "Ontology_term"); # Clean Ontology_term attribute
         foreach my $data (@{$functionData{$function_type}{$ID}}) {
           $feature->add_tag_value('Ontology_term', $data);
           $data_list .= "$data,";
@@ -738,6 +767,7 @@ sub addFunctions {
         }
       }
       else {
+        clean_attribute($feature, "Dbxref"); # Clean Dbxref attribute
         foreach my $data (@{$functionData{$function_type}{$ID}}) {
           $feature->add_tag_value('Dbxref', $data);
           $data_list .= "$data,";
@@ -1042,7 +1072,7 @@ sub parse_interpro_tsv {
         my @tuple = split(/:/, $pathway_tuple); #cut at character :
         my $db_name = $tuple[0];
         print "pathway info: ".$pathway_tuple."\n" if ($opt_verbose);
-
+        next if ($pathway_tuple eq "-"); # avoid empty pathway tuple
         if (! grep( /^\Q$pathway_tuple\E$/, @{$functionData{$db_name}{$mRNAID}} ) ) { # to avoid duplicate
           $TotalTerm{$db_name}++;
           push ( @{$functionData{$db_name}{$mRNAID}} , $pathway_tuple );
@@ -1145,12 +1175,35 @@ =head1 OPTIONS
 
 =item B<-b> or B<--blast>
 
-String - Input blast ( outfmt 6 = tabular ) file that will be used to complement the features
-read from the first file (specified with --ref).
+String - Input blast ( outfmt 6 = tabular ) usually made by blasting the proteins resulting from the GFF/GTF file provided as input
+and a confident protein database (e.g. Swissprot/Uniprot). The file makse a bridge between the feature ID from the GFF/GTF and the 
+best protein ID matched in the used database. Thanks to that link the Name and products (sometimes called descriptions) information 
+will be extracted from the database fasta file and added in the GFF file. You must provide the same database via --db as the one used 
+to create this blast output file.
+
+=item B<--clean_name> 
+
+Bolean - When activated, if the Name attribute already exists, it we be cleaned. Otherwise Name retrieved by --blast + --db options 
+will be appended. Default False (Name attribute not cleaned).
+
+=item B<--clean_product> 
+
+Bolean - When activated, if the product attribute already exists, it we be cleaned. Otherwise product retrieved by --blast + --db options 
+will be appended. Default False (product attribute not cleaned).
+
+=item B<--clean_dbxref> 
+
+Bolean - When activated, if the Dbxref attribute already exists, it we be cleaned. Otherwise Dbxref retrieved by --interpro option 
+will be appended. Default False (Dbxref attribute not cleaned).
+
+=item B<--clean_ontology> 
+
+Bolean - When activated, if the Ontology_term attribute already exists, it we be cleaned. Otherwise Ontology_term retrieved by --interpro option 
+will be appended. Default False (Ontology_term attribute not cleaned).
 
 =item B<-d> or B<--db>
 
-String - The fasta file that has been used as DB for the blast. Gene names and products/descriptions will be fished from this file.
+String - The fasta file that has been used as DB for the blast. Gene names and products  (sometimes called descriptions) will be fished from this file.
 
 =item B<--be> or B<--blast_evalue>
 

docs/tools/agat_sp_manage_functional_annotation.md

@@ -79,8 +79,29 @@ agat_sp_manage_functional_annotation.pl --help
 
 - **-b** or **--blast**
 
-    String - Input blast ( outfmt 6 = tabular ) file that will be used to complement the features
-    read from the first file (specified with --ref).
+    String - Input blast ( outfmt 6 = tabular ) usually made by blasting the proteins resulting from the GFF/GTF file provided as input
+    and a confident protein database (e.g. Swissprot/Uniprot). The file makse a bridge between the feature ID from the GFF/GTF and the 
+    best protein ID matched in the used database. Thanks to that link the Name and products (sometimes called descriptions) information will be extracted from the database fasta file and added in the GFF file. You must provide the same database via --db as the one used to create
+    this blast output file.
+
+- **--clean_name**
+
+    Bolean - When activated, if the Name attribute already exists, it we be cleaned. Otherwise Name retrieved by --blast + --db options 
+    will be appended. Default False (Name attribute not cleaned).
+
+- **--clean_product**
+
+    Bolean - When activated, if the product attribute already exists, it we be cleaned. Otherwise product retrieved by --blast + --db options 
+    will be appended. Default False (product attribute not cleaned).
+
+- **--clean_dbxref**
+
+    Bolean - When activated, if the Dbxref attribute already exists, it we be cleaned. Otherwise Dbxref retrieved by --interpro option 
+    will be appended. Default False (Dbxref attribute not cleaned).
+
+- **--clean_ontology**
+
+    Bolean - When activated, if the Ontology_term attribute already exists, it we be cleaned. Otherwise Ontology_term retrieved by --interpro option will be appended. Default False (Ontology_term attribute not cleaned).
 
 - **-d** or **--db**
 

t/scripts_output.t

@@ -586,7 +586,7 @@ unlink $outtmp;
 
 $script = $script_prefix."bin/agat_sp_manage_functional_annotation.pl";
 $result = "$output_folder/agat_sp_manage_functional_annotation_1.gff";
-system(" $script --gff $input_folder/agat_sp_manage_functional_annotation/02413F.gff --db $input_folder/agat_sp_manage_functional_annotation/uniprot_sprot_test.fasta -b $input_folder/agat_sp_manage_functional_annotation/02413F_blast.out -i $input_folder/agat_sp_manage_functional_annotation/02413F_interpro.tsv -o $outtmp 2>&1 1>/dev/null");
+system(" $script --gff $input_folder/agat_sp_manage_functional_annotation/02413F.gff --db $input_folder/agat_sp_manage_functional_annotation/uniprot_sprot_test.fasta -b $input_folder/agat_sp_manage_functional_annotation/02413F_blast.out -i $input_folder/agat_sp_manage_functional_annotation/02413F_interpro.tsv --clean_name -o $outtmp 2>&1 1>/dev/null");
 #run test
 ok( system( "diff $result $outtmp/02413F.gff" ) == 0, "output $script");
 rmtree $outtmp;