fix #350 (#354)

* fix indentation * remove verbosity option from the help, it is now handled by the config * add get_uniq_id function to make unique ID on the fly for spread features that can shre identical IDs * add splice3 and splice5 level3 features * fix #350 / use push in infosequential instead of omniscient for Push-L3-omiscient-3: level3 - Use Unique ID even for CDS to avoid confusion in location and level3 checks - remove strand when cloning L3 to create a l2 --------- Co-authored-by: Jacques Dainat <jacques.dainat@ird.fr>
NBISweden · Apr 25, 2023 · 02d2023 · 02d2023
1 parent f07ca0b
commit 02d2023
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Showing 12 changed files with 1,982 additions and 1,929 deletions.
diff --git a/bin/agat_convert_sp_gxf2gxf.pl b/bin/agat_convert_sp_gxf2gxf.pl
@@ -13,7 +13,6 @@
 my $config = get_agat_config();
 my $start_run = time();
 my $opt_gfffile;
-my $opt_verbose = 1;
 my $opt_output;
 my $opt_help;
 
@@ -99,10 +98,6 @@ =head1 OPTIONS
 
 String - Input GTF/GFF file. Compressed file with .gz extension is accepted.
 
-=item B<-v>
-
-Integer - Verbose option. To modify verbosity. Default is 1. 0 is quiet, 2 and 3 are increasing verbosity.
-
 =item B<-o> or B<--output>
 
 String - Output GFF file.  If no output file is specified, the output will be

diff --git a/lib/AGAT/OmniscientI.pm b/lib/AGAT/OmniscientI.pm
@@ -17,6 +17,7 @@ use Exporter;
 use Term::ProgressBar;
 use AGAT::AGAT;
 use AGAT::OmniscientTool;
+use AGAT::OmniscientO;
 use AGAT::Levels;
 use AGAT::Utilities;
 use AGAT::BioperlGFF;
@@ -448,7 +449,10 @@ sub slurp_gff3_file_JD {
 		dual_print ($log, file_text_line({ string => "	 done in ".(time() - $previous_time)." seconds", char => "-" }), $verbose );
 		$check_cpt++; $previous_time = time();
 	}
-
+	my $out =prepare_gffout();
+	print_omniscient( {omniscient => \%omniscient,
+					  output => $out
+                } );
 	if( $config->{check_l2_linked_to_l3} ) {
 			#Check relationship between l3 and l2
 			dual_print ($log, file_text_line({ string => "Check$check_cpt: l2 linked to l3", char => "-", prefix => "\n" }), $verbose );
@@ -690,9 +694,9 @@ sub manage_one_feature{
 				# get Parent #
 				#GFF case
 				if($feature->has_tag('Parent')){
-							$parent = $feature->_tag_value('Parent');
-							$locusTAGvalue = $parent;
-							_save_common_tag_value_top_feature($feature, $locusTAG_uniq, 'level2');
+						$parent = $feature->_tag_value('Parent');
+						$locusTAGvalue = $parent;
+						_save_common_tag_value_top_feature($feature, $locusTAG_uniq, 'level2');
 				}
 
 				#GTF case
@@ -874,7 +878,7 @@ sub manage_one_feature{
 								#######################
 
 								# case were locus already met before (feature are spread within the file), we link the L3 to the last l2 of this locus.
-								if( exists_keys($locusTAG_uniq, ('level2', lc($locusTAGvalue) ) ) ){
+								if( $locusTAGvalue and exists_keys($locusTAG_uniq, ('level2', lc($locusTAGvalue) ) ) ){
 										dual_print ($log, "Complex case L3 1 !!!\n", $verbose) if ($debug);
 										$last_l2_f = @{$locusTAG_uniq->{'level2'}{lc($locusTAGvalue)}}[$#{$locusTAG_uniq->{'level2'}{lc($locusTAGvalue)}}];
 										$l2_id = $last_l2_f->_tag_value('ID');
@@ -920,7 +924,6 @@ sub manage_one_feature{
 						# We don't play this game only if we decided finally to take the same parent
 						# value as previous feature
 						if ($play_this_game){
-
 								create_or_replace_tag($feature,'Parent',$l2_id); #modify Parent To keep only one
 
 								#############
@@ -954,10 +957,9 @@ sub manage_one_feature{
 														$last_l1_f->primary_tag('gene');
 												}
 
-												#push( @{$infoSequential->{'locus'}{lc($l1_id)}{lc($l2_id)}{'level3'}}, $feature );
-												#$infoSequential->{'id'}{lc($l2_id)} = $l2_id;
+												push( @{$infoSequential->{'locus'}{lc($l1_id)}{lc($l2_id)}{'level3'}}, $feature );
+												$infoSequential->{'id'}{lc($l2_id)} = $l2_id;
 												dual_print ($log, "::::::::::Push-L3-omiscient-3: level3 ".$primary_tag." || ".lc($l2_id)." == ".$feature->gff_string."\n", $verbose) if ($debug);
-												push (@{$omniscient->{"level3"}{$primary_tag}{lc($l2_id)}}, $feature);
 												return $l2_id, $last_l1_f, $last_l2_f, $feature, $feature, $lastL1_new;								#### STOP HERE AND RETURN
 										}
 								}
@@ -1868,14 +1870,14 @@ sub _check_all_level3_locations{
 
 	foreach my $type_l3 (keys %{$hash_omniscient->{'level3'}}){
 		foreach my $id_l2 (keys %{$hash_omniscient->{'level3'}{$type_l3}}){
-      if(! exists_keys($hash_omniscient,('other','level', 'skip_merge_l3', $type_l3) ) ){
-  			if( exists_keys($hash_omniscient,('level3', $type_l3, $id_l2) ) ){
-  				#CONDITION ? EVALUATE_IF_CONDITION_WAS_TRUE : EVALUATE_IF_CONDITION_WAS_FALSE
-  				my $method;
-  				exists_keys($hash_omniscient,('other', 'level', 'spread', $type_l3) ) ? $method = "adjacent" : $method = "all";
-  				$nb_merged = merge_features( $hash_omniscient, 'level3', $type_l3, $id_l2, $method, $log);
-  			}
-      }
+			if(! exists_keys($hash_omniscient,('other','level', 'skip_merge_l3', $type_l3) ) ){
+					if( exists_keys($hash_omniscient,('level3', $type_l3, $id_l2) ) ){
+						#CONDITION ? EVALUATE_IF_CONDITION_WAS_TRUE : EVALUATE_IF_CONDITION_WAS_FALSE
+						my $method;
+						exists_keys($hash_omniscient,('other', 'level', 'spread', $type_l3) ) ? $method = "adjacent" : $method = "all";
+						$nb_merged = merge_features( $hash_omniscient, 'level3', $type_l3, $id_l2, $method, $log);
+					}
+			}
 		}
 		if($nb_merged){
 			$resume_cases{$type_l3}+=$nb_merged;
@@ -2083,8 +2085,8 @@ sub _check_exons{
 										if(! $feature_example){
 											$feature_example=$l3_feature;
 										}
-
-										push @{$list_location_NoExon_tmp}, [[$l3_feature->_tag_value('ID')] ,int($l3_feature->start), int($l3_feature->end)]; #list of all feature that has been checked in overlap mode
+										my $IDunique = get_uniq_id($hash_omniscient, $l3_feature); # be safe in case of spread feature that might have same ID
+										push @{$list_location_NoExon_tmp}, [[$IDunique] ,int($l3_feature->start), int($l3_feature->end)]; #list of all feature that has been checked in overlap mode
 									}
 								}
 							}
@@ -2575,19 +2577,20 @@ sub merge_features{
 		#    ==========
 		#         ========= <-
 		# To avoid rare case like this one we need to skip consumed feature that can be not consecutive.
-		if( exists_keys( \%skip_because_consumed, (lc($l3_feature->_tag_value("ID"))) ) ){
+		my $IDunique = get_uniq_id($hash_omniscient, $l3_feature); # to be safe with spread feature sharing same ID
+		if( exists_keys( \%skip_because_consumed, (lc($IDunique)) ) ){
 			next;
 		}
 
 		foreach my $l3_feature_next (@sorted_features){
-
+			my $IDunique_next = get_uniq_id($hash_omniscient, $l3_feature_next);# to be safe with spread feature sharing same ID
 			#Check if adjacent
 			if ($method eq "adjacent"){
 				if ( $l3_feature->end()+1 == $l3_feature_next->start() ){ #locations are consecutives consecutive
 						my $message = "Features adjacents we merge them:\n".$l3_feature->gff_string()."\n".$l3_feature_next->gff_string()."\n";
 						dual_print($log, $message, 0); #print log only
-						$l3_feature->end($l3_feature_next->end());
-						$skip_because_consumed{lc($l3_feature_next->_tag_value("ID"))}++; # Save consumed feature ID
+						$l3_feature->end($l3_feature_next->end()) if ($l3_feature_next->end() > $l3_feature->end());
+						$skip_because_consumed{lc($IDunique_next)}++; # Save consumed feature ID
 						$modification_occured++;
 				}
 				#if after we stop
@@ -2599,8 +2602,8 @@ sub merge_features{
 				if ( ($l3_feature_next->start() <= $l3_feature->end()+1) and ($l3_feature_next->end()+1 >= $l3_feature->start() ) ){ #it overlaps or are consecutive/adjacent
 						my $message = "Features adjacents we merge them:\n".$l3_feature->gff_string()."\n".$l3_feature_next->gff_string()."\n";
 						dual_print($log, $message, 0); #print log only
-						$l3_feature->end($l3_feature_next->end());
-						$skip_because_consumed{lc($l3_feature_next->_tag_value("ID"))}++; # Save consumed feature ID
+						$l3_feature->end($l3_feature_next->end()) if ($l3_feature_next->end() > $l3_feature->end());
+						$skip_because_consumed{lc($IDunique_next)}++; # Save consumed feature ID
 						$modification_occured++;
 				}
 				#if after we stop
@@ -2896,6 +2899,9 @@ sub _check_sequential{ # Goes through from L3 to l1
 			 						$must_create_l2=1;
 			 						$feature_l2 = clone($infoSequential->{'locus'}{$locusNameHIS}{$bucket}{'level3'}[0]);#create a copy of the first mRNA feature;
 
+									# remove strand if any
+									$feature_l2->frame(".");
+
 									#manage primary tag
 									my $primary_tag_l2='RNA';
 									foreach my $feature_L3 (@{$infoSequential->{'locus'}{$locusNameHIS}{$bucket}{'level3'}} ){

diff --git a/lib/AGAT/OmniscientTool.pm b/lib/AGAT/OmniscientTool.pm
@@ -31,7 +31,7 @@ remove_shortest_isoforms check_gene_overlap_at_level3 gather_and_sort_l1_by_seq_
 gather_and_sort_l1_by_seq_id_for_l1type collect_l1_info_sorted_by_seqid_and_location
 remove_l1_and_relatives remove_l2_and_relatives remove_l3_and_relatives get_longest_cds_start_end
 check_mrna_positions check_features_overlap initialize_omni_from
-create_omniscient get_cds_from_l2 merge_overlap_loci );
+create_omniscient get_cds_from_l2 merge_overlap_loci get_uniq_id );
 
 sub import {
   AGAT::OmniscientTool->export_to_level(1, @_); # to be able to load the EXPORT functions when direct call; (normal case)
@@ -607,7 +607,7 @@ sub merge_overlap_loci{
 										my $kept_l2 = shift @$commons; # first is the one we append
 										my $id_l2 = lc($kept_l2->_tag_value('ID'));
 										foreach my $common (@{$commons}){
-                      $resume_identic++;
+                      						$resume_identic++;
 											my @list_tag_l2 = $common->get_all_tags();
 											foreach my $tag (@list_tag_l2){
 												create_or_append_tag($kept_l2, "merged_".$tag ,$common->get_tag_values($tag));
@@ -2916,6 +2916,20 @@ return $result
 #				   |+----------------------------------------------------+|
 #				   +------------------------------------------------------+
 
+# secure way to get ID because if spread feature e.g. CDS the ID can be share by multiple feature
+sub get_uniq_id {
+	my ($hash_omniscient, $feature) = @_;
+
+	my $id;
+	if ( exists_keys($hash_omniscient,('other', 'level', 'spread', lc($feature->primary_tag()) ) ) )
+	 {
+		$id = $feature->_tag_value('ID')."_".$feature->start()."_".$feature->end();
+	} 
+	else {
+		$id = $feature->_tag_value('ID');
+	}
+	return $id;
+}
 #				   +------------------------------------------------------+
 #				   |+----------------------------------------------------+|
 #				   || 			Info from id/feature 					 ||

diff --git a/share/feature_levels.yaml b/share/feature_levels.yaml
@@ -169,6 +169,8 @@ level3:
   pseudogenic_exon: 1
   selenocysteine: 1
   sig_peptide: exon
+  splice3 : intron
+  splice5 : intron
   start_codon: exon
   stop_codon: exon
   stop_codon_read_through: exon

diff --git a/t/gff_syntax.t b/t/gff_syntax.t
@@ -2,7 +2,7 @@
 
 use strict;
 use warnings;
-use Test::More tests => 44;
+use Test::More tests => 45;
 
 =head1 DESCRIPTION
 

diff --git a/t/gff_syntax/README b/t/gff_syntax/README
@@ -52,6 +52,7 @@ This is an explanations of the different test files used to check the GFF3 parse
 	scaffold_1	AUGUSTUS	transcript	3211	5134	0.7	+	.	anno1.g20064.t1
 42: No attribute tag in L1; No attribute tag in L2; No attribute tag in L3; Single value in 9th column (GFF1)
 43: Issue 290 - level3 features (exons CDS) directly attached to the gene, while it exists an mRNA feature. The mRNA feature is also attached to the gene.
+44: Issue 350 - Exonerate output - No L2, ID only for L1.
 
 /!\ If only level3 features are defined, and no locus tag present (see test 26), the tool cannot deal with it. I will create by default one umbrella level1, or if you on attribute as uniq locus ID, It will create a l1 for each feature => If only exon or only CDS features so the result will be fine, but if there are two different features that has to be linked together (two CDS or a CDS and a signal peptide as in the test case 26) , the tool will not perform properly.
 

diff --git a/t/gff_syntax/in/44_test.gff b/t/gff_syntax/in/44_test.gff
@@ -0,0 +1,16 @@
+ptg000001l	exonerate:protein2genome:local	gene	13733550	13734381	1150	-	.	gene_id 1 ; sequence XP_021634939.1 ; gene_orientation +
+ptg000001l	exonerate:protein2genome:local	cds	13734028	13734381	.	-	.
+ptg000001l	exonerate:protein2genome:local	exon	13734028	13734381	.	-	.	insertions 0 ; deletions 0
+ptg000001l	exonerate:protein2genome:local	splice5	13734026	13734027	.	-	.	intron_id 1 ; splice_site "GT"
+ptg000001l	exonerate:protein2genome:local	intron	13733971	13734027	.	-	.	intron_id 1
+ptg000001l	exonerate:protein2genome:local	splice3	13733971	13733972	.	-	.	intron_id 0 ; splice_site "AG"
+ptg000001l	exonerate:protein2genome:local	cds	13733550	13733970	.	-	.
+ptg000001l	exonerate:protein2genome:local	exon	13733550	13733970	.	-	.	insertions 0 ; deletions 0 ; frameshifts 1
+ptg000001l	exonerate:protein2genome:local	gene	6876023	6876853	1131	-	.	gene_id 2 ; sequence XP_021634939.1 ; gene_orientation +
+ptg000001l	exonerate:protein2genome:local	cds	6876500	6876853	.	-	.
+ptg000001l	exonerate:protein2genome:local	exon	6876500	6876853	.	-	.	insertions 0 ; deletions 0
+ptg000001l	exonerate:protein2genome:local	splice5	6876498	6876499	.	-	.	intron_id 1 ; splice_site "GT"
+ptg000001l	exonerate:protein2genome:local	intron	6876443	6876499	.	-	.	intron_id 1
+ptg000001l	exonerate:protein2genome:local	splice3	6876443	6876444	.	-	.	intron_id 0 ; splice_site "AG"
+ptg000001l	exonerate:protein2genome:local	cds	6876023	6876442	.	-	.
+ptg000001l	exonerate:protein2genome:local	exon	6876023	6876442	.	-	.	insertions 0 ; deletions 0
diff --git a/t/gff_syntax/out/42_correct_output.gff b/t/gff_syntax/out/42_correct_output.gff
@@ -1,7 +1,7 @@
 ##gff-version 3
 # GFF1 only one value as attribute
-scaffold_5	JGI	gene	42603	45653	.	+	0	ID=nbis-gene-2;common_tag=geneB
-scaffold_5	JGI	mRNA	42603	45653	.	+	0	ID=nbis-rna-2;Parent=nbis-gene-2;common_tag=geneB
+scaffold_5	JGI	gene	42603	45653	.	+	.	ID=nbis-gene-2;common_tag=geneB
+scaffold_5	JGI	mRNA	42603	45653	.	+	.	ID=nbis-rna-2;Parent=nbis-gene-2;common_tag=geneB
 scaffold_5	JGI	exon	42603	43344	.	+	0	ID=geneB;Parent=nbis-rna-2;common_tag=geneB
 scaffold_5	JGI	exon	43530	43531	.	+	0	ID=nbis-exon-3;Parent=nbis-rna-2;common_tag=geneB
 scaffold_5	JGI	exon	43569	45653	.	+	0	ID=nbis-exon-4;Parent=nbis-rna-2;common_tag=geneB
@@ -10,8 +10,8 @@ scaffold_5	JGI	CDS	43530	43531	.	+	2	ID=nbis-cds-5;Parent=nbis-rna-2;common_tag=
 scaffold_5	JGI	CDS	43569	45653	.	+	0	ID=nbis-cds-6;Parent=nbis-rna-2;common_tag=geneB
 scaffold_5	JGI	start_codon	42603	42605	.	+	0	ID=nbis-start_codon-2;Parent=nbis-rna-2;common_tag=geneB
 scaffold_5	JGI	stop_codon	45651	45653	.	+	0	ID=nbis-stop_codon-2;Parent=nbis-rna-2;common_tag=geneB
-scaffold_5	JGI	gene	442603	445653	.	+	0	ID=nbis-gene-1;common_tag=geneA
-scaffold_5	JGI	mRNA	442603	445653	.	+	0	ID=nbis-rna-1;Parent=nbis-gene-1;common_tag=geneA
+scaffold_5	JGI	gene	442603	445653	.	+	.	ID=nbis-gene-1;common_tag=geneA
+scaffold_5	JGI	mRNA	442603	445653	.	+	.	ID=nbis-rna-1;Parent=nbis-gene-1;common_tag=geneA
 scaffold_5	JGI	exon	442603	443344	.	+	0	ID=geneA;Parent=nbis-rna-1;common_tag=geneA
 scaffold_5	JGI	exon	443530	443531	.	+	0	ID=nbis-exon-1;Parent=nbis-rna-1;common_tag=geneA
 scaffold_5	JGI	exon	443569	445653	.	+	0	ID=nbis-exon-2;Parent=nbis-rna-1;common_tag=geneA

diff --git a/t/gff_syntax/out/44_correct_output.gff b/t/gff_syntax/out/44_correct_output.gff
@@ -0,0 +1,19 @@
+##gff-version 3
+ptg000001l	exonerate:protein2genome:local	gene	6876023	6876853	1131	-	.	ID=2;gene_id=2;gene_orientation=+;sequence=XP_021634939.1
+ptg000001l	exonerate:protein2genome:local	mRNA	6876023	6876853	.	-	.	ID=nbis-rna-2;Parent=2
+ptg000001l	exonerate:protein2genome:local	exon	6876023	6876442	.	-	.	ID=exon-4;Parent=nbis-rna-2;deletions=0;insertions=0
+ptg000001l	exonerate:protein2genome:local	exon	6876500	6876853	.	-	.	ID=exon-3;Parent=nbis-rna-2;deletions=0;insertions=0
+ptg000001l	exonerate:protein2genome:local	cds	6876023	6876442	.	-	.	ID=cds-4;Parent=nbis-rna-2
+ptg000001l	exonerate:protein2genome:local	cds	6876500	6876853	.	-	.	ID=cds-3;Parent=nbis-rna-2
+ptg000001l	exonerate:protein2genome:local	intron	6876443	6876499	.	-	.	ID=nbis-intron-2;Parent=nbis-rna-2;intron_id=1
+ptg000001l	exonerate:protein2genome:local	splice3	6876443	6876444	.	-	.	ID=splice3-2;Parent=nbis-rna-2;intron_id=0;splice_site=AG
+ptg000001l	exonerate:protein2genome:local	splice5	6876498	6876499	.	-	.	ID=splice5-2;Parent=nbis-rna-2;intron_id=1;splice_site=GT
+ptg000001l	exonerate:protein2genome:local	gene	13733550	13734381	1150	-	.	ID=1;gene_id=1;gene_orientation=+;sequence=XP_021634939.1
+ptg000001l	exonerate:protein2genome:local	mRNA	13733550	13734381	.	-	.	ID=nbis-rna-1;Parent=1
+ptg000001l	exonerate:protein2genome:local	exon	13733550	13733970	.	-	.	ID=exon-2;Parent=nbis-rna-1;deletions=0;frameshifts=1;insertions=0
+ptg000001l	exonerate:protein2genome:local	exon	13734028	13734381	.	-	.	ID=exon-1;Parent=nbis-rna-1;deletions=0;insertions=0
+ptg000001l	exonerate:protein2genome:local	cds	13733550	13733970	.	-	.	ID=cds-2;Parent=nbis-rna-1
+ptg000001l	exonerate:protein2genome:local	cds	13734028	13734381	.	-	.	ID=cds-1;Parent=nbis-rna-1
+ptg000001l	exonerate:protein2genome:local	intron	13733971	13734027	.	-	.	ID=nbis-intron-1;Parent=nbis-rna-1;intron_id=1
+ptg000001l	exonerate:protein2genome:local	splice3	13733971	13733972	.	-	.	ID=splice3-1;Parent=nbis-rna-1;intron_id=0;splice_site=AG
+ptg000001l	exonerate:protein2genome:local	splice5	13734026	13734027	.	-	.	ID=splice5-1;Parent=nbis-rna-1;intron_id=1;splice_site=GT
diff --git a/t/gff_syntax/out/8_correct_output.gff b/t/gff_syntax/out/8_correct_output.gff
@@ -1,19 +1,19 @@
 ##gff-version 3
-Tob1_contig1	Prodigal:2.60	gene	476	670	.	-	0	ID=nbis-gene-1;locus_tag=Tob1_00001;product=hypothetical protein
-Tob1_contig1	Prodigal:2.60	mRNA	476	670	.	-	0	ID=nbis-rna-1;Parent=nbis-gene-1;locus_tag=Tob1_00001;product=hypothetical protein
+Tob1_contig1	Prodigal:2.60	gene	476	670	.	-	.	ID=nbis-gene-1;locus_tag=Tob1_00001;product=hypothetical protein
+Tob1_contig1	Prodigal:2.60	mRNA	476	670	.	-	.	ID=nbis-rna-1;Parent=nbis-gene-1;locus_tag=Tob1_00001;product=hypothetical protein
 Tob1_contig1	Prodigal:2.60	exon	476	670	.	-	.	ID=nbis-exon-1;Parent=nbis-rna-1;locus_tag=Tob1_00001;product=hypothetical protein
 Tob1_contig1	Prodigal:2.60	CDS	476	670	.	-	0	ID=Tob1_00001;Parent=nbis-rna-1;locus_tag=Tob1_00001;product=hypothetical protein
-Tob1_contig1	Prodigal:2.60	gene	34266	35222	.	+	0	ID=nbis-gene-2;locus_tag=Tob1_00024;product=hypothetical protein
-Tob1_contig1	Prodigal:2.60	mRNA	34266	35222	.	+	0	ID=nbis-rna-2;Parent=nbis-gene-2;locus_tag=Tob1_00024;product=hypothetical protein
+Tob1_contig1	Prodigal:2.60	gene	34266	35222	.	+	.	ID=nbis-gene-2;locus_tag=Tob1_00024;product=hypothetical protein
+Tob1_contig1	Prodigal:2.60	mRNA	34266	35222	.	+	.	ID=nbis-rna-2;Parent=nbis-gene-2;locus_tag=Tob1_00024;product=hypothetical protein
 Tob1_contig1	Prodigal:2.60	exon	34266	35222	.	+	.	ID=nbis-exon-2;Parent=nbis-rna-2;locus_tag=Tob1_00024;product=hypothetical protein
 Tob1_contig1	Prodigal:2.60	CDS	34266	35222	.	+	0	ID=Tob1_00024;Parent=nbis-rna-2;locus_tag=Tob1_00024;product=hypothetical protein
 Tob1_contig1	SignalP:4.1	sig_peptide	34266	34298	.	+	0	ID=sig_peptide-1;Parent=nbis-rna-2;inference=ab initio prediction:SignalP:4.1;note=predicted cleavage at residue 33;product=putative signal peptide
-Tob1_contig1	Prodigal:2.60	gene	35267	37444	.	-	0	ID=nbis-gene-3;locus_tag=Tob1_00025
-Tob1_contig1	Prodigal:2.60	mRNA	35267	37444	.	-	0	ID=nbis-rna-3;Parent=nbis-gene-3;locus_tag=Tob1_00025
+Tob1_contig1	Prodigal:2.60	gene	35267	37444	.	-	.	ID=nbis-gene-3;locus_tag=Tob1_00025
+Tob1_contig1	Prodigal:2.60	mRNA	35267	37444	.	-	.	ID=nbis-rna-3;Parent=nbis-gene-3;locus_tag=Tob1_00025
 Tob1_contig1	Prodigal:2.60	exon	35267	37444	.	-	.	ID=nbis-exon-3;Parent=nbis-rna-3;locus_tag=Tob1_00025
 Tob1_contig1	Prodigal:2.60	CDS	35267	37444	.	-	0	ID=Tob1_00025;Parent=nbis-rna-3;locus_tag=Tob1_00025
 Tob1_contig1	SignalP:4.1	sig_peptide	37420	37444	.	-	0	ID=sig_peptide-2;Parent=nbis-rna-3;inference=ab initio prediction:SignalP:4.1;note=predicted cleavage at residue 25;product=putative signal peptide
-Tob1_contig1	Prodigal:2.60	gene	38304	39338	.	-	0	ID=nbis-gene-4;locus_tag=Tob1_00026
-Tob1_contig1	Prodigal:2.60	mRNA	38304	39338	.	-	0	ID=nbis-rna-4;Parent=nbis-gene-4;locus_tag=Tob1_00026
+Tob1_contig1	Prodigal:2.60	gene	38304	39338	.	-	.	ID=nbis-gene-4;locus_tag=Tob1_00026
+Tob1_contig1	Prodigal:2.60	mRNA	38304	39338	.	-	.	ID=nbis-rna-4;Parent=nbis-gene-4;locus_tag=Tob1_00026
 Tob1_contig1	Prodigal:2.60	exon	38304	39338	.	-	.	ID=nbis-exon-4;Parent=nbis-rna-4;locus_tag=Tob1_00026
 Tob1_contig1	Prodigal:2.60	CDS	38304	39338	.	-	0	ID=Tob1_00026;Parent=nbis-rna-4;locus_tag=Tob1_00026