NBISweden · Juke34 · Sep 17, 2024 · Sep 17, 2024 · Sep 17, 2024 · Sep 17, 2024
diff --git a/bin/agat_sp_compare_two_annotations.pl b/bin/agat_sp_compare_two_annotations.pl
@@ -729,18 +729,18 @@ =head1 DESCRIPTION
 
 =head1 SYNOPSIS
 
-    agat_sp_compare_two_annotations.pl -gff1 infile.gff [ -o outfile ]
+    agat_sp_compare_two_annotations.pl -gff1 infile1.gff -gff2 infile2.gff  [ -o outfile ]
     agat_sp_compare_two_annotations.pl --help
 
 =head1 OPTIONS
 
 =over 8
 
-=item B<-gff1>
+=item B<--gff1>
 
 Input GTF/GFF file1.
 
-=item B<-gff2>
+=item B<--gff2>
 
 Input GTF/GFF file2.
 

diff --git a/docs/tools/agat_sp_compare_two_annotations.md b/docs/tools/agat_sp_compare_two_annotations.md
@@ -3,15 +3,15 @@
 ## DESCRIPTION
 
 The script aims to compare two annotation of the same assembly. It provided
-information about split/fusion of genes between the two annotations.
-The most common case are:
-1 => 0 ( gene uniq to file1)
-0 => 1 ( gene uniq to file2)
-1 => 1 ( 1 gene from file 1 overlaps only 1 gene from file2)
-1 => &lt;many> ( 1 gene from file 1 overlaps &lt;many> genes from file2) => split case (with file 1 as reference)
+information about split/fusion of genes between the two annotations.  
+The most common case are:  
+1 => 0 ( gene uniq to file1)  
+0 => 1 ( gene uniq to file2)  
+1 => 1 ( 1 gene from file 1 overlaps only 1 gene from file2)  
+1 => &lt;many> ( 1 gene from file 1 overlaps &lt;many> genes from file2) => split case (with file 1 as reference)  
 &lt;many> => 1 ( &lt;many> genes from file 1 overlap only 1 gene from file2) => fusion case (with file 1 as reference)
 
-Then you can get more complex cases:
+Then you can get more complex cases:  
 &lt;many> => &lt;many>  (&lt;many> genes from file 1 overlap &lt;many> genes from file2)
 
 The script output a folder containing a report of number of different cases as well as a file
@@ -20,17 +20,17 @@ per case type listing per line the gene feature's ID involved in each case.
 ## SYNOPSIS
 
 ```
-agat_sp_compare_two_annotations.pl -gff1 infile.gff [ -o outfile ]
+agat_sp_compare_two_annotations.pl --gff1 infile1.gff -gff2 infile2.gff [ -o outfile ]
 agat_sp_compare_two_annotations.pl --help
 ```
 
 ## OPTIONS
 
-- **-gff1**
+- **--gff1**
 
     Input GTF/GFF file1.
 
-- **-gff2**
+- **--gff2**
 
     Input GTF/GFF file2.
 

diff --git a/lib/AGAT/OmniscientTool.pm b/lib/AGAT/OmniscientTool.pm
@@ -1314,14 +1314,21 @@ sub clean_clone{
 		}
 	}
 
-	# remove Parent attribute if level1
+	# remove Parent and transcript_id attributes if level1. 
+	# We check is Level1 using the primary_tag of the feature
 	if ($omniscient){
 		if ($cloned_feature->has_tag("Parent")){
 			my $hash_level = $omniscient->{'other'}{'level'};
 			if( exists_keys($hash_level,'level1',lc($cloned_feature->primary_tag)) ){
 				$cloned_feature->remove_tag("Parent");
 			}
 		}
+		if ($cloned_feature->has_tag("transcript_id")){
+			my $hash_level = $omniscient->{'other'}{'level'};
+			if( exists_keys($hash_level,'level1',lc($cloned_feature->primary_tag)) ){
+				$cloned_feature->remove_tag("transcript_id");
+			}
+		}
 	}
 	# new id
 	create_or_replace_tag($cloned_feature,'ID',$new_id) if $new_id;

diff --git a/t/gff_other/out/issue441.gtf b/t/gff_other/out/issue441.gtf
@@ -1,6 +1,6 @@
 ##gtf-version X
 # GFF-like GTF i.e. not checked against any GTF specification. Conversion based on GFF input, standardised by AGAT.
-Scaffold170	AGAT	gene	2883887	2888594	.	+	.	gene_id "GBI_15721"; transcript_id "GBI_15721-RE"; ID "GBI_15721"; gene_name "GBI_15721";
+Scaffold170	AGAT	gene	2883887	2888594	.	+	.	gene_id "GBI_15721"; ID "GBI_15721"; gene_name "GBI_15721";
 Scaffold170	AGAT	mRNA	2883887	2888594	.	+	.	gene_id "GBI_15721"; transcript_id "GBI_15721-RE"; ID "GBI_15721-RE"; Parent "GBI_15721"; gene_name "GBI_15721";
 Scaffold170	maker	exon	2883887	2884591	.	+	.	gene_id "GBI_15721"; transcript_id "GBI_15721-RE"; ID "agat-exon-1"; Parent "GBI_15721-RE"; gene_name "GBI_15721";
 Scaffold170	maker	exon	2885735	2885878	.	+	.	gene_id "GBI_15721"; transcript_id "GBI_15721-RE"; ID "agat-exon-2"; Parent "GBI_15721-RE"; gene_name "GBI_15721";

diff --git a/t/gff_syntax/out/30_correct_output.gff b/t/gff_syntax/out/30_correct_output.gff
@@ -1,10 +1,10 @@
 ##gff-version 3
-000000F|arrow	AGAT	gene	898	1804	.	+	.	ID=P12103_109_S2_L002.1;gene_id=P12103_109_S2_L002.1;transcript_id=P12103_109_S2_L002.1.1
+000000F|arrow	AGAT	gene	898	1804	.	+	.	ID=P12103_109_S2_L002.1;gene_id=P12103_109_S2_L002.1
 000000F|arrow	StringTie	transcript	898	1804	1000	+	.	ID=P12103_109_S2_L002.1.1;Parent=P12103_109_S2_L002.1;gene_id=P12103_109_S2_L002.1;transcript_id=P12103_109_S2_L002.1.1
 000000F|arrow	StringTie	exon	898	1804	1000	+	.	ID=agat-exon-1;Parent=P12103_109_S2_L002.1.1;gene_id=P12103_109_S2_L002.1;transcript_id=P12103_109_S2_L002.1.1
 000000F|arrow	StringTie	pseudogene	1147	3802	1000	-	.	ID=P12103_109_S2_L002.2;gene_id=P12103_109_S2_L002.2;transcript_id=P12103_109_S2_L002.2.1
 000000F|arrow	AGAT	RNA	1147	3802	.	-	.	ID=P12103_109_S2_L002.2.1;Parent=P12103_109_S2_L002.2;gene_id=P12103_109_S2_L002.2;transcript_id=P12103_109_S2_L002.2.1
 000000F|arrow	StringTie	exon	1147	3802	1000	-	.	ID=agat-exon-2;Parent=P12103_109_S2_L002.2.1;gene_id=P12103_109_S2_L002.2;transcript_id=P12103_109_S2_L002.2.1
-000000F|arrow	AGAT	gene	6990	7449	.	-	.	ID=P12103_109_S2_L002.4;gene_id=P12103_109_S2_L002.4;transcript_id=P12103_109_S2_L002.4.1
+000000F|arrow	AGAT	gene	6990	7449	.	-	.	ID=P12103_109_S2_L002.4;gene_id=P12103_109_S2_L002.4
 000000F|arrow	StringTie	transcript	6990	7449	1000	-	.	ID=P12103_109_S2_L002.4.1;Parent=P12103_109_S2_L002.4;gene_id=P12103_109_S2_L002.4;transcript_id=P12103_109_S2_L002.4.1
 000000F|arrow	StringTie	exon	6990	7449	1000	-	.	ID=agat-exon-3;Parent=P12103_109_S2_L002.4.1;gene_id=P12103_109_S2_L002.4;transcript_id=P12103_109_S2_L002.4.1
diff --git a/t/gff_syntax/out/36_correct_output.gff b/t/gff_syntax/out/36_correct_output.gff
@@ -1,5 +1,5 @@
 ##gff-version 3
-001269F_0	AGAT	gene	540236	558650	.	+	.	ID=ENSG00000105497.3;ccdsid=CCDS12837.1;exon_id=ENSE00000842706.1;exon_number=2;gene_id=ENSG00000105497.3;gene_name=ZNF175;gene_status=KNOWN;gene_type=protein_coding;havana_gene=OTTHUMG00000167771.3;havana_transcript=OTTHUMT00000396205.1;level=2;protein_id=ENSP00000262259.2;tag=basic,appris_principal,CCDS;transcript_id=ENST00000262259.2;transcript_name=ZNF175-001;transcript_status=KNOWN;transcript_type=protein_coding
+001269F_0	AGAT	gene	540236	558650	.	+	.	ID=ENSG00000105497.3;ccdsid=CCDS12837.1;exon_id=ENSE00000842706.1;exon_number=2;gene_id=ENSG00000105497.3;gene_name=ZNF175;gene_status=KNOWN;gene_type=protein_coding;havana_gene=OTTHUMG00000167771.3;havana_transcript=OTTHUMT00000396205.1;level=2;protein_id=ENSP00000262259.2;tag=basic,appris_principal,CCDS;transcript_name=ZNF175-001;transcript_status=KNOWN;transcript_type=protein_coding
 001269F_0	AGAT	mRNA	542087	558627	.	+	.	ID=ENST00000262259.2;Parent=ENSG00000105497.3;ccdsid=CCDS12837.1;exon_id=ENSE00000842706.1;exon_number=2;gene_id=ENSG00000105497.3;gene_name=ZNF175;gene_status=KNOWN;gene_type=protein_coding;havana_gene=OTTHUMG00000167771.3;havana_transcript=OTTHUMT00000396205.1;level=2;protein_id=ENSP00000262259.2;tag=basic,appris_principal,CCDS;transcript_id=ENST00000262259.2;transcript_name=ZNF175-001;transcript_status=KNOWN;transcript_type=protein_coding
 001269F_0	HAVANA	exon	542087	542338	.	+	.	ID=exon:ENST00000262259.2:2;Parent=ENST00000262259.2;ccdsid=CCDS12837.1;exon_id=ENSE00000842706.1;exon_number=2;gene_id=ENSG00000105497.3;gene_name=ZNF175;gene_status=KNOWN;gene_type=protein_coding;havana_gene=OTTHUMG00000167771.3;havana_transcript=OTTHUMT00000396205.1;level=2;protein_id=ENSP00000262259.2;tag=basic,appris_principal,CCDS;transcript_id=ENST00000262259.2;transcript_name=ZNF175-001;transcript_status=KNOWN;transcript_type=protein_coding
 001269F_0	HAVANA	exon	550309	550435	.	+	.	ID=exon:ENST00000262259.2:3;Parent=ENST00000262259.2;ccdsid=CCDS12837.1;exon_id=ENSE00002436360.1;exon_number=3;gene_id=ENSG00000105497.3;gene_name=ZNF175;gene_status=KNOWN;gene_type=protein_coding;havana_gene=OTTHUMG00000167771.3;havana_transcript=OTTHUMT00000396205.1;level=2;protein_id=ENSP00000262259.2;tag=basic,appris_principal,CCDS;transcript_id=ENST00000262259.2;transcript_name=ZNF175-001;transcript_status=KNOWN;transcript_type=protein_coding
@@ -36,15 +36,15 @@
 001269F_0	HAVANA	CDS	558460	558503	.	+	2	ID=CDS:ENST00000436511.2:4;Parent=ENST00000436511.2;exon_id=ENSE00002268856.1;exon_number=4;gene_id=ENSG00000105497.3;gene_name=ZNF175;gene_status=KNOWN;gene_type=protein_coding;havana_gene=OTTHUMG00000167771.3;havana_transcript=OTTHUMT00000396206.1;level=1;protein_id=ENSP00000440578.1;tag=basic,exp_conf;transcript_id=ENST00000436511.2;transcript_name=ZNF175-003;transcript_status=PUTATIVE;transcript_type=protein_coding
 001269F_0	AGAT	five_prime_UTR	542265	542266	.	+	.	ID=agat-five_prime_utr-3;Parent=ENST00000436511.2;exon_id=ENSE00002298653.1;exon_number=1;gene_id=ENSG00000105497.3;gene_name=ZNF175;gene_status=KNOWN;gene_type=protein_coding;havana_gene=OTTHUMG00000167771.3;havana_transcript=OTTHUMT00000396206.1;level=1;protein_id=ENSP00000440578.1;tag=basic,exp_conf;transcript_id=ENST00000436511.2;transcript_name=ZNF175-003;transcript_status=PUTATIVE;transcript_type=protein_coding
 001269F_0	AGAT	three_prime_UTR	558504	558650	.	+	.	ID=agat-three_prime_utr-5;Parent=ENST00000436511.2;exon_id=ENSE00002298653.1;exon_number=1;gene_id=ENSG00000105497.3;gene_name=ZNF175;gene_status=KNOWN;gene_type=protein_coding;havana_gene=OTTHUMG00000167771.3;havana_transcript=OTTHUMT00000396206.1;level=1;protein_id=ENSP00000440578.1;tag=basic,exp_conf;transcript_id=ENST00000436511.2;transcript_name=ZNF175-003;transcript_status=PUTATIVE;transcript_type=protein_coding
-001269F_0	AGAT	gene	560695	563290	.	-	.	ID=ENSG00000167765.3;gene_id=ENSG00000167765.3;gene_name=AC018755.1;gene_status=KNOWN;gene_type=protein_coding;level=1;protein_id=ENSP00000301439.2;tag=basic,appris_principal,exp_conf;transcript_id=ENST00000301439.3;transcript_name=AC018755.1-201;transcript_status=KNOWN;transcript_type=protein_coding
+001269F_0	AGAT	gene	560695	563290	.	-	.	ID=ENSG00000167765.3;gene_id=ENSG00000167765.3;gene_name=AC018755.1;gene_status=KNOWN;gene_type=protein_coding;level=1;protein_id=ENSP00000301439.2;tag=basic,appris_principal,exp_conf;transcript_name=AC018755.1-201;transcript_status=KNOWN;transcript_type=protein_coding
 001269F_0	ENSEMBL	transcript	560695	563290	.	-	.	ID=ENST00000301439.3;Parent=ENSG00000167765.3;gene_id=ENSG00000167765.3;gene_name=AC018755.1;gene_status=KNOWN;gene_type=protein_coding;level=1;protein_id=ENSP00000301439.2;tag=basic,appris_principal,exp_conf;transcript_id=ENST00000301439.3;transcript_name=AC018755.1-201;transcript_status=KNOWN;transcript_type=protein_coding
 001269F_0	ENSEMBL	exon	560695	561963	.	-	.	ID=exon:ENST00000301439.3:2;Parent=ENST00000301439.3;exon_id=ENSE00001116661.1;exon_number=2;gene_id=ENSG00000167765.3;gene_name=AC018755.1;gene_status=KNOWN;gene_type=protein_coding;level=1;protein_id=ENSP00000301439.2;tag=basic,appris_principal,exp_conf;transcript_id=ENST00000301439.3;transcript_name=AC018755.1-201;transcript_status=KNOWN;transcript_type=protein_coding
 001269F_0	ENSEMBL	exon	562861	563290	.	-	.	ID=exon:ENST00000301439.3:1;Parent=ENST00000301439.3;exon_id=ENSE00001116660.3;exon_number=1;gene_id=ENSG00000167765.3;gene_name=AC018755.1;gene_status=KNOWN;gene_type=protein_coding;level=1;protein_id=ENSP00000301439.2;tag=basic,appris_principal,exp_conf;transcript_id=ENST00000301439.3;transcript_name=AC018755.1-201;transcript_status=KNOWN;transcript_type=protein_coding
 001269F_0	ENSEMBL	CDS	561548	561963	.	-	1	ID=CDS:ENST00000301439.3:2;Parent=ENST00000301439.3;exon_id=ENSE00001116661.1;exon_number=2;gene_id=ENSG00000167765.3;gene_name=AC018755.1;gene_status=KNOWN;gene_type=protein_coding;level=1;protein_id=ENSP00000301439.2;tag=basic,appris_principal,exp_conf;transcript_id=ENST00000301439.3;transcript_name=AC018755.1-201;transcript_status=KNOWN;transcript_type=protein_coding
 001269F_0	ENSEMBL	CDS	562861	563234	.	-	0	ID=CDS:ENST00000301439.3:1;Parent=ENST00000301439.3;exon_id=ENSE00001116660.3;exon_number=1;gene_id=ENSG00000167765.3;gene_name=AC018755.1;gene_status=KNOWN;gene_type=protein_coding;level=1;protein_id=ENSP00000301439.2;tag=basic,appris_principal,exp_conf;transcript_id=ENST00000301439.3;transcript_name=AC018755.1-201;transcript_status=KNOWN;transcript_type=protein_coding
 001269F_0	AGAT	five_prime_UTR	563235	563290	.	-	.	ID=agat-five_prime_utr-2;Parent=ENST00000301439.3;exon_id=ENSE00001116661.1;exon_number=2;gene_id=ENSG00000167765.3;gene_name=AC018755.1;gene_status=KNOWN;gene_type=protein_coding;level=1;protein_id=ENSP00000301439.2;tag=basic,appris_principal,exp_conf;transcript_id=ENST00000301439.3;transcript_name=AC018755.1-201;transcript_status=KNOWN;transcript_type=protein_coding
 001269F_0	AGAT	three_prime_UTR	560695	561547	.	-	.	ID=agat-three_prime_utr-3;Parent=ENST00000301439.3;exon_id=ENSE00001116661.1;exon_number=2;gene_id=ENSG00000167765.3;gene_name=AC018755.1;gene_status=KNOWN;gene_type=protein_coding;level=1;protein_id=ENSP00000301439.2;tag=basic,appris_principal,exp_conf;transcript_id=ENST00000301439.3;transcript_name=AC018755.1-201;transcript_status=KNOWN;transcript_type=protein_coding
-001269F_0	AGAT	gene	580439	599250	.	-	.	ID=ENSG00000105501.7;ccdsid=CCDS33088.1;gene_id=ENSG00000105501.7;gene_name=SIGLEC5;gene_status=KNOWN;gene_type=protein_coding;havana_gene=OTTHUMG00000165510.5;level=3;protein_id=ENSP00000455510.2;tag=basic,appris_principal,CCDS;transcript_id=ENST00000570106.2;transcript_name=SIGLEC5-202;transcript_status=KNOWN;transcript_type=protein_coding
+001269F_0	AGAT	gene	580439	599250	.	-	.	ID=ENSG00000105501.7;ccdsid=CCDS33088.1;gene_id=ENSG00000105501.7;gene_name=SIGLEC5;gene_status=KNOWN;gene_type=protein_coding;havana_gene=OTTHUMG00000165510.5;level=3;protein_id=ENSP00000455510.2;tag=basic,appris_principal,CCDS;transcript_name=SIGLEC5-202;transcript_status=KNOWN;transcript_type=protein_coding
 001269F_0	ENSEMBL	transcript	580439	598551	.	-	.	ID=ENST00000222107.4;Parent=ENSG00000105501.7
 001269F_0	ENSEMBL	exon	580439	581333	.	-	.	ID=exon:ENST00000222107.4:9;Parent=ENST00000222107.4;exon_id=ENSE00000842709.5;exon_number=9;gene_id=ENSG00000105501.7;gene_name=SIGLEC5;gene_status=KNOWN;gene_type=protein_coding;havana_gene=OTTHUMG00000165510.5;level=3;protein_id=ENSP00000222107.4;tag=basic,appris_principal;transcript_id=ENST00000222107.4;transcript_name=SIGLEC5-201;transcript_status=KNOWN;transcript_type=protein_coding
 001269F_0	ENSEMBL	exon	594943	595024	.	-	.	ID=exon:ENST00000222107.4:8;Parent=ENST00000222107.4;exon_id=ENSE00003665149.1;exon_number=8;gene_id=ENSG00000105501.7;gene_name=SIGLEC5;gene_status=KNOWN;gene_type=protein_coding;havana_gene=OTTHUMG00000165510.5;level=3;protein_id=ENSP00000222107.4;tag=basic,appris_principal;transcript_id=ENST00000222107.4;transcript_name=SIGLEC5-201;transcript_status=KNOWN;transcript_type=protein_coding

diff --git a/t/gff_syntax/out/37_correct_output.gff b/t/gff_syntax/out/37_correct_output.gff
@@ -1,5 +1,5 @@
 ##gff-version 3
-xfSc0000000	AGAT	gene	7096	13319	.	-	.	ID=BL03703;exon_number=1;gene_id=BL03703;gene_name=CHRND;oldID=BlTCONS00149301;status=both;transcript_id=BL03703_cuf1
+xfSc0000000	AGAT	gene	7096	13319	.	-	.	ID=BL03703;exon_number=1;gene_id=BL03703;gene_name=CHRND;oldID=BlTCONS00149301;status=both
 xfSc0000000	AGAT	mRNA	7096	10149	.	-	.	ID=BL03703_cuf1;Parent=BL03703;exon_number=1;gene_id=BL03703;gene_name=CHRND;oldID=BlTCONS00149301;status=both;transcript_id=BL03703_cuf1
 xfSc0000000	protein_coding	exon	7096	8697	.	-	.	ID=agat-exon-6;Parent=BL03703_cuf1;exon_number=2;gene_id=BL03703;gene_name=CHRND;oldID=BlTCONS00149301;status=both;transcript_id=BL03703_cuf1
 xfSc0000000	protein_coding	exon	9847	10149	.	-	.	ID=agat-exon-5;Parent=BL03703_cuf1;exon_number=1;gene_id=BL03703;gene_name=CHRND;oldID=BlTCONS00149301;status=both;transcript_id=BL03703_cuf1
@@ -14,7 +14,7 @@ xfSc0000000	protein_coding	CDS	12803	13024	.	-	2	ID=agat-cds-3;Parent=BL03703_ev
 xfSc0000000	protein_coding	CDS	13283	13319	.	-	0	ID=agat-cds-2;Parent=BL03703_evm0;exon_number=1;gene_id=BL03703;gene_name=CHRND;oldID=Blg02918.0;status=both;transcript_id=BL03703_evm0
 xfSc0000000	AGAT	RNA	7096	9184	.	-	.	ID=BL03703_cuf0;Parent=BL03703;exon_number=1;gene_id=BL03703;gene_name=CHRND;oldID=BlTCONS00149300;status=both;transcript_id=BL03703_cuf0
 xfSc0000000	protein_coding	exon	7096	9184	.	-	.	ID=agat-exon-4;Parent=BL03703_cuf0;exon_number=1;gene_id=BL03703;gene_name=CHRND;oldID=BlTCONS00149300;status=both;transcript_id=BL03703_cuf0
-xfSc0000437	AGAT	gene	3712	3937	.	-	.	ID=BL03702;exon_number=2;gene_id=BL03702;gene_name=AHR;oldID=Blg03689.3;status=both;transcript_id=BL03702_evm3
+xfSc0000437	AGAT	gene	3712	3937	.	-	.	ID=BL03702;exon_number=2;gene_id=BL03702;gene_name=AHR;oldID=Blg03689.3;status=both
 xfSc0000437	AGAT	mRNA	3712	3937	.	-	.	ID=BL03702_evm3;Parent=BL03702;exon_number=2;gene_id=BL03702;gene_name=AHR;oldID=Blg03689.3;status=both;transcript_id=BL03702_evm3
 xfSc0000437	protein_coding	exon	3712	3937	.	-	.	ID=agat-exon-1;Parent=BL03702_evm3;exon_number=3;gene_id=BL03702;gene_name=AHR;oldID=Blg03689.3;status=both;transcript_id=BL03702_evm3
 xfSc0000437	protein_coding	CDS	3712	3937	.	-	1	ID=agat-cds-1;Parent=BL03702_evm3;exon_number=2;gene_id=BL03702;gene_name=AHR;oldID=Blg03689.3;status=both;transcript_id=BL03702_evm3
diff --git a/t/gff_syntax/out/stop_split_over_two_exons_correct_output.gff b/t/gff_syntax/out/stop_split_over_two_exons_correct_output.gff
@@ -1,5 +1,5 @@
 ##gff-version 3
-chr6	AGAT	gene	143060901	143061606	.	+	.	ID=ENSG00000146416.19;gene_id=ENSG00000146416.19;gene_name=AIG1;gene_type=protein_coding;transcript_id=ENST00000367596.5
+chr6	AGAT	gene	143060901	143061606	.	+	.	ID=ENSG00000146416.19;gene_id=ENSG00000146416.19;gene_name=AIG1;gene_type=protein_coding
 chr6	HAVANA	transcript	143060901	143061606	.	+	.	ID=ENST00000367596.5;Parent=ENSG00000146416.19;gene_id=ENSG00000146416.19;gene_name=AIG1;gene_type=protein_coding;transcript_id=ENST00000367596.5
 chr6	HAVANA	exon	143060901	143061066	.	+	.	ID=agat-exon-1;Parent=ENST00000367596.5;gene_id=ENSG00000146416.19;gene_name=AIG1;gene_type=protein_coding;transcript_id=ENST00000367596.5
 chr6	HAVANA	exon	143061214	143061606	.	+	.	ID=agat-exon-2;Parent=ENST00000367596.5;gene_id=ENSG00000146416.19;gene_name=AIG1;gene_type=protein_coding;transcript_id=ENST00000367596.5

diff --git a/t/gff_syntax/out/stop_start_an_exon_correct_output.gff b/t/gff_syntax/out/stop_start_an_exon_correct_output.gff
@@ -1,5 +1,5 @@
 ##gff-version 3
-chr6	AGAT	gene	143060901	143061606	.	+	.	ID=ENSG00000146416.19;gene_id=ENSG00000146416.19;gene_name=AIG1;gene_type=protein_coding;transcript_id=ENST00000367596.5
+chr6	AGAT	gene	143060901	143061606	.	+	.	ID=ENSG00000146416.19;gene_id=ENSG00000146416.19;gene_name=AIG1;gene_type=protein_coding
 chr6	HAVANA	transcript	143060901	143061606	.	+	.	ID=ENST00000367596.5;Parent=ENSG00000146416.19;gene_id=ENSG00000146416.19;gene_name=AIG1;gene_type=protein_coding;transcript_id=ENST00000367596.5
 chr6	HAVANA	exon	143060901	143061066	.	+	.	ID=agat-exon-1;Parent=ENST00000367596.5;gene_id=ENSG00000146416.19;gene_name=AIG1;gene_type=protein_coding;transcript_id=ENST00000367596.5
 chr6	HAVANA	exon	143061214	143061606	.	+	.	ID=agat-exon-2;Parent=ENST00000367596.5;gene_id=ENSG00000146416.19;gene_name=AIG1;gene_type=protein_coding;transcript_id=ENST00000367596.5

diff --git a/t/level_missing/out/testA_output.gff b/t/level_missing/out/testA_output.gff
@@ -1,13 +1,13 @@
 ##gff-version 3
-chr12	AGAT	gene	100	500	.	+	.	ID=agat-gene-1;common_tag="gene1";gene_info="gene1";transcript_id="transcript1"
+chr12	AGAT	gene	100	500	.	+	.	ID=agat-gene-1;common_tag="gene1";gene_info="gene1"
 chr12	HAVANA	transcript	100	500	.	+	.	ID="bbb";Parent=agat-gene-1;common_tag="gene1";gene_info="gene1";transcript_id="transcript1"
 chr12	HAVANA	exon	100	500	.	+	.	ID="ccc";Parent="bbb";common_tag="gene1"
 chr12	HAVANA	CDS	100	500	.	+	0	ID="ddd";Parent="bbb";common_tag="gene1"
-chr12	AGAT	gene	100	600	.	+	.	ID=agat-gene-2;common_tag="gene1";gene_info="gene1";transcript_id="transcript2"
+chr12	AGAT	gene	100	600	.	+	.	ID=agat-gene-2;common_tag="gene1";gene_info="gene1"
 chr12	HAVANA	transcript	100	600	.	+	.	ID="bbb2";Parent=agat-gene-2;common_tag="gene1";gene_info="gene1";transcript_id="transcript2"
 chr12	HAVANA	exon	100	600	.	+	.	ID="ccc2";Parent="bbb2";common_tag="gene1"
 chr12	HAVANA	CDS	100	600	.	+	0	ID="ddd2";Parent="bbb2";common_tag="gene1"
-chr12	AGAT	gene	1000	5000	.	+	.	ID=agat-gene-3;common_tag="gene2";gene_info="gene2";transcript_id="transcript3"
+chr12	AGAT	gene	1000	5000	.	+	.	ID=agat-gene-3;common_tag="gene2";gene_info="gene2"
 chr12	HAVANA	transcript	1000	5000	.	+	.	ID="yyy";Parent=agat-gene-3;common_tag="gene2";gene_info="gene2";transcript_id="transcript3"
 chr12	HAVANA	exon	1000	5000	.	+	.	ID="zzz";Parent="yyy";common_tag="gene2"
 chr12	HAVANA	CDS	1000	5000	.	+	0	ID="www";Parent="yyy";common_tag="gene2"