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Clean l1 (#491)
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* remove transcript ID in Level1 feature when creating it from another feature used as template (clean_clone)
* fix test to reflect that transcript_id not part of level1
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@Juke34
Juke34 authored Sep 17, 2024
1 parent bc41f87 commit 64702ff
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Showing 12 changed files with 29 additions and 22 deletions.
9 changes: 8 additions & 1 deletion lib/AGAT/OmniscientTool.pm
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Expand Up @@ -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;
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2 changes: 1 addition & 1 deletion t/gff_other/out/issue441.gtf
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@@ -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";
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4 changes: 2 additions & 2 deletions t/gff_syntax/out/30_correct_output.gff
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##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
6 changes: 3 additions & 3 deletions t/gff_syntax/out/36_correct_output.gff
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##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
Expand Down Expand Up @@ -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
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4 changes: 2 additions & 2 deletions t/gff_syntax/out/37_correct_output.gff
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@@ -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
Expand All @@ -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
2 changes: 1 addition & 1 deletion t/gff_syntax/out/stop_split_over_two_exons_correct_output.gff
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##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
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2 changes: 1 addition & 1 deletion t/gff_syntax/out/stop_start_an_exon_correct_output.gff
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@@ -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
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6 changes: 3 additions & 3 deletions t/level_missing/out/testA_output.gff
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@@ -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"
4 changes: 2 additions & 2 deletions t/level_missing/out/testA_output2.gff
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##gff-version 3
chr12 AGAT gene 100 600 . + . ID="gene1";common_tag="gene1";gene_info="gene1";transcript_id="transcript1"
chr12 AGAT gene 100 600 . + . ID="gene1";common_tag="gene1";gene_info="gene1"
chr12 HAVANA transcript 100 500 . + . ID="bbb";Parent="gene1";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 HAVANA transcript 100 600 . + . ID="bbb2";Parent="gene1";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="gene2";common_tag="gene2";gene_info="gene2";transcript_id="transcript3"
chr12 AGAT gene 1000 5000 . + . ID="gene2";common_tag="gene2";gene_info="gene2"
chr12 HAVANA transcript 1000 5000 . + . ID="yyy";Parent="gene2";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"
4 changes: 2 additions & 2 deletions t/level_missing/out/testA_output3.gff
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##gff-version 3
chr12 AGAT gene 100 600 . + . ID="gene1";common_tag="gene1";gene_info="gene1";transcript_id="transcript1"
chr12 AGAT gene 100 600 . + . ID="gene1";common_tag="gene1";gene_info="gene1"
chr12 HAVANA transcript 100 500 . + . ID="bbb";Parent="gene1";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 HAVANA transcript 100 600 . + . ID="bbb2";Parent="gene1";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="gene2";common_tag="gene2";gene_info="gene2";transcript_id="transcript3"
chr12 AGAT gene 1000 5000 . + . ID="gene2";common_tag="gene2";gene_info="gene2"
chr12 HAVANA transcript 1000 5000 . + . ID="yyy";Parent="gene2";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"
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