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add a second test with extensiojn option activated, and update test t…
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…o reflect last updates
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@Juke34
Juke34 committed Feb 22, 2024
1 parent ce370d7 commit 03cad91
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Showing 3 changed files with 108 additions and 16 deletions.
7 changes: 7 additions & 0 deletions t/scripts_output.t
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Original file line number Diff line number Diff line change
Expand Up @@ -213,6 +213,13 @@ system(" $script --gff $input_folder/agat_sp_add_start_and_stop.gff --fasta $inp
ok( system("diff $result $outtmp") == 0, "output $script");
unlink $outtmp;

$script = $script_prefix."bin/agat_sp_add_start_and_stop.pl";
$result = "$output_folder/agat_sp_add_start_and_stop_2.gff";
system(" $script --gff $input_folder/agat_sp_add_start_and_stop.gff --fasta $input_folder/1.fa -e --ni -o $outtmp 2>&1 1>/dev/null");
#run test
ok( system("diff $result $outtmp") == 0, "output $script");
unlink $outtmp;

# -------------------------- check agat_sp_statistics --------------------------

$script = $script_prefix."bin/agat_sp_alignment_output_style.pl";
Expand Down
30 changes: 14 additions & 16 deletions t/scripts_output/out/agat_sp_add_start_and_stop_1.gff
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Original file line number Diff line number Diff line change
@@ -1,12 +1,10 @@
##gff-version 3
1 AGAT gene 34 123 . + . ID=agat-cds-2
1 AGAT mRNA 34 123 . + . ID=transcriptX;Parent=agat-cds-2
1 irgsp gene 34 123 . + . ID=geneX
1 irgsp mRNA 34 123 . + . ID=transcriptX;Parent=geneX
1 irgsp exon 34 123 . + . ID=agat-exon-2;Parent=transcriptX
1 irgsp CDS 34 123 . + 0 ID=agat-cds-2;Parent=transcriptX
1 AGAT start_codon 34 36 . + . ID=start_added-1;Parent=transcriptX
1 AGAT stop_codon 121 123 . + . ID=stop_added-1;Parent=transcriptX
1 irgsp gene 34 123 . + . ID=geneX
1 irgsp mRNA 34 123 . + . ID=agat-mrna-1;Parent=geneX
1 AGAT start_codon 34 36 . + . ID=start_added-6;Parent=transcriptX
1 AGAT stop_codon 121 123 . + . ID=stop_added-6;Parent=transcriptX
1 irgsp gene 25861 26424 . - . ID=gene:Os01g0100650;biotype=protein_coding;description=Hypothetical gene. (Os01t0100650-00);gene_id=Os01g0100650;logic_name=irgspv1.0-20170804-genes
1 irgsp mRNA 25861 26424 . - . ID=transcript:Os01t0100650-00;Parent=gene:Os01g0100650;biotype=protein_coding;transcript_id=Os01t0100650-00
1 irgsp exon 25861 26424 . - . ID=Os01t0100650-00.exon1;Parent=transcript:Os01t0100650-00;Name=Os01t0100650-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100650-00.exon1;rank=1
Expand All @@ -30,8 +28,8 @@
1 irgsp CDS 306171 306245 . + 0 ID=CDS:Os01t0105700-01;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
1 irgsp CDS 306353 306493 . + 0 ID=CDS:Os01t0105700-01;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
1 irgsp five_prime_UTR 303233 303328 . + . ID=agat-five_prime_utr-1;Parent=transcript:Os01t0105700-01
1 AGAT start_codon 303329 303331 . + . ID=start_added-3;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
1 AGAT stop_codon 306491 306493 . + . ID=stop_added-3;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
1 AGAT start_codon 303329 303331 . + . ID=start_added-2;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
1 AGAT stop_codon 306491 306493 . + . ID=stop_added-2;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
1 irgsp three_prime_UTR 306491 306736 . + . ID=agat-three_prime_utr-1;Parent=transcript:Os01t0105700-01
1 irgsp gene 306871 308842 . - . ID=gene:Os01g0105800;Name=IRON-SULFUR CLUSTER PROTEIN 9;biotype=protein_coding;description=Similar to Iron sulfur assembly protein 1. (Os01t0105800-01);gene_id=Os01g0105800;logic_name=irgspv1.0-20170804-genes
1 irgsp mRNA 306871 308842 . - . ID=transcript:Os01t0105800-01;Parent=gene:Os01g0105800;biotype=protein_coding;transcript_id=Os01t0105800-01
Expand All @@ -44,8 +42,8 @@
1 irgsp CDS 308397 308601 . - 0 ID=CDS:Os01t0105800-01;Parent=transcript:Os01t0105800-01;protein_id=Os01t0105800-01
1 irgsp five_prime_UTR 308602 308626 . - . ID=agat-five_prime_utr-2;Parent=transcript:Os01t0105800-01
1 irgsp five_prime_UTR 308703 308842 . - . ID=agat-five_prime_utr-3;Parent=transcript:Os01t0105800-01
1 AGAT start_codon 308599 308601 . - . ID=start_added-4;Parent=transcript:Os01t0105800-01;protein_id=Os01t0105800-01
1 AGAT stop_codon 307124 307126 . - . ID=stop_added-4;Parent=transcript:Os01t0105800-01;protein_id=Os01t0105800-01
1 AGAT start_codon 308599 308601 . - . ID=start_added-3;Parent=transcript:Os01t0105800-01;protein_id=Os01t0105800-01
1 AGAT stop_codon 307124 307126 . - . ID=stop_added-3;Parent=transcript:Os01t0105800-01;protein_id=Os01t0105800-01
1 irgsp three_prime_UTR 306871 307126 . - . ID=agat-three_prime_utr-2;Parent=transcript:Os01t0105800-01
1 irgsp gene 309520 313170 . - . ID=gene:Os01g0105900;biotype=protein_coding;description=Carbohydrate/purine kinase domain containing protein. (Os01t0105900-01);gene_id=Os01g0105900;logic_name=irgspv1.0-20170804-genes
1 irgsp mRNA 309520 313170 . - . ID=transcript:Os01t0105900-01;Parent=gene:Os01g0105900;biotype=protein_coding;transcript_id=Os01t0105900-01
Expand All @@ -66,8 +64,8 @@
1 irgsp CDS 311163 311426 . - 0 ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
1 irgsp CDS 312867 313064 . - 0 ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
1 irgsp five_prime_UTR 313065 313170 . - . ID=agat-five_prime_utr-4;Parent=transcript:Os01t0105900-01
1 AGAT start_codon 313062 313064 . - . ID=start_added-5;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
1 AGAT stop_codon 309822 309824 . - . ID=stop_added-5;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
1 AGAT start_codon 313062 313064 . - . ID=start_added-4;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
1 AGAT stop_codon 309822 309824 . - . ID=stop_added-4;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
1 irgsp three_prime_UTR 309520 309824 . - . ID=agat-three_prime_utr-3;Parent=transcript:Os01t0105900-01
1 irgsp gene 319754 322205 . + . ID=gene:Os01g0106200;biotype=protein_coding;description=Similar to RER1A protein (AtRER1A). (Os01t0106200-01);gene_id=Os01g0106200;logic_name=irgspv1.0-20170804-genes
1 irgsp mRNA 319754 322205 . + . ID=transcript:Os01t0106200-01;Parent=gene:Os01g0106200;biotype=protein_coding;transcript_id=Os01t0106200-01
Expand All @@ -78,12 +76,12 @@
1 irgsp CDS 321468 321648 . + 1 ID=CDS:Os01t0106200-01;Parent=transcript:Os01t0106200-01;protein_id=Os01t0106200-01
1 irgsp CDS 321928 321975 . + 0 ID=CDS:Os01t0106200-01;Parent=transcript:Os01t0106200-01;protein_id=Os01t0106200-01
1 irgsp five_prime_UTR 319754 319874 . + . ID=agat-five_prime_utr-5;Parent=transcript:Os01t0106200-01
1 AGAT start_codon 319875 319877 . + . ID=start_added-6;Parent=transcript:Os01t0106200-01;protein_id=Os01t0106200-01
1 AGAT stop_codon 321973 321975 . + . ID=stop_added-6;Parent=transcript:Os01t0106200-01;protein_id=Os01t0106200-01
1 AGAT start_codon 319875 319877 . + . ID=start_added-5;Parent=transcript:Os01t0106200-01;protein_id=Os01t0106200-01
1 AGAT stop_codon 321973 321975 . + . ID=stop_added-5;Parent=transcript:Os01t0106200-01;protein_id=Os01t0106200-01
1 irgsp three_prime_UTR 321973 322205 . + . ID=agat-three_prime_utr-4;Parent=transcript:Os01t0106200-01
1 irgsp gene 43270900 43270919 . + . ID=geneA
1 irgsp mRNA 43270900 43270919 . + . ID=transcriptA;Parent=geneA
1 irgsp exon 43270900 43270919 . + . ID=agat-exon-1;Parent=transcriptA
1 irgsp CDS 43270900 43270919 . + 0 ID=agat-cds-1;Parent=transcriptA
1 AGAT start_codon 43270900 43270902 . + . ID=start_added-2;Parent=transcriptA
1 AGAT stop_codon 43270917 43270919 . + . ID=stop_added-2;Parent=transcriptA
1 AGAT start_codon 43270900 43270902 . + . ID=start_added-1;Parent=transcriptA
1 AGAT stop_codon 43270917 43270919 . + . ID=stop_added-1;Parent=transcriptA
87 changes: 87 additions & 0 deletions t/scripts_output/out/agat_sp_add_start_and_stop_2.gff
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Original file line number Diff line number Diff line change
@@ -0,0 +1,87 @@
##gff-version 3
1 irgsp gene 34 1011 . + . ID=geneX
1 irgsp mRNA 34 1011 . + . ID=transcriptX;Parent=geneX
1 irgsp exon 34 1011 . + . ID=agat-exon-2;Parent=transcriptX
1 irgsp CDS 34 1011 . + 0 ID=agat-cds-2;Parent=transcriptX
1 AGAT stop_codon 1009 1011 . + . ID=stop_added-6;Parent=transcriptX
1 irgsp gene 25861 26447 . - . ID=gene:Os01g0100650;biotype=protein_coding;description=Hypothetical gene. (Os01t0100650-00);gene_id=Os01g0100650;logic_name=irgspv1.0-20170804-genes
1 irgsp mRNA 25861 26447 . - . ID=transcript:Os01t0100650-00;Parent=gene:Os01g0100650;biotype=protein_coding;transcript_id=Os01t0100650-00
1 irgsp exon 25861 26447 . - . ID=Os01t0100650-00.exon1;Parent=transcript:Os01t0100650-00;Name=Os01t0100650-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100650-00.exon1;rank=1
1 irgsp CDS 26040 26447 . - 0 ID=CDS:Os01t0100650-00;Parent=transcript:Os01t0100650-00;protein_id=Os01t0100650-00
1 irgsp five_prime_UTR 26424 26424 . - . ID=agat-five_prime_utr-6;Parent=transcript:Os01t0100650-00
1 AGAT start_codon 26445 26447 . - . ID=start_added-2;Parent=transcript:Os01t0100650-00;protein_id=Os01t0100650-00
1 AGAT stop_codon 26040 26042 . - . ID=stop_added-1;Parent=transcript:Os01t0100650-00;protein_id=Os01t0100650-00
1 irgsp three_prime_UTR 25861 26039 . - . ID=agat-three_prime_utr-5;Parent=transcript:Os01t0100650-00
1 irgsp gene 303233 306736 . + . ID=gene:Os01g0105700;Name=basic helix-loop-helix protein 071;biotype=protein_coding;description=Basic helix-loop-helix dimerisation region bHLH domain containing protein. (Os01t0105700-01);gene_id=Os01g0105700;logic_name=irgspv1.0-20170804-genes
1 irgsp mRNA 303233 306736 . + . ID=transcript:Os01t0105700-01;Parent=gene:Os01g0105700;biotype=protein_coding;transcript_id=Os01t0105700-01
1 irgsp exon 303233 303471 . + . ID=Os01t0105700-01.exon1;Parent=transcript:Os01t0105700-01;Name=Os01t0105700-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0105700-01.exon1;rank=1
1 irgsp exon 303981 304509 . + . ID=Os01t0105700-01.exon2;Parent=transcript:Os01t0105700-01;Name=Os01t0105700-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0105700-01.exon2;rank=2
1 irgsp exon 305572 305718 . + . ID=Os01t0105700-01.exon3;Parent=transcript:Os01t0105700-01;Name=Os01t0105700-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105700-01.exon3;rank=3
1 irgsp exon 305834 305899 . + . ID=Os01t0105700-01.exon4;Parent=transcript:Os01t0105700-01;Name=Os01t0105700-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105700-01.exon4;rank=4
1 irgsp exon 305993 306058 . + . ID=Os01t0105700-01.exon5;Parent=transcript:Os01t0105700-01;Name=Os01t0105700-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105700-01.exon5;rank=5
1 irgsp exon 306171 306245 . + . ID=Os01t0105700-01.exon6;Parent=transcript:Os01t0105700-01;Name=Os01t0105700-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105700-01.exon6;rank=6
1 irgsp exon 306353 306736 . + . ID=Os01t0105700-01.exon7;Parent=transcript:Os01t0105700-01;Name=Os01t0105700-01.exon7;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0105700-01.exon7;rank=7
1 irgsp CDS 303329 303471 . + 0 ID=CDS:Os01t0105700-01;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
1 irgsp CDS 303981 304509 . + 1 ID=CDS:Os01t0105700-01;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
1 irgsp CDS 305572 305718 . + 0 ID=CDS:Os01t0105700-01;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
1 irgsp CDS 305834 305899 . + 0 ID=CDS:Os01t0105700-01;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
1 irgsp CDS 305993 306058 . + 0 ID=CDS:Os01t0105700-01;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
1 irgsp CDS 306171 306245 . + 0 ID=CDS:Os01t0105700-01;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
1 irgsp CDS 306353 306493 . + 0 ID=CDS:Os01t0105700-01;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
1 irgsp five_prime_UTR 303233 303328 . + . ID=agat-five_prime_utr-1;Parent=transcript:Os01t0105700-01
1 AGAT start_codon 303329 303331 . + . ID=start_added-3;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
1 AGAT stop_codon 306491 306493 . + . ID=stop_added-2;Parent=transcript:Os01t0105700-01;protein_id=Os01t0105700-01
1 irgsp three_prime_UTR 306494 306736 . + . ID=agat-three_prime_utr-1;Parent=transcript:Os01t0105700-01
1 irgsp gene 306871 308842 . - . ID=gene:Os01g0105800;Name=IRON-SULFUR CLUSTER PROTEIN 9;biotype=protein_coding;description=Similar to Iron sulfur assembly protein 1. (Os01t0105800-01);gene_id=Os01g0105800;logic_name=irgspv1.0-20170804-genes
1 irgsp mRNA 306871 308842 . - . ID=transcript:Os01t0105800-01;Parent=gene:Os01g0105800;biotype=protein_coding;transcript_id=Os01t0105800-01
1 irgsp exon 306871 307217 . - . ID=Os01t0105800-01.exon4;Parent=transcript:Os01t0105800-01;Name=Os01t0105800-01.exon4;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0105800-01.exon4;rank=4
1 irgsp exon 307296 307413 . - . ID=Os01t0105800-01.exon3;Parent=transcript:Os01t0105800-01;Name=Os01t0105800-01.exon3;constitutive=1;ensembl_end_phase=2;ensembl_phase=1;exon_id=Os01t0105800-01.exon3;rank=3
1 irgsp exon 308397 308626 . - . ID=Os01t0105800-01.exon2;Parent=transcript:Os01t0105800-01;Name=Os01t0105800-01.exon2;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Os01t0105800-01.exon2;rank=2
1 irgsp exon 308703 308842 . - . ID=Os01t0105800-01.exon1;Parent=transcript:Os01t0105800-01;Name=Os01t0105800-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0105800-01.exon1;rank=1
1 irgsp CDS 307124 307217 . - 1 ID=CDS:Os01t0105800-01;Parent=transcript:Os01t0105800-01;protein_id=Os01t0105800-01
1 irgsp CDS 307296 307413 . - 2 ID=CDS:Os01t0105800-01;Parent=transcript:Os01t0105800-01;protein_id=Os01t0105800-01
1 irgsp CDS 308397 308601 . - 0 ID=CDS:Os01t0105800-01;Parent=transcript:Os01t0105800-01;protein_id=Os01t0105800-01
1 irgsp five_prime_UTR 308602 308626 . - . ID=agat-five_prime_utr-2;Parent=transcript:Os01t0105800-01
1 irgsp five_prime_UTR 308703 308842 . - . ID=agat-five_prime_utr-3;Parent=transcript:Os01t0105800-01
1 AGAT start_codon 308599 308601 . - . ID=start_added-4;Parent=transcript:Os01t0105800-01;protein_id=Os01t0105800-01
1 AGAT stop_codon 307124 307126 . - . ID=stop_added-3;Parent=transcript:Os01t0105800-01;protein_id=Os01t0105800-01
1 irgsp three_prime_UTR 306871 307123 . - . ID=agat-three_prime_utr-2;Parent=transcript:Os01t0105800-01
1 irgsp gene 309520 313170 . - . ID=gene:Os01g0105900;biotype=protein_coding;description=Carbohydrate/purine kinase domain containing protein. (Os01t0105900-01);gene_id=Os01g0105900;logic_name=irgspv1.0-20170804-genes
1 irgsp mRNA 309520 313170 . - . ID=transcript:Os01t0105900-01;Parent=gene:Os01g0105900;biotype=protein_coding;transcript_id=Os01t0105900-01
1 irgsp exon 309520 310070 . - . ID=Os01t0105900-01.exon8;Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon8;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0105900-01.exon8;rank=8
1 irgsp exon 310256 310367 . - . ID=Os01t0105900-01.exon7;Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0105900-01.exon7;rank=7
1 irgsp exon 310455 310552 . - . ID=Os01t0105900-01.exon6;Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon6;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0105900-01.exon6;rank=6
1 irgsp exon 310632 310739 . - . ID=Os01t0105900-01.exon5;Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105900-01.exon5;rank=5
1 irgsp exon 310880 310918 . - . ID=Os01t0105900-01.exon4;Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105900-01.exon4;rank=4
1 irgsp exon 311002 311073 . - . ID=Os01t0105900-01.exon3;Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105900-01.exon3;rank=3
1 irgsp exon 311163 311426 . - . ID=Os01t0105900-01.exon2;Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0105900-01.exon2;rank=2
1 irgsp exon 312867 313170 . - . ID=Os01t0105900-01.exon1;Parent=transcript:Os01t0105900-01;Name=Os01t0105900-01.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0105900-01.exon1;rank=1
1 irgsp CDS 309822 310070 . - 0 ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
1 irgsp CDS 310256 310367 . - 1 ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
1 irgsp CDS 310455 310552 . - 0 ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
1 irgsp CDS 310632 310739 . - 0 ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
1 irgsp CDS 310880 310918 . - 0 ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
1 irgsp CDS 311002 311073 . - 0 ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
1 irgsp CDS 311163 311426 . - 0 ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
1 irgsp CDS 312867 313064 . - 0 ID=CDS:Os01t0105900-01;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
1 irgsp five_prime_UTR 313065 313170 . - . ID=agat-five_prime_utr-4;Parent=transcript:Os01t0105900-01
1 AGAT start_codon 313062 313064 . - . ID=start_added-5;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
1 AGAT stop_codon 309822 309824 . - . ID=stop_added-4;Parent=transcript:Os01t0105900-01;protein_id=Os01t0105900-01
1 irgsp three_prime_UTR 309520 309821 . - . ID=agat-three_prime_utr-3;Parent=transcript:Os01t0105900-01
1 irgsp gene 319754 322205 . + . ID=gene:Os01g0106200;biotype=protein_coding;description=Similar to RER1A protein (AtRER1A). (Os01t0106200-01);gene_id=Os01g0106200;logic_name=irgspv1.0-20170804-genes
1 irgsp mRNA 319754 322205 . + . ID=transcript:Os01t0106200-01;Parent=gene:Os01g0106200;biotype=protein_coding;transcript_id=Os01t0106200-01
1 irgsp exon 319754 320236 . + . ID=Os01t0106200-01.exon1;Parent=transcript:Os01t0106200-01;Name=Os01t0106200-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0106200-01.exon1;rank=1
1 irgsp exon 321468 321648 . + . ID=Os01t0106200-01.exon2;Parent=transcript:Os01t0106200-01;Name=Os01t0106200-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0106200-01.exon2;rank=2
1 irgsp exon 321928 322205 . + . ID=Os01t0106200-01.exon3;Parent=transcript:Os01t0106200-01;Name=Os01t0106200-01.exon3;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0106200-01.exon3;rank=3
1 irgsp CDS 319875 320236 . + 0 ID=CDS:Os01t0106200-01;Parent=transcript:Os01t0106200-01;protein_id=Os01t0106200-01
1 irgsp CDS 321468 321648 . + 1 ID=CDS:Os01t0106200-01;Parent=transcript:Os01t0106200-01;protein_id=Os01t0106200-01
1 irgsp CDS 321928 321975 . + 0 ID=CDS:Os01t0106200-01;Parent=transcript:Os01t0106200-01;protein_id=Os01t0106200-01
1 irgsp five_prime_UTR 319754 319874 . + . ID=agat-five_prime_utr-5;Parent=transcript:Os01t0106200-01
1 AGAT start_codon 319875 319877 . + . ID=start_added-6;Parent=transcript:Os01t0106200-01;protein_id=Os01t0106200-01
1 AGAT stop_codon 321973 321975 . + . ID=stop_added-5;Parent=transcript:Os01t0106200-01;protein_id=Os01t0106200-01
1 irgsp three_prime_UTR 321976 322205 . + . ID=agat-three_prime_utr-4;Parent=transcript:Os01t0106200-01
1 irgsp gene 43269907 43270922 . + . ID=geneA
1 irgsp mRNA 43269907 43270922 . + . ID=transcriptA;Parent=geneA
1 irgsp exon 43269907 43270922 . + . ID=agat-exon-1;Parent=transcriptA
1 irgsp CDS 43269907 43270922 . + 0 ID=agat-cds-1;Parent=transcriptA
1 AGAT start_codon 43269907 43269909 . + . ID=start_added-1;Parent=transcriptA

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