From 03cad914c51678287e02d71533d23e338d8a28da Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Thu, 22 Feb 2024 12:38:41 +0100 Subject: [PATCH] add a second test with extensiojn option activated, and update test to reflect last updates --- t/scripts_output.t | 7 ++ .../out/agat_sp_add_start_and_stop_1.gff | 30 +++---- .../out/agat_sp_add_start_and_stop_2.gff | 87 +++++++++++++++++++ 3 files changed, 108 insertions(+), 16 deletions(-) create mode 100644 t/scripts_output/out/agat_sp_add_start_and_stop_2.gff diff --git a/t/scripts_output.t b/t/scripts_output.t index 3cf8f3ac..ec26dd7a 100644 --- a/t/scripts_output.t +++ b/t/scripts_output.t @@ -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"; diff --git a/t/scripts_output/out/agat_sp_add_start_and_stop_1.gff b/t/scripts_output/out/agat_sp_add_start_and_stop_1.gff index 80e454a4..d26d0a32 100644 --- a/t/scripts_output/out/agat_sp_add_start_and_stop_1.gff +++ b/t/scripts_output/out/agat_sp_add_start_and_stop_1.gff @@ -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 @@ -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 @@ -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 @@ -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 @@ -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 diff --git a/t/scripts_output/out/agat_sp_add_start_and_stop_2.gff b/t/scripts_output/out/agat_sp_add_start_and_stop_2.gff new file mode 100644 index 00000000..ab0f8e89 --- /dev/null +++ b/t/scripts_output/out/agat_sp_add_start_and_stop_2.gff @@ -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