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add test data & expected output + script to fetch them
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| ##gff-version 3 | ||
| scaffold625 maker gene 337818 343277 . + . ID=CLUHARG00000005458;Name=TUBB3_2 | ||
| scaffold625 maker mRNA 337818 343277 . + . ID=CLUHART00000008717;Parent=CLUHARG00000005458 | ||
| scaffold625 maker exon 337818 337971 . + . ID=CLUHART00000008717:exon:1404;Parent=CLUHART00000008717 | ||
| scaffold625 maker exon 340733 340841 . + . ID=CLUHART00000008717:exon:1405;Parent=CLUHART00000008717 | ||
| scaffold625 maker exon 341518 341628 . + . ID=CLUHART00000008717:exon:1406;Parent=CLUHART00000008717 | ||
| scaffold625 maker exon 341964 343277 . + . ID=CLUHART00000008717:exon:1407;Parent=CLUHART00000008717 | ||
| scaffold625 maker CDS 337915 337971 . + 0 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717 | ||
| scaffold625 maker CDS 340733 340841 . + 0 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717 | ||
| scaffold625 maker CDS 341518 341628 . + 2 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717 | ||
| scaffold625 maker CDS 341964 343033 . + 2 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717 | ||
| scaffold625 maker five_prime_UTR 337818 337914 . + . ID=CLUHART00000008717:five_prime_utr;Parent=CLUHART00000008717 | ||
| scaffold625 maker three_prime_UTR 343034 343277 . + . ID=CLUHART00000008717:three_prime_utr;Parent=CLUHART00000008717 | ||
| scaffold789 maker gene 558184 564780 . + . ID=CLUHARG00000003852;Name=PF11_0240 | ||
| scaffold789 maker mRNA 558184 564780 . + . ID=CLUHART00000006146;Parent=CLUHARG00000003852 | ||
| scaffold789 maker exon 558184 560123 . + . ID=CLUHART00000006146:exon:995;Parent=CLUHART00000006146 | ||
| scaffold789 maker exon 561401 561519 . + . ID=CLUHART00000006146:exon:996;Parent=CLUHART00000006146 | ||
| scaffold789 maker exon 564171 564235 . + . ID=CLUHART00000006146:exon:997;Parent=CLUHART00000006146 | ||
| scaffold789 maker exon 564372 564780 . + . ID=CLUHART00000006146:exon:998;Parent=CLUHART00000006146 | ||
| scaffold789 maker CDS 558191 560123 . + 0 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146 | ||
| scaffold789 maker CDS 561401 561519 . + 2 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146 | ||
| scaffold789 maker CDS 564171 564235 . + 0 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146 | ||
| scaffold789 maker CDS 564372 564588 . + 1 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146 | ||
| scaffold789 maker five_prime_UTR 558184 558190 . + . ID=CLUHART00000006146:five_prime_utr;Parent=CLUHART00000006146 | ||
| scaffold789 maker three_prime_UTR 564589 564780 . + . ID=CLUHART00000006146:three_prime_utr;Parent=CLUHART00000006146 | ||
| scaffold789 maker mRNA 558184 564780 . + . ID=CLUHART00000006147;Parent=CLUHARG00000003852 | ||
| scaffold789 maker exon 558184 560123 . + . ID=CLUHART00000006147:exon:997;Parent=CLUHART00000006147 | ||
| scaffold789 maker exon 561401 561519 . + . ID=CLUHART00000006147:exon:998;Parent=CLUHART00000006147 | ||
| scaffold789 maker exon 562057 562121 . + . ID=CLUHART00000006147:exon:999;Parent=CLUHART00000006147 | ||
| scaffold789 maker exon 564372 564780 . + . ID=CLUHART00000006147:exon:1000;Parent=CLUHART00000006147 | ||
| scaffold789 maker CDS 558191 560123 . + 0 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147 | ||
| scaffold789 maker CDS 561401 561519 . + 2 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147 | ||
| scaffold789 maker CDS 562057 562121 . + 0 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147 | ||
| scaffold789 maker CDS 564372 564588 . + 1 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147 | ||
| scaffold789 maker five_prime_UTR 558184 558190 . + . ID=CLUHART00000006147:five_prime_utr;Parent=CLUHART00000006147 | ||
| scaffold789 maker three_prime_UTR 564589 564780 . + . ID=CLUHART00000006147:three_prime_utr;Parent=CLUHART00000006147 |
36 changes: 36 additions & 0 deletions
36
src/agat/agat_sp_ensembl_output_style/test_data/agat_sp_ensembl_output_style_1.gff
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,36 @@ | ||
| ##gff-version 3 | ||
| scaffold625 maker gene 337818 343277 . + . ID=CLUHARG00000005458;Name=TUBB3_2;gene_id=CLUHARG00000005458 | ||
| scaffold625 maker transcript 337818 343277 . + . ID=CLUHART00000008717;Parent=CLUHARG00000005458;transcript_id=CLUHART00000008717 | ||
| scaffold625 maker exon 337818 337971 . + . ID=CLUHART00000008717:exon:1404;Parent=CLUHART00000008717;exon_id=CLUHART00000008717:exon:1404 | ||
| scaffold625 maker exon 340733 340841 . + . ID=CLUHART00000008717:exon:1405;Parent=CLUHART00000008717;exon_id=CLUHART00000008717:exon:1405 | ||
| scaffold625 maker exon 341518 341628 . + . ID=CLUHART00000008717:exon:1406;Parent=CLUHART00000008717;exon_id=CLUHART00000008717:exon:1406 | ||
| scaffold625 maker exon 341964 343277 . + . ID=CLUHART00000008717:exon:1407;Parent=CLUHART00000008717;exon_id=CLUHART00000008717:exon:1407 | ||
| scaffold625 maker CDS 337915 337971 . + 0 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717 | ||
| scaffold625 maker CDS 340733 340841 . + 0 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717 | ||
| scaffold625 maker CDS 341518 341628 . + 2 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717 | ||
| scaffold625 maker CDS 341964 343033 . + 2 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717 | ||
| scaffold625 maker five_prime_UTR 337818 337914 . + . ID=CLUHART00000008717:five_prime_utr;Parent=CLUHART00000008717 | ||
| scaffold625 maker three_prime_UTR 343034 343277 . + . ID=CLUHART00000008717:three_prime_utr;Parent=CLUHART00000008717 | ||
| scaffold789 maker gene 558184 564780 . + . ID=CLUHARG00000003852;Name=PF11_0240;gene_id=CLUHARG00000003852 | ||
| scaffold789 maker transcript 558184 564780 . + . ID=CLUHART00000006146;Parent=CLUHARG00000003852;transcript_id=CLUHART00000006146 | ||
| scaffold789 maker exon 558184 560123 . + . ID=CLUHART00000006146:exon:995;Parent=CLUHART00000006146;exon_id=CLUHART00000006146:exon:995 | ||
| scaffold789 maker exon 561401 561519 . + . ID=CLUHART00000006146:exon:996;Parent=CLUHART00000006146;exon_id=CLUHART00000006146:exon:996 | ||
| scaffold789 maker exon 564171 564235 . + . ID=CLUHART00000006146:exon:997;Parent=CLUHART00000006146;exon_id=CLUHART00000006146:exon:997 | ||
| scaffold789 maker exon 564372 564780 . + . ID=CLUHART00000006146:exon:998;Parent=CLUHART00000006146;exon_id=CLUHART00000006146:exon:998 | ||
| scaffold789 maker CDS 558191 560123 . + 0 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146 | ||
| scaffold789 maker CDS 561401 561519 . + 2 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146 | ||
| scaffold789 maker CDS 564171 564235 . + 0 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146 | ||
| scaffold789 maker CDS 564372 564588 . + 1 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146 | ||
| scaffold789 maker five_prime_UTR 558184 558190 . + . ID=CLUHART00000006146:five_prime_utr;Parent=CLUHART00000006146 | ||
| scaffold789 maker three_prime_UTR 564589 564780 . + . ID=CLUHART00000006146:three_prime_utr;Parent=CLUHART00000006146 | ||
| scaffold789 maker transcript 558184 564780 . + . ID=CLUHART00000006147;Parent=CLUHARG00000003852;transcript_id=CLUHART00000006147 | ||
| scaffold789 maker exon 558184 560123 . + . ID=CLUHART00000006147:exon:997;Parent=CLUHART00000006147;exon_id=CLUHART00000006147:exon:997 | ||
| scaffold789 maker exon 561401 561519 . + . ID=CLUHART00000006147:exon:998;Parent=CLUHART00000006147;exon_id=CLUHART00000006147:exon:998 | ||
| scaffold789 maker exon 562057 562121 . + . ID=CLUHART00000006147:exon:999;Parent=CLUHART00000006147;exon_id=CLUHART00000006147:exon:999 | ||
| scaffold789 maker exon 564372 564780 . + . ID=CLUHART00000006147:exon:1000;Parent=CLUHART00000006147;exon_id=CLUHART00000006147:exon:1000 | ||
| scaffold789 maker CDS 558191 560123 . + 0 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147 | ||
| scaffold789 maker CDS 561401 561519 . + 2 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147 | ||
| scaffold789 maker CDS 562057 562121 . + 0 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147 | ||
| scaffold789 maker CDS 564372 564588 . + 1 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147 | ||
| scaffold789 maker five_prime_UTR 558184 558190 . + . ID=CLUHART00000006147:five_prime_utr;Parent=CLUHART00000006147 | ||
| scaffold789 maker three_prime_UTR 564589 564780 . + . ID=CLUHART00000006147:three_prime_utr;Parent=CLUHART00000006147 |
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| #!/bin/bash | ||
|
|
||
| # clone repo | ||
| if [ ! -d /tmp/agat_source ]; then | ||
| git clone --depth 1 --single-branch --branch master https://github.com/NBISweden/AGAT /tmp/agat_source | ||
| fi | ||
|
|
||
| # copy test data | ||
| cp -r /tmp/agat_source/t/scripts_output/in/0.gff src/agat/agat_sp_ensembl_output_style/test_data/ | ||
| cp -r /tmp/agat_source/t/scripts_output/out/agat_sp_ensembl_output_style_1.gff src/agat/agat_sp_ensembl_output_style/test_data/ |