/dports/biology/bcftools/bcftools-1.14/test/csq/ENST00000422159/ |
H A D | short.gff | 6 3 havana CDS 278 328 . - 0 ID=CDS:ENSP00000405464;Parent=transcript:ENST00000422159;protein_id=ENSP… 8 3 havana CDS 4196 4312 . - 0 ID=CDS:ENSP00000405464;Parent=transcript:ENST00000422159;protein_id=EN… 9 3 havana CDS 4507 4614 . - 0 ID=CDS:ENSP00000405464;Parent=transcript:ENST00000422159;protein_id=EN…
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/dports/biology/bio-mocha/bcftools-1.14/test/csq/ENST00000422159/ |
H A D | short.gff | 6 3 havana CDS 278 328 . - 0 ID=CDS:ENSP00000405464;Parent=transcript:ENST00000422159;protein_id=ENSP… 8 3 havana CDS 4196 4312 . - 0 ID=CDS:ENSP00000405464;Parent=transcript:ENST00000422159;protein_id=EN… 9 3 havana CDS 4507 4614 . - 0 ID=CDS:ENSP00000405464;Parent=transcript:ENST00000422159;protein_id=EN…
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/dports/biology/py-gffutils/gffutils-0.10.1/gffutils/test/data/ |
H A D | hybrid1.gff3 | 8 chr17 UCSC CDS 62468039 62468236 . - 1 Parent=A00469 9 chr17 UCSC CDS 62468490 62468654 . - 2 Parent=A00469 10 chr17 UCSC CDS 62468747 62468866 . - 1 Parent=A00469 11 chr17 UCSC CDS 62469076 62469236 . - 1 Parent=A00469 12 chr17 UCSC CDS 62469497 62469506 . - 0 Parent=A00469
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/dports/biology/bio-mocha/bcftools-1.14/test/csq/ENST00000518414/ |
H A D | ENST00000518414.gff | 7 8 havana CDS 8495 8506 . + 0 ID=CDS:ENSP00000430552;Parent=transcript:ENST00000518414;protein_id=EN… 9 8 havana CDS 10486 10612 . + 0 ID=CDS:ENSP00000430552;Parent=transcript:ENST00000518414;protein_id=… 11 8 havana CDS 11321 11400 . + 2 ID=CDS:ENSP00000430552;Parent=transcript:ENST00000518414;protein_id=…
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/dports/biology/bcftools/bcftools-1.14/test/csq/ENST00000518414/ |
H A D | ENST00000518414.gff | 7 8 havana CDS 8495 8506 . + 0 ID=CDS:ENSP00000430552;Parent=transcript:ENST00000518414;protein_id=EN… 9 8 havana CDS 10486 10612 . + 0 ID=CDS:ENSP00000430552;Parent=transcript:ENST00000518414;protein_id=… 11 8 havana CDS 11321 11400 . + 2 ID=CDS:ENSP00000430552;Parent=transcript:ENST00000518414;protein_id=…
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/dports/biology/p5-Bio-GFF3/Bio-GFF3-2.0/t/data/ |
H A D | knownGene_out_of_order.gff3 | 2 chr17 UCSC CDS 62468039 62468236 . - 1 Parent=A00469 4 chr17 UCSC CDS 62468490 62468654 . - 2 Parent=A00469 7 chr17 UCSC CDS 62468747 62468866 . - 1 Parent=A00469 8 chr17 UCSC CDS 62469076 62469236 . - 1 Parent=A00469 9 chr17 UCSC CDS 62469497 62469506 . - 0 Parent=A00469 15 chr9 UCSC CDS 90518842 90519167 . - 1 Parent=AB000114 16 chr9 UCSC CDS 90520309 90521248 . - 0 Parent=AB000114
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H A D | gff3_with_syncs.dumped_result | 110 'CDS:Solyc00g005000.2.1.1' 128 'type' => 'CDS' 185 'CDS:Solyc00g005000.2.1.2' 203 'type' => 'CDS' 327 'CDS:Solyc00g005020.1.1.1' 345 'type' => 'CDS' 402 'CDS:Solyc00g005020.1.1.2' 420 'type' => 'CDS' 477 'CDS:Solyc00g005020.1.1.3' 495 'type' => 'CDS'
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/dports/biology/bio-mocha/bcftools-1.14/test/csq/ENST00000357367/ |
H A D | ENST00000357367.gff | 5 1 ensembl_havana CDS 357 918 . - 1 ID=CDS:ENSP00000349931;Parent=transcript:ENST00000357367;protein… 7 1 ensembl_havana CDS 1833 2408 . - 1 ID=CDS:ENSP00000349931;Parent=transcript:ENST00000357367;prote… 8 1 ensembl_havana CDS 2791 3077 . - 0 ID=CDS:ENSP00000349931;Parent=transcript:ENST00000357367;prote…
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/dports/biology/bcftools/bcftools-1.14/test/csq/ENST00000357367/ |
H A D | ENST00000357367.gff | 5 1 ensembl_havana CDS 357 918 . - 1 ID=CDS:ENSP00000349931;Parent=transcript:ENST00000357367;protein… 7 1 ensembl_havana CDS 1833 2408 . - 1 ID=CDS:ENSP00000349931;Parent=transcript:ENST00000357367;prote… 8 1 ensembl_havana CDS 2791 3077 . - 0 ID=CDS:ENSP00000349931;Parent=transcript:ENST00000357367;prote…
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/unit_test/5colftblreader_test_cases/ |
H A D | gb-7414.tbl | 4 19 1719 CDS 16 6 1415 CDS 22 11 769 CDS 27 11 36 CDS 34 19 1719 CDS
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/dports/biology/bio-mocha/bcftools-1.14/test/csq/ENST00000479739/ |
H A D | ENST00000479739.gff | 9 2 havana CDS 13260 13482 . - 1 ID=CDS:ENSP00000441266;Parent=transcript:ENST00000479739;protein_id=… 11 2 havana CDS 15392 15520 . - 1 ID=CDS:ENSP00000441266;Parent=transcript:ENST00000479739;protein_id=… 13 2 havana CDS 16451 16563 . - 0 ID=CDS:ENSP00000441266;Parent=transcript:ENST00000479739;protein_id=… 14 2 havana CDS 25089 25091 . - 0 ID=CDS:ENSP00000441266;Parent=transcript:ENST00000479739;protein_id=…
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/dports/biology/bcftools/bcftools-1.14/test/csq/ENST00000479739/ |
H A D | ENST00000479739.gff | 9 2 havana CDS 13260 13482 . - 1 ID=CDS:ENSP00000441266;Parent=transcript:ENST00000479739;protein_id=… 11 2 havana CDS 15392 15520 . - 1 ID=CDS:ENSP00000441266;Parent=transcript:ENST00000479739;protein_id=… 13 2 havana CDS 16451 16563 . - 0 ID=CDS:ENSP00000441266;Parent=transcript:ENST00000479739;protein_id=… 14 2 havana CDS 25089 25091 . - 0 ID=CDS:ENSP00000441266;Parent=transcript:ENST00000479739;protein_id=…
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/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/ |
H A D | gencode.and.this.is.a.valid.one.too.table.gtf | 10 KI270734.1 ENSEMBL CDS 156289 156446 . - 0 gene_id "ENSG00000277196.4"; transcript_id "ENST00000615… 13 KI270734.1 ENSEMBL CDS 150987 151021 . - 1 gene_id "ENSG00000277196.4"; transcript_id "ENST00000615… 15 KI270734.1 ENSEMBL CDS 150350 150499 . - 2 gene_id "ENSG00000277196.4"; transcript_id "ENST00000615… 17 KI270734.1 ENSEMBL CDS 148414 148478 . - 2 gene_id "ENSG00000277196.4"; transcript_id "ENST00000615… 19 KI270734.1 ENSEMBL CDS 148116 148232 . - 0 gene_id "ENSG00000277196.4"; transcript_id "ENST00000615… 21 KI270734.1 ENSEMBL CDS 147624 147703 . - 0 gene_id "ENSG00000277196.4"; transcript_id "ENST00000615… 23 KI270734.1 ENSEMBL CDS 146640 146721 . - 1 gene_id "ENSG00000277196.4"; transcript_id "ENST00000615… 25 KI270734.1 ENSEMBL CDS 145004 145096 . - 0 gene_id "ENSG00000277196.4"; transcript_id "ENST00000615… 27 KI270734.1 ENSEMBL CDS 144749 144895 . - 0 gene_id "ENSG00000277196.4"; transcript_id "ENST00000615… 29 KI270734.1 ENSEMBL CDS 143614 143789 . - 0 gene_id "ENSG00000277196.4"; transcript_id "ENST00000615… [all …]
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/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/__testing/ |
H A D | longest_orfs.gff3 | 5 CUFF.38.1 transdecoder CDS 3859 5772 . + 0 ID=cds.CUFF.38.1.p1;Parent=CUFF.38.1.p1 12 CUFF.38.1 transdecoder CDS 1759 3411 . + 0 ID=cds.CUFF.38.1.p2;Parent=CUFF.38.1.p2 19 CUFF.38.1 transdecoder CDS 5907 7274 . - 0 ID=cds.CUFF.38.1.p3;Parent=CUFF.38.1.p3 32 CUFF.38.1 transdecoder CDS 6937 7326 . + 0 ID=cds.CUFF.38.1.p5;Parent=CUFF.38.1.p5 39 CUFF.24.1 transdecoder CDS 689 2356 . + 0 ID=cds.CUFF.24.1.p1;Parent=CUFF.24.1.p1 46 CUFF.35.1 transdecoder CDS 542 994 . + 0 ID=cds.CUFF.35.1.p1;Parent=CUFF.35.1.p1 53 CUFF.17.1 transdecoder CDS 231 1286 . + 0 ID=cds.CUFF.17.1.p1;Parent=CUFF.17.1.p1 67 CUFF.49.1 transdecoder CDS 214 804 . + 0 ID=cds.CUFF.49.1.p2;Parent=CUFF.49.1.p2 122 CUFF.3.1 transdecoder CDS 207 1073 . + 0 ID=cds.CUFF.3.1.p1;Parent=CUFF.3.1.p1 371 CUFF.5.1 transdecoder CDS 207 713 . + 0 ID=cds.CUFF.5.1.p1;Parent=CUFF.5.1.p1 [all …]
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/dports/biology/bcftools/bcftools-1.14/test/csq/ENST00000423372/ |
H A D | snps.vcf | 24 1 3621 . G A . . EXP=3_prime_utr|AL627309.1|ENST00000423372|protein_coding;type=CDS:-9 25 1 3622 . C A . . EXP=3_prime_utr|AL627309.1|ENST00000423372|protein_coding;type=CDS:-8 26 1 3626 . A C . . EXP=3_prime_utr|AL627309.1|ENST00000423372|protein_coding;type=CDS:-4 27 1 3627 . C A . . EXP=3_prime_utr|AL627309.1|ENST00000423372|protein_coding;type=CDS:-3 28 1 3628 . A C . . EXP=3_prime_utr|AL627309.1|ENST00000423372|protein_coding;type=CDS:-2 29 …. EXP=@3632;EXPL=stop_lost|AL627309.1|ENST00000423372|protein_coding|-|260*>260C|3630T>A;type=CDS:0 30 …T>A+3632A>C;EXPL=stop_lost|AL627309.1|ENST00000423372|protein_coding|-|260*>260G|3632A>C;type=CDS:2 31 … . EXP=@3634;EXPL=missense|AL627309.1|ENST00000423372|protein_coding|-|259L>259F|3633T>A;type=CDS:3 32 …A+3634A>C;EXPL=stop_gained|AL627309.1|ENST00000423372|protein_coding|-|259L>259*|3634A>C;type=CDS:4 33 …638 . T A . . EXP=missense|AL627309.1|ENST00000423372|protein_coding|-|258N>258Y|3638T>A;type=CDS:8 [all …]
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/dports/biology/bio-mocha/bcftools-1.14/test/csq/ENST00000423372/ |
H A D | snps.vcf | 24 1 3621 . G A . . EXP=3_prime_utr|AL627309.1|ENST00000423372|protein_coding;type=CDS:-9 25 1 3622 . C A . . EXP=3_prime_utr|AL627309.1|ENST00000423372|protein_coding;type=CDS:-8 26 1 3626 . A C . . EXP=3_prime_utr|AL627309.1|ENST00000423372|protein_coding;type=CDS:-4 27 1 3627 . C A . . EXP=3_prime_utr|AL627309.1|ENST00000423372|protein_coding;type=CDS:-3 28 1 3628 . A C . . EXP=3_prime_utr|AL627309.1|ENST00000423372|protein_coding;type=CDS:-2 29 …. EXP=@3632;EXPL=stop_lost|AL627309.1|ENST00000423372|protein_coding|-|260*>260C|3630T>A;type=CDS:0 30 …T>A+3632A>C;EXPL=stop_lost|AL627309.1|ENST00000423372|protein_coding|-|260*>260G|3632A>C;type=CDS:2 31 … . EXP=@3634;EXPL=missense|AL627309.1|ENST00000423372|protein_coding|-|259L>259F|3633T>A;type=CDS:3 32 …A+3634A>C;EXPL=stop_gained|AL627309.1|ENST00000423372|protein_coding|-|259L>259*|3634A>C;type=CDS:4 33 …638 . T A . . EXP=missense|AL627309.1|ENST00000423372|protein_coding|-|258N>258Y|3638T>A;type=CDS:8 [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/unit_test/gff3writer_test_cases/ |
H A D | modevidence-gnomon.annot.gff3 | 10 …29286.1 Gnomon CDS 2018 2055 . + 0 ID=cds-NW_004929286.1:2018..3467;Parent=rna-NW_004929286.1:1559… 11 …29286.1 Gnomon CDS 2423 2549 . + 1 ID=cds-NW_004929286.1:2018..3467;Parent=rna-NW_004929286.1:1559… 12 …29286.1 Gnomon CDS 3231 3467 . + 0 ID=cds-NW_004929286.1:2018..3467;Parent=rna-NW_004929286.1:1559…
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/dports/biology/wise/wise2.4.1/src/models/ |
H A D | genomewise9.dy | 66 source CDS 81 source CDS offj="2" 85 source CDS offj="4" 101 query_label CDS 108 source CDS offj="8" 119 source CDS offj="9" 130 source CDS offj="10" 138 source CDS 148 source CDS 194 source CDS offj="0" [all …]
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/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/ |
H A D | gencode.v19.MUC16.non-basic.gtf | 9 chr19 HAVANA CDS 9002501 9002673 . - 1 gene_id "ENSG00000181143.11"; transcript_id "ENST00000596768… 11 chr19 HAVANA CDS 9002153 9002188 . - 2 gene_id "ENSG00000181143.11"; transcript_id "ENST00000596768… 13 chr19 HAVANA CDS 9001831 9001896 . - 2 gene_id "ENSG00000181143.11"; transcript_id "ENST00000596768… 15 chr19 HAVANA CDS 9000442 9000566 . - 2 gene_id "ENSG00000181143.11"; transcript_id "ENST00000596768… 17 chr19 HAVANA CDS 9000147 9000214 . - 0 gene_id "ENSG00000181143.11"; transcript_id "ENST00000596768… 19 chr19 HAVANA CDS 8999392 8999564 . - 1 gene_id "ENSG00000181143.11"; transcript_id "ENST00000596768… 21 chr19 HAVANA CDS 8999025 8999060 . - 2 gene_id "ENSG00000181143.11"; transcript_id "ENST00000596768… 23 chr19 HAVANA CDS 8998698 8998763 . - 2 gene_id "ENSG00000181143.11"; transcript_id "ENST00000596768… 25 chr19 HAVANA CDS 8997412 8997536 . - 2 gene_id "ENSG00000181143.11"; transcript_id "ENST00000596768… 151 chr19 HAVANA CDS 9006642 9006766 . - 2 gene_id "ENSG00000181143.11"; transcript_id "ENST00000599436… [all …]
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/dports/dns/bind-tools/bind-9.16.27/bin/tests/system/cds/ |
H A D | setup.sh | 50 sed 's/ IN DS / IN CDS /' <DS.$n >>CDS.$n 105 cat sig.null CDS.1 >brk.unsigned-cds 107 cat db.null CDS.1 | sign cds.1 108 cat db.null CDS.2 | sign cds.2 109 cat db.null CDS.1 CDS.2 | sign cds.both 114 cat db.null CDS.2 CDNSKEY.2 | sign cds.cdnskey.2
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/dports/dns/bind916/bind-9.16.27/bin/tests/system/cds/ |
H A D | setup.sh | 50 sed 's/ IN DS / IN CDS /' <DS.$n >>CDS.$n 105 cat sig.null CDS.1 >brk.unsigned-cds 107 cat db.null CDS.1 | sign cds.1 108 cat db.null CDS.2 | sign cds.2 109 cat db.null CDS.1 CDS.2 | sign cds.both 114 cat db.null CDS.2 CDNSKEY.2 | sign cds.cdnskey.2
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/dports/dns/samba-nsupdate/bind-9.16.5/bin/tests/system/cds/ |
H A D | setup.sh | 48 sed 's/ IN DS / IN CDS /' <DS.$n >>CDS.$n 103 cat sig.null CDS.1 >brk.unsigned-cds 105 cat db.null CDS.1 | sign cds.1 106 cat db.null CDS.2 | sign cds.2 107 cat db.null CDS.1 CDS.2 | sign cds.both 112 cat db.null CDS.2 CDNSKEY.2 | sign cds.cdnskey.2
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/dports/biology/bcftools/bcftools-1.14/test/csq/EMN908947/ |
H A D | ribosomal-slippage.gff | 5 MN908947.3 feature CDS 13463 13468 . + 0 ID=CDS:YP_009724389.1;Parent=transcript:ORF1ab;biotype=pro… 6 MN908947.3 feature CDS 13468 13473 . + 0 ID=CDS:YP_009724389.1;Parent=transcript:ORF1ab;biotype=pro…
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/dports/biology/bio-mocha/bcftools-1.14/test/csq/EMN908947/ |
H A D | ribosomal-slippage.gff | 5 MN908947.3 feature CDS 13463 13468 . + 0 ID=CDS:YP_009724389.1;Parent=transcript:ORF1ab;biotype=pro… 6 MN908947.3 feature CDS 13468 13473 . + 0 ID=CDS:YP_009724389.1;Parent=transcript:ORF1ab;biotype=pro…
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/import/unit_test/data/input/ |
H A D | test-classified-exons.gtf | 7 140 Twinscan CDS 66996 66999 . - 1 gene_id "140.000"; transcript_id "140.000.1"; 9 140 Twinscan CDS 70207 70294 . - 2 gene_id "140.000"; transcript_id "140.000.1"; 10 140 Twinscan CDS 71696 71807 . - 0 gene_id "140.000"; transcript_id "140.000.1"; 13 140 Twinscan CDS 73222 73222 . - 0 gene_id "140.000"; transcript_id "140.000.1";
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