/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/sample_data/supertranscripts_example/ |
H A D | supertranscripts.gtf | 1 Calx Trinity_gene exon 631 864 . + . gene_id "Calx"; transcript_id "Calx_i7" 2 Calx Trinity_gene exon 1803 4077 . + . gene_id "Calx"; transcript_id "Calx_i7" 3 Calx Trinity_gene exon 4078 4092 . + . gene_id "Calx"; transcript_id "Calx_i7" 4 Calx Trinity_gene exon 4093 4831 . + . gene_id "Calx"; transcript_id "Calx_i7" 5 Calx Trinity_gene exon 4832 4870 . + . gene_id "Calx"; transcript_id "Calx_i7" 6 Calx Trinity_gene exon 4871 5506 . + . gene_id "Calx"; transcript_id "Calx_i7" 7 Calx Trinity_gene exon 5537 5551 . + . gene_id "Calx"; transcript_id "Calx_i7" 8 Calx Trinity_gene exon 5552 6706 . + . gene_id "Calx"; transcript_id "Calx_i7" 9 Calx Trinity_gene exon 6707 7292 . + . gene_id "Calx"; transcript_id "Calx_i7" 14 Calx Trinity_gene exon 865 930 . + . gene_id "Calx"; transcript_id "Calx_i6" [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/ |
H A D | magicblast_unit_test.cpp | 198 SExon exon; in BOOST_AUTO_TEST_CASE() local 225 exon.donor = ""; in BOOST_AUTO_TEST_CASE() 250 exon.donor = ""; in BOOST_AUTO_TEST_CASE() 275 exon.donor = ""; in BOOST_AUTO_TEST_CASE() 300 exon.donor = ""; in BOOST_AUTO_TEST_CASE() 396 SExon exon; in BOOST_AUTO_TEST_CASE() local 414 exon.donor = ""; in BOOST_AUTO_TEST_CASE() 429 exon.donor = ""; in BOOST_AUTO_TEST_CASE() 444 exon.donor = ""; in BOOST_AUTO_TEST_CASE() 459 exon.donor = ""; in BOOST_AUTO_TEST_CASE() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/ |
H A D | magicblast_unit_test.cpp | 198 SExon exon; in BOOST_AUTO_TEST_CASE() local 225 exon.donor = ""; in BOOST_AUTO_TEST_CASE() 250 exon.donor = ""; in BOOST_AUTO_TEST_CASE() 275 exon.donor = ""; in BOOST_AUTO_TEST_CASE() 300 exon.donor = ""; in BOOST_AUTO_TEST_CASE() 396 SExon exon; in BOOST_AUTO_TEST_CASE() local 414 exon.donor = ""; in BOOST_AUTO_TEST_CASE() 429 exon.donor = ""; in BOOST_AUTO_TEST_CASE() 444 exon.donor = ""; in BOOST_AUTO_TEST_CASE() 459 exon.donor = ""; in BOOST_AUTO_TEST_CASE() [all …]
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/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/sample_data/stringtie_example/ |
H A D | stringtie_merged.gtf | 4 chrX StringTie exon 322514 323718 1000 . . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_numbe… 6 chrX StringTie exon 304750 305197 1000 - . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_numbe… 7 chrX StringTie exon 307360 307512 1000 - . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_numbe… 8 chrX StringTie exon 307732 307880 1000 - . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_numbe… 9 chrX StringTie exon 311419 311627 1000 - . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_numbe… 10 chrX StringTie exon 312766 312924 1000 - . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_numbe… 11 chrX StringTie exon 314150 314217 1000 - . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_numbe… 12 chrX StringTie exon 314890 315020 1000 - . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_numbe… 13 chrX StringTie exon 315229 315299 1000 - . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_numbe… 14 chrX StringTie exon 316914 317051 1000 - . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_numbe… [all …]
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/dports/biology/emboss/EMBOSS-6.6.0/ajax/ensembl/ |
H A D | ensexon.c | 1372 return (exon) ? exon->Adaptor : NULL; in ensExonGetAdaptor() 1393 return (exon) ? exon->Constitutive : ajFalse; in ensExonGetConstitutive() 1415 return (exon) ? exon->Current : ajFalse; in ensExonGetCurrent() 1436 return (exon) ? exon->DateCreation : NULL; in ensExonGetDateCreation() 1457 return (exon) ? exon->DateModification : NULL; in ensExonGetDateModification() 1481 return (exon) ? exon->Feature : NULL; in ensExonGetFeature() 1502 return (exon) ? exon->Identifier : 0U; in ensExonGetIdentifier() 1523 return (exon) ? exon->PhaseEnd : 0; in ensExonGetPhaseEnd() 1567 return (exon) ? exon->PhaseStart : 0; in ensExonGetPhaseStart() 1609 return (exon) ? exon->Version : 0U; in ensExonGetVersion() [all …]
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H A D | ensexon.h | 151 EnsPExon ensExonNewRef(EnsPExon exon); 157 AjBool ensExonGetConstitutive(const EnsPExon exon); 159 AjBool ensExonGetCurrent(const EnsPExon exon); 161 AjPStr ensExonGetDateCreation(const EnsPExon exon); 167 ajuint ensExonGetIdentifier(const EnsPExon exon); 169 ajint ensExonGetPhaseEnd(const EnsPExon exon); 171 ajint ensExonGetPhaseStart(const EnsPExon exon); 175 ajuint ensExonGetVersion(const EnsPExon exon); 203 ajint ensExonCalculateFrame(const EnsPExon exon); 231 EnsPExon ensExonTransform(EnsPExon exon, [all …]
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/dports/biology/py-crossmap/CrossMap-0.5.4/test/ |
H A D | test08_hg19.gtf | 2 chr1 hg19_refGene exon 66081691 66081907 0.000000 + . gene_id "NM_002303"; transcript_id "NM_002303… 4 chr1 hg19_refGene exon 172017752 172017890 0.000000 + . gene_id "NM_001136127"; transcript_id "NM_0… 9 chr1 hg19_refGene exon 3417741 3417872 0.000000 - . gene_id "NM_001409"; transcript_id "NM_001409"; 10 chr1 hg19_refGene exon 10190773 10190871 0.000000 + . gene_id "NM_006048"; transcript_id "NM_006048… 11 chr1 hg19_refGene exon 11805860 11805894 0.000000 + . gene_id "NM_020350"; transcript_id "NM_020350… 20 chr1 hg19_refGene exon 68591041 68592018 0.000000 - . gene_id "NM_024911"; transcript_id "NM_024911… 21 chr1 hg19_refGene exon 68619200 68619336 0.000000 - . gene_id "NM_024911"; transcript_id "NM_024911… 24 chr1 hg19_refGene exon 94476356 94476485 0.000000 - . gene_id "NM_000350"; transcript_id "NM_000350… 25 chr1 hg19_refGene exon 94982608 94984219 0.000000 + . gene_id "NM_002858"; transcript_id "NM_002858… 50 chr1 hg19_refGene exon 2318858 2318968 0.000000 - . gene_id "NM_024848"; transcript_id "NM_024848"; [all …]
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/dports/biology/p5-Bio-GFF3/Bio-GFF3-2.0/t/data/ |
H A D | mm9_sample_ensembl.gff3 | 106 12 Ensembl exon 57796848 57796851 . + 0 Name=;Parent=CCDS25924.1 107 12 Ensembl exon 57797561 57798187 . + 1 Name=;Parent=CCDS25924.1 108 12 Ensembl exon 57800999 57801141 . + 1 Name=;Parent=CCDS25924.1 109 12 Ensembl exon 57810640 57810894 . + 0 Name=;Parent=CCDS25924.1 113 12 Ensembl exon 58297860 58297926 . - 1 Name=;Parent=CCDS25925.1 114 12 Ensembl exon 58029252 58029300 . - 2 Name=;Parent=CCDS25925.1 115 12 Ensembl exon 57959014 57959097 . - 2 Name=;Parent=CCDS25925.1 116 12 Ensembl exon 57876313 57876379 . - 0 Name=;Parent=CCDS25925.1 117 12 Ensembl exon 57871140 57871199 . - 0 Name=;Parent=CCDS25925.1 118 12 Ensembl exon 57867005 57867112 . - 0 Name=;Parent=CCDS25925.1 [all …]
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H A D | tomato_chr4_head.gff3 | 5 chr04 EuGene exon 12512 12955 . + 0 ID=exon:chr04.1.1;Parent=mRNA:chr04.1;Ontology_term=SO:0000147 10 chr04 EuGene exon 15510 15947 . + 0 ID=exon:chr04.2.1;Parent=mRNA:chr04.2;Ontology_term=SO:0000200 11 chr04 EuGene exon 18837 21038 . + 0 ID=exon:chr04.2.2;Parent=mRNA:chr04.2;Ontology_term=SO:0000004 12 chr04 EuGene exon 21529 21687 . + 0 ID=exon:chr04.2.3;Parent=mRNA:chr04.2;Ontology_term=SO:0000202 19 chr04 EuGene exon 31909 32480 . - 2 ID=exon:chr04.3.2;Parent=mRNA:chr04.3;Ontology_term=SO:0000202 20 chr04 EuGene exon 32566 33004 . - 0 ID=exon:chr04.3.1;Parent=mRNA:chr04.3;Ontology_term=SO:0000200 26 chr04 EuGene exon 87944 89482 . + 0 ID=exon:chr04.4.1;Parent=mRNA:chr04.4;Ontology_term=SO:0000147 31 chr04 EuGene exon 90341 90490 . - 0 ID=exon:chr04.5.8;Parent=mRNA:chr04.5;Ontology_term=SO:0000202 32 chr04 EuGene exon 91259 91391 . - 1 ID=exon:chr04.5.7;Parent=mRNA:chr04.5;Ontology_term=SO:0000004 33 chr04 EuGene exon 91984 92287 . - 2 ID=exon:chr04.5.6;Parent=mRNA:chr04.5;Ontology_term=SO:0000004 [all …]
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H A D | tomato_test.gff3 | 5 SL2.40ch01 ITAG_eugene exon 80999140 80999496 . + . ID=exon:Solyc01g098840.2.1.1;Parent=mRNA:Solyc0… 9 SL2.40ch01 ITAG_eugene exon 81000283 81000520 . + 0 ID=exon:Solyc01g098840.2.1.2;Parent=mRNA:Solyc0… 12 SL2.40ch01 ITAG_eugene exon 81000613 81000866 . + 2 ID=exon:Solyc01g098840.2.1.3;Parent=mRNA:Solyc0… 15 SL2.40ch01 ITAG_eugene exon 81002584 81002997 . + 1 ID=exon:Solyc01g098840.2.1.4;Parent=mRNA:Solyc0… 18 SL2.40ch01 ITAG_eugene exon 81003924 81004317 . + 2 ID=exon:Solyc01g098840.2.1.5;Parent=mRNA:Solyc0… 24 SL2.40ch01 ITAG_eugene exon 81004479 81004659 . - . ID=exon:Solyc01g098850.2.1.4;Parent=mRNA:Solyc0… 28 SL2.40ch01 ITAG_eugene exon 81004761 81005119 . - 2 ID=exon:Solyc01g098850.2.1.3;Parent=mRNA:Solyc0… 31 SL2.40ch01 ITAG_eugene exon 81005213 81005589 . - 1 ID=exon:Solyc01g098850.2.1.2;Parent=mRNA:Solyc0… 34 SL2.40ch01 ITAG_eugene exon 81005961 81006268 . - 0 ID=exon:Solyc01g098850.2.1.1;Parent=mRNA:Solyc0… 40 SL2.40ch01 ITAG_eugene exon 81006669 81006873 . + . ID=exon:Solyc01g098860.2.1.1;Parent=mRNA:Solyc0… [all …]
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/dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/docs/web/examples/data/ |
H A D | D_melanogaster_2Rslice.cds | 1 D_melanogaster_2Rslice Dpseudo initial-exon 4473 4605 . - . 2R_CG14748.1 2 D_melanogaster_2Rslice Dpseudo internal-exon 2533 3735 . - . 2R_CG14748.1 3 D_melanogaster_2Rslice Dpseudo internal-exon 1823 2164 . - . 2R_CG14748.1 4 D_melanogaster_2Rslice Dpseudo internal-exon 1416 1733 . - . 2R_CG14748.1 5 D_melanogaster_2Rslice Dpseudo internal-exon 1205 1352 . - . 2R_CG14748.1 6 D_melanogaster_2Rslice Dpseudo internal-exon 937 1142 . - . 2R_CG14748.1 7 D_melanogaster_2Rslice Dpseudo internal-exon 425 608 . - . 2R_CG14748.1 8 D_melanogaster_2Rslice Dpseudo last-exon 23 347 . - . 2R_CG14748.1 9 D_melanogaster_2Rslice Dpseudo initial-exon 8532 8638 . - . 2R_CG14747.1 11 D_melanogaster_2Rslice Dpseudo last-exon 7176 7258 . - . 2R_CG14747.1 [all …]
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H A D | D_melanogaster_2Rslice.utr | 1 D_melanogaster_2Rslice Dpseudo initial-exon 4473 4834 . - . 2R_CG14748.1 2 D_melanogaster_2Rslice Dpseudo internal-exon 2533 3735 . - . 2R_CG14748.1 3 D_melanogaster_2Rslice Dpseudo internal-exon 1823 2164 . - . 2R_CG14748.1 4 D_melanogaster_2Rslice Dpseudo internal-exon 1416 1733 . - . 2R_CG14748.1 5 D_melanogaster_2Rslice Dpseudo internal-exon 1205 1352 . - . 2R_CG14748.1 6 D_melanogaster_2Rslice Dpseudo internal-exon 937 1142 . - . 2R_CG14748.1 7 D_melanogaster_2Rslice Dpseudo internal-exon 425 608 . - . 2R_CG14748.1 8 D_melanogaster_2Rslice Dpseudo last-exon 1 347 . - . 2R_CG14748.1 9 D_melanogaster_2Rslice Dpseudo initial-exon 8532 8638 . - . 2R_CG14747.1 11 D_melanogaster_2Rslice Dpseudo last-exon 7176 7258 . - . 2R_CG14747.1 [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 | rw-1080.entry.gff3 | 11 NM_002020.5 RefSeq exon 1 113 . + . ID=id-FLT4;Parent=gene-FLT4;Dbxref=GeneID:2324,HGNC:HGNC:3767,M… 12 NM_002020.5 RefSeq exon 114 210 . + . ID=id-FLT4-2;Parent=gene-FLT4;Dbxref=GeneID:2324,HGNC:HGNC:37… 13 NM_002020.5 RefSeq exon 211 455 . + . ID=id-FLT4-3;Parent=gene-FLT4;Dbxref=GeneID:2324,HGNC:HGNC:37… 14 NM_002020.5 RefSeq exon 456 568 . + . ID=id-FLT4-4;Parent=gene-FLT4;Dbxref=GeneID:2324,HGNC:HGNC:37… 15 NM_002020.5 RefSeq exon 569 731 . + . ID=id-FLT4-5;Parent=gene-FLT4;Dbxref=GeneID:2324,HGNC:HGNC:37… 16 NM_002020.5 RefSeq exon 732 871 . + . ID=id-FLT4-6;Parent=gene-FLT4;Dbxref=GeneID:2324,HGNC:HGNC:37… 17 NM_002020.5 RefSeq exon 872 1040 . + . ID=id-FLT4-7;Parent=gene-FLT4;Dbxref=GeneID:2324,HGNC:HGNC:3… 18 NM_002020.5 RefSeq exon 1041 1158 . + . ID=id-FLT4-8;Parent=gene-FLT4;Dbxref=GeneID:2324,HGNC:HGNC:… 19 NM_002020.5 RefSeq exon 1159 1313 . + . ID=id-FLT4-9;Parent=gene-FLT4;Dbxref=GeneID:2324,HGNC:HGNC:… 20 NM_002020.5 RefSeq exon 1314 1476 . + . ID=id-FLT4-10;Parent=gene-FLT4;Dbxref=GeneID:2324,HGNC:HGNC… [all …]
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H A D | spliced-seg.annot.asn | 34 donor-after-exon { 49 donor-after-exon { 64 donor-after-exon { 79 donor-after-exon { 94 donor-after-exon { 109 donor-after-exon { 126 donor-after-exon { 186 donor-after-exon { 201 donor-after-exon { 216 donor-after-exon { [all …]
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/dports/biology/gffread/gffread-0.12.7/examples/output/ |
H A D | ann_simple.gff | 5 NT_187562.1 BestRefSeq exon 411 495 . + . Parent=rna157470 6 NT_187562.1 BestRefSeq exon 1995 2051 . + . Parent=rna157470 7 NT_187562.1 BestRefSeq exon 2602 2726 . + . Parent=rna157470 8 NT_187562.1 BestRefSeq exon 9665 9753 . + . Parent=rna157470 9 NT_187562.1 BestRefSeq exon 12115 12164 . + . Parent=rna157470 10 NT_187562.1 BestRefSeq exon 12577 12744 . + . Parent=rna157470 11 NT_187562.1 BestRefSeq exon 14174 14326 . + . Parent=rna157470 12 NT_187562.1 BestRefSeq exon 14664 14864 . + . Parent=rna157470 13 NT_187562.1 BestRefSeq exon 16634 16788 . + . Parent=rna157470 14 NT_187562.1 BestRefSeq exon 17438 17606 . + . Parent=rna157470 [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/ngs_roi/example/ |
H A D | dmel.gtf | 1 2L dm3_flyBaseGene exon 8384467 8384895 0.000000 + . gene_id "CG13384-RD"; transcript_id "CG13384-R… 2 2L dm3_flyBaseGene exon 8384997 8385097 0.000000 + . gene_id "CG13384-RD"; transcript_id "CG13384-R… 5 2L dm3_flyBaseGene exon 8386217 8386385 0.000000 + . gene_id "CG13384-RD"; transcript_id "CG13384-R… 7 2L dm3_flyBaseGene exon 8386484 8387378 0.000000 + . gene_id "CG13384-RD"; transcript_id "CG13384-R… 9 2L dm3_flyBaseGene exon 8387659 8387831 0.000000 + . gene_id "CG13384-RD"; transcript_id "CG13384-R… 12 2L dm3_flyBaseGene exon 8387891 8388803 0.000000 + . gene_id "CG13384-RD"; transcript_id "CG13384-R… 13 2L dm3_flyBaseGene exon 8384467 8384540 0.000000 + . gene_id "CG13384-RC"; transcript_id "CG13384-R… 16 2L dm3_flyBaseGene exon 8384700 8384895 0.000000 + . gene_id "CG13384-RC"; transcript_id "CG13384-R… 18 2L dm3_flyBaseGene exon 8386217 8386385 0.000000 + . gene_id "CG13384-RC"; transcript_id "CG13384-R… 20 2L dm3_flyBaseGene exon 8386487 8387378 0.000000 + . gene_id "CG13384-RC"; transcript_id "CG13384-R… [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/unit_test/ |
H A D | unit_test_gene_model.cpp | 541 exons.push_back(exon); in BOOST_AUTO_TEST_CASE() 547 exons.push_back(exon); in BOOST_AUTO_TEST_CASE() 581 exons.push_back(exon); in BOOST_AUTO_TEST_CASE() 605 exons.push_back(exon); in BOOST_AUTO_TEST_CASE() 612 exons.push_back(exon); in BOOST_AUTO_TEST_CASE() 658 exons.push_back(exon); in BOOST_AUTO_TEST_CASE() 684 exons.push_back(exon); in BOOST_AUTO_TEST_CASE() 693 exons.push_back(exon); in BOOST_AUTO_TEST_CASE() 867 exons.push_back(exon); in BOOST_AUTO_TEST_CASE() 893 exons.push_back(exon); in BOOST_AUTO_TEST_CASE() [all …]
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/dports/biology/subread/subread-2.0.2-source/test/featureCounts/data/ |
H A D | test-minimum.GTF | 1 chr3 FCTEST exon 100 10000 . + 0 gene_id "simu_gene1"; transcript_id "TR:simu_gene1" 2 chr3 FCTEST exon 20000 30000 . + 0 gene_id "simu_gene1"; transcript_id "TR:simu_gene1" 3 chr3 FCTEST exon 40000 89000 . + 0 gene_id "simu_gene1"; transcript_id "TR:simu_gene1" 4 chr3 FCTEST exon 100010 101000 . + 0 gene_id "simu_gene2"; transcript_id "TR:simu_gene2" 5 chr3 FCTEST exon 102000 103000 . + 0 gene_id "simu_gene2"; transcript_id "TR:simu_gene2" 6 chr3 FCTEST exon 104000 129000 . + 0 gene_id "simu_gene2"; transcript_id "TR:simu_gene2" 7 chr3 FCTEST exon 102000 131000 . + 0 gene_id "simu_gene2"; transcript_id "TR:simu_gene2" 8 chr3 FCTEST exon 500010 501000 . - 0 gene_id "simu_gene3"; transcript_id "TR:simu_gene3" 9 chr3 FCTEST exon 502000 503000 . - 0 gene_id "simu_gene3"; transcript_id "TR:simu_gene3" 10 chr3 FCTEST exon 504000 529000 . - 0 gene_id "simu_gene3"; transcript_id "TR:simu_gene3" [all …]
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H A D | test-chralias.GTF | 1 chr3 SAF exon 100 10000 . + 0 gene_id "simu_gene1"; transcript_id "TRN_simu_gene1"; exon_id "EXON_s… 2 chr3 SAF exon 20000 30000 . + 0 gene_id "simu_gene1"; transcript_id "TRN_simu_gene1"; exon_id "EXON… 3 chr3 SAF exon 40000 89000 . + 0 gene_id "simu_gene1"; transcript_id "TRN_simu_gene1"; exon_id "EXON… 4 chr3 SAF exon 100010 101000 . + 0 gene_id "simu_gene2"; transcript_id "TRN_simu_gene2"; exon_id "EX… 5 chr3 SAF exon 102000 103000 . + 0 gene_id "simu_gene2"; transcript_id "TRN_simu_gene2"; exon_id "EX… 6 chr3 SAF exon 104000 129000 . + 0 gene_id "simu_gene2"; transcript_id "TRN_simu_gene2"; exon_id "EX… 7 chr3 SAF exon 102000 131000 . + 0 gene_id "simu_gene2"; transcript_id "TRN_simu_gene2"; exon_id "EX… 8 chr3 SAF exon 500010 501000 . - 0 gene_id "simu_gene3"; transcript_id "TRN_simu_gene3"; exon_id "EX… 9 chr3 SAF exon 502000 503000 . - 0 gene_id "simu_gene3"; transcript_id "TRN_simu_gene3"; exon_id "EX… 10 chr3 SAF exon 504000 529000 . - 0 gene_id "simu_gene3"; transcript_id "TRN_simu_gene3"; exon_id "EX… [all …]
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/Tools/ |
H A D | Sim4.t | 22 my $exon = 1; 25 is $exons[$exon]->strand(), -1; 26 is $exons[$exon]->start(), 1048; 27 is $exons[$exon]->end(), 1117; 28 is $exons[$exon]->score, 93; 40 $exon = 1; 43 is $exons[$exon]->strand(), 1; 45 is $exons[$exon]->end(), 1500; 46 is $exons[$exon]->score, 99; 54 is $exons[$exon]->strand(), 1; [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/unit_test/gtfreader_test_cases/ |
H A D | gene-mrna-exon-cds.gtf | 3 Chr1 TAIR10 exon 3631 3913 . + . gene_id "AT1G01010"; transcript_id "AT1G01010.1" 5 Chr1 TAIR10 exon 3996 4276 . + . gene_id "AT1G01010"; transcript_id "AT1G01010.1" 7 Chr1 TAIR10 exon 4486 4605 . + . gene_id "AT1G01010"; transcript_id "AT1G01010.1" 9 Chr1 TAIR10 exon 4706 5095 . + . gene_id "AT1G01010"; transcript_id "AT1G01010.1" 11 Chr1 TAIR10 exon 5174 5326 . + . gene_id "AT1G01010"; transcript_id "AT1G01010.1" 13 Chr1 TAIR10 exon 5439 5899 . + . gene_id "AT1G01010"; transcript_id "AT1G01010.1" 18 Chr1 TAIR10 exon 8571 8737 . - . gene_id "AT1G01020"; transcript_id "AT1G01020.1" 20 Chr1 TAIR10 exon 8417 8464 . - . gene_id "AT1G01020"; transcript_id "AT1G01020.1" 22 Chr1 TAIR10 exon 8236 8325 . - . gene_id "AT1G01020"; transcript_id "AT1G01020.1" 24 Chr1 TAIR10 exon 7942 7987 . - . gene_id "AT1G01020"; transcript_id "AT1G01020.1" [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/unit_test/pslwriter_test_cases/ |
H A D | rw-255-1k.asn1 | 117 donor-after-exon { 142 donor-after-exon { 334 donor-after-exon { 359 donor-after-exon { 384 donor-after-exon { 409 donor-after-exon { 434 donor-after-exon { 459 donor-after-exon { 484 donor-after-exon { 509 donor-after-exon { [all …]
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H A D | rw-255-100.asn1 | 117 donor-after-exon { 142 donor-after-exon { 167 donor-after-exon { 192 donor-after-exon { 217 donor-after-exon { 242 donor-after-exon { 267 donor-after-exon { 292 donor-after-exon { 317 donor-after-exon { 342 donor-after-exon { [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/gff_io/ |
H A D | example_with_errors.gff | 7 gtg123 . exon 8 atg123 . exon 9 btg123 . exon 1050 10 ctg123 . exon 1050 11 dtg123 . exon 1050 1500 12 etg123 . exon 1050 1500 13 ftg123 . exon 1050 1500 . 14 gtg123 . exon 1050 1500 . 15 htg123 . exon 1050 1500 . + 16 itg123 . exon 1050 1500 . + [all …]
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/dports/biology/wise/wise2.4.1/src/models/ |
H A D | est_evidence.dy | 25 EstExon ** exon !list 67 EstExon * exon; 91 if( sscanf(buffer,"exon %d %d %d",&exon->start,&exon->end,&exon->intron_3_score) < 2 ) { 95 exon->start--; 96 exon->end--; 100 sscanf(buffer,"cds %d %d %d",&exon->start,&exon->end,&exon->phase); 101 exon->start--; 102 exon->end--; 103 if( exon->phase > 2 || exon->phase < 0 ) { 282 if( est->exon[i]->start <= jposition && jposition <= est->exon[i]->end ) { [all …]
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