/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/py-crossmap/CrossMap-0.5.4/test/ |
H A D | test08_hg19.gtf | 1 chr1 hg19_refGene CDS 48267145 48267291 0.000000 - 0 gene_id "NM_001194986"; transcript_id "NM_0011… 2 chr1 hg19_refGene exon 66081691 66081907 0.000000 + . gene_id "NM_002303"; transcript_id "NM_002303… 3 chr1 hg19_refGene CDS 145334684 145334792 0.000000 + 2 gene_id "NM_001039703"; transcript_id "NM_00… 7 chr1 hg19_refGene CDS 235850249 235850347 0.000000 - 0 gene_id "NM_000081"; transcript_id "NM_00008… 8 chr1 hg19_refGene CDS 235880012 235880078 0.000000 - 1 gene_id "NM_000081"; transcript_id "NM_00008… 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… 13 chr1 hg19_refGene CDS 22207832 22207995 0.000000 - 2 gene_id "NM_005529"; transcript_id "NM_005529"… 14 chr1 hg19_refGene CDS 26899715 26899852 0.000000 + 0 gene_id "NM_002953"; transcript_id "NM_002953"… [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… 3 2L dm3_flyBaseGene start_codon 8386247 8386249 0.000000 + . gene_id "CG13384-RD"; transcript_id "CG… 4 2L dm3_flyBaseGene CDS 8386247 8386385 0.000000 + 0 gene_id "CG13384-RD"; transcript_id "CG13384-RD… 5 2L dm3_flyBaseGene exon 8386217 8386385 0.000000 + . gene_id "CG13384-RD"; transcript_id "CG13384-R… 6 2L dm3_flyBaseGene CDS 8386484 8387378 0.000000 + 2 gene_id "CG13384-RD"; transcript_id "CG13384-RD… 7 2L dm3_flyBaseGene exon 8386484 8387378 0.000000 + . gene_id "CG13384-RD"; transcript_id "CG13384-R… 8 2L dm3_flyBaseGene CDS 8387659 8387831 0.000000 + 1 gene_id "CG13384-RD"; transcript_id "CG13384-RD… 9 2L dm3_flyBaseGene exon 8387659 8387831 0.000000 + . gene_id "CG13384-RD"; transcript_id "CG13384-R… 10 2L dm3_flyBaseGene CDS 8387891 8388132 0.000000 + 2 gene_id "CG13384-RD"; transcript_id "CG13384-RD… [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 | 1 Chr1 TAIR10 gene 3631 5899 . + . gene_id "AT1G01010" 2 Chr1 TAIR10 mRNA 3631 5899 . + . gene_id "AT1G01010"; transcript_id "AT1G01010.1" 3 Chr1 TAIR10 exon 3631 3913 . + . gene_id "AT1G01010"; transcript_id "AT1G01010.1" 4 Chr1 TAIR10 CDS 3760 3913 . + 0 gene_id "AT1G01010"; transcript_id "AT1G01010.1" 5 Chr1 TAIR10 exon 3996 4276 . + . gene_id "AT1G01010"; transcript_id "AT1G01010.1" 6 Chr1 TAIR10 CDS 3996 4276 . + 2 gene_id "AT1G01010"; transcript_id "AT1G01010.1" 7 Chr1 TAIR10 exon 4486 4605 . + . gene_id "AT1G01010"; transcript_id "AT1G01010.1" 8 Chr1 TAIR10 CDS 4486 4605 . + 0 gene_id "AT1G01010"; transcript_id "AT1G01010.1" 15 Chr1 TAIR10 gene 5928 8737 . - . gene_id "AT1G01020" 52 Chr1 TAIR10 gene 11649 13714 . - . gene_id "AT1G01030" [all …]
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H A D | exon-cds.gtf | 2 381 Twinscan exon 300 401 . + . gene_id "381.000"; transcript_id "381.000.1"; amb… 3 381 Twinscan exon 800 851 . + . gene_id "381.000"; transcript_id "381.000.1"; amb… 4 381 Twinscan CDS 380 401 . + 0 gene_id "381.000"; transcript_id "381.000.1"; 5 381 Twinscan exon 501 650 . + . gene_id "381.000"; transcript_id "381.000.1"; rea… 6 381 Twinscan CDS 501 650 . + 2 gene_id "381.000"; transcript_id "381.000.1"; 7 381 Twinscan exon 700 800 . + . gene_id "381.000"; transcript_id "381.000.1"; rea… 8 381 Twinscan CDS 700 707 . + 2 gene_id "381.000"; transcript_id "381.000.1"; 9 381 Twinscan exon 900 1000 . + . gene_id "381.000"; transcript_id "381.000.1"; rea… 10 381 Twinscan exon 1100 1200 . + . gene_id "381.000"; transcript_id "381.000.1"; rea… 11 381 Twinscan start_codon 380 382 . + 0 gene_id "381.000"; transcript_id "381.000.1"; [all …]
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/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/sample_data/stringtie_example/ |
H A D | stringtie_merged.gtf | 3 chrX StringTie transcript 322514 323718 1000 . . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; 4 chrX StringTie exon 322514 323718 1000 . . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_numbe… 5 chrX StringTie transcript 304750 318701 1000 - . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; 33 chrX StringTie transcript 255489 304287 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; 46 chrX StringTie transcript 276330 303355 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.3"; 55 chrX StringTie transcript 276330 303355 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.4"; 71 chrX StringTie transcript 283484 303355 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.6"; 80 chrX StringTie transcript 278953 280243 1000 - . gene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; 83 chrX StringTie transcript 303357 303632 1000 - . gene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; 85 chrX StringTie transcript 990316 991744 1000 . . gene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; [all …]
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/dports/biology/gffread/gffread-0.12.7/examples/output/ |
H A D | annotation.gtf | 1 NT_187562.1 BestRefSeq transcript 411 68627 . + . transcript_id "rna157470"; gene_id "gene55473"; g… 2 NT_187562.1 BestRefSeq exon 411 495 . + . transcript_id "rna157470"; gene_id "gene55473"; gene_name… 3 NT_187562.1 BestRefSeq exon 1995 2051 . + . transcript_id "rna157470"; gene_id "gene55473"; gene_na… 4 NT_187562.1 BestRefSeq exon 2602 2726 . + . transcript_id "rna157470"; gene_id "gene55473"; gene_na… 5 NT_187562.1 BestRefSeq exon 9665 9753 . + . transcript_id "rna157470"; gene_id "gene55473"; gene_na… 6 NT_187562.1 BestRefSeq exon 12115 12164 . + . transcript_id "rna157470"; gene_id "gene55473"; gene_… 7 NT_187562.1 BestRefSeq exon 12577 12744 . + . transcript_id "rna157470"; gene_id "gene55473"; gene_… 8 NT_187562.1 BestRefSeq exon 14174 14326 . + . transcript_id "rna157470"; gene_id "gene55473"; gene_… 9 NT_187562.1 BestRefSeq exon 14664 14864 . + . transcript_id "rna157470"; gene_id "gene55473"; gene_… 10 NT_187562.1 BestRefSeq exon 16634 16788 . + . transcript_id "rna157470"; gene_id "gene55473"; gene_… [all …]
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/dports/biology/bcftools/bcftools-1.14/misc/ |
H A D | gff2gff.py | 24 def __init__(self, gene_id): argument 26 self.id = gene_id 67 if gene_id not in feature_groups: 68 feature_groups[gene_id] = FeatureGroup(gene_id) 82 feature_groups[gene_id] = FeatureGroup(gene_id) 90 feature_groups[gene_id] = FeatureGroup(gene_id) 99 feature_groups[gene_id] = FeatureGroup(gene_id) 121 for gene_id in feature_groups: 131 … feature_groups[gene_id].transcript = make_transcript_pseudofeature(feature_groups[gene_id].CDSs) 134 for gene_id in feature_groups: [all …]
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/dports/biology/bio-mocha/bcftools-1.14/misc/ |
H A D | gff2gff.py | 24 def __init__(self, gene_id): argument 26 self.id = gene_id 67 if gene_id not in feature_groups: 68 feature_groups[gene_id] = FeatureGroup(gene_id) 82 feature_groups[gene_id] = FeatureGroup(gene_id) 90 feature_groups[gene_id] = FeatureGroup(gene_id) 99 feature_groups[gene_id] = FeatureGroup(gene_id) 121 for gene_id in feature_groups: 131 … feature_groups[gene_id].transcript = make_transcript_pseudofeature(feature_groups[gene_id].CDSs) 134 for gene_id in feature_groups: [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/unit_test/gtfwriter_test_cases/ |
H A D | rw-836-3.entry.gtf | 2 AP000423.1 DDBJ gene 4 76 . - . gene_id "trnH"; transcript_id ""; gbkey "Gene"; gene "trnH"; gene_b… 5 AP000423.1 DDBJ gene 383 1444 . - . gene_id "psbA"; transcript_id ""; gbkey "Gene"; gene "psbA"; ge… 9 AP000423.1 DDBJ gene 4311 4347 . - . gene_id "trnK"; transcript_id ""; gbkey "Gene"; gene "trnK"; g… 23 AP000423.1 DDBJ gene 6616 6687 . - . gene_id "trnQ"; transcript_id ""; gbkey "Gene"; gene "trnQ"; g… 34 AP000423.1 DDBJ gene 7785 7872 . + . gene_id "trnS"; transcript_id ""; gbkey "Gene"; gene "trnS"; g… 42 AP000423.1 DDBJ gene 9590 9661 . + . gene_id "trnR"; transcript_id ""; gbkey "Gene"; gene "trnR"; g… 79 AP000423.1 DDBJ gene 27373 27443 . + . gene_id "trnC"; transcript_id ""; gbkey "Gene"; gene "trnC";… 90 AP000423.1 DDBJ gene 29801 29874 . - . gene_id "trnD"; transcript_id ""; gbkey "Gene"; gene "trnD";… 93 AP000423.1 DDBJ gene 30323 30406 . - . gene_id "trnY"; transcript_id ""; gbkey "Gene"; gene "trnY";… 96 AP000423.1 DDBJ gene 30466 30538 . - . gene_id "trnE"; transcript_id ""; gbkey "Gene"; gene "trnE";… [all …]
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H A D | 1.annot.gtf | 16 NC_000018.10 miRNA exon 48162 48272 . + . gene_id "ENSG00000221441"; transcript_id "ENST00000408514… 19 NC_000018.10 protein_coding exon 158483 158714 . + . gene_id "ENSG00000101557"; transcript_id "ENST… 20 NC_000018.10 protein_coding exon 163308 163453 . + . gene_id "ENSG00000101557"; transcript_id "ENST… 21 NC_000018.10 protein_coding exon 166787 166819 . + . gene_id "ENSG00000101557"; transcript_id "ENST… 22 NC_000018.10 protein_coding exon 178933 179037 . + . gene_id "ENSG00000101557"; transcript_id "ENST… 23 NC_000018.10 protein_coding exon 180236 180339 . + . gene_id "ENSG00000101557"; transcript_id "ENST… 24 NC_000018.10 protein_coding exon 192842 192900 . + . gene_id "ENSG00000101557"; transcript_id "ENST… 25 NC_000018.10 protein_coding exon 196637 196767 . + . gene_id "ENSG00000101557"; transcript_id "ENST… 26 NC_000018.10 protein_coding exon 197616 197696 . + . gene_id "ENSG00000101557"; transcript_id "ENST… 27 NC_000018.10 protein_coding exon 198047 198132 . + . gene_id "ENSG00000101557"; transcript_id "ENST… [all …]
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H A D | rw-329.annot.gtf | 2 Zv8_NA7 . gene 67958 88253 . - . gene_id "ENSDART00000076400"; transcript_id ""; gbkey "Gene"; gene… 14 Zv8_NA7 . CDS 88161 88253 . - 0 gene_id "ENSDART00000076400"; transcript_id "xxENSDART00000076400";… 15 Zv8_NA7 . CDS 86374 86421 . - 0 gene_id "ENSDART00000076400"; transcript_id "xxENSDART00000076400";… 16 Zv8_NA7 . CDS 85732 85937 . - 0 gene_id "ENSDART00000076400"; transcript_id "xxENSDART00000076400";… 17 Zv8_NA7 . CDS 83834 83954 . - 1 gene_id "ENSDART00000076400"; transcript_id "xxENSDART00000076400";… 18 Zv8_NA7 . CDS 83077 83158 . - 0 gene_id "ENSDART00000076400"; transcript_id "xxENSDART00000076400";… 19 Zv8_NA7 . CDS 79151 79257 . - 2 gene_id "ENSDART00000076400"; transcript_id "xxENSDART00000076400";… 20 Zv8_NA7 . CDS 76806 76878 . - 0 gene_id "ENSDART00000076400"; transcript_id "xxENSDART00000076400";… 21 Zv8_NA7 . CDS 74583 74678 . - 2 gene_id "ENSDART00000076400"; transcript_id "xxENSDART00000076400";… 22 Zv8_NA7 . CDS 72549 72610 . - 2 gene_id "ENSDART00000076400"; transcript_id "xxENSDART00000076400";… [all …]
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H A D | rw-836-2.entry.gtf | 50 AJ507799.2 EMBL gene 11305 11308 . + . gene_id "BCR2"; transcript_id ""; gbkey "Gene"; gene "BCR2";… 51 AJ507799.2 EMBL gene 11336 11480 . + . gene_id "EBNA"; transcript_id ""; gbkey "Gene"; gene "EBNA";… 132 AJ507799.2 EMBL gene 41471 41476 . + . gene_id "BHF1"; transcript_id ""; gbkey "Gene"; gene "BHF1";… 189 AJ507799.2 EMBL gene 62729 62729 . + . gene_id "BORF1"; transcript_id ""; gbkey "Gene"; gene "BORF1… 195 AJ507799.2 EMBL gene 63881 63881 . + . gene_id "BORF2"; transcript_id ""; gbkey "Gene"; gene "BORF2… 200 AJ507799.2 EMBL gene 66516 66521 . + . gene_id "BaRF1"; transcript_id ""; gbkey "Gene"; gene "BaRF1… 205 AJ507799.2 EMBL gene 67552 67557 . + . gene_id "BMRF1"; transcript_id ""; gbkey "Gene"; gene "BMRF1… 216 AJ507799.2 EMBL gene 70454 70459 . - . gene_id "SM"; transcript_id ""; gbkey "Gene"; gene "SM"; gen… 235 AJ507799.2 EMBL gene 72063 72068 . - . gene_id "SM_1"; transcript_id ""; gbkey "Gene"; gene "SM"; g… 242 AJ507799.2 EMBL gene 75320 75325 . - . gene_id "BLL3"; transcript_id ""; gbkey "Gene"; gene "BLL3";… [all …]
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H A D | rw-836-1.entry.gtf | 2 NC_016163.1 RefSeq gene 2 262389 . + . gene_id "phiR1-37_gp367"; transcript_id ""; db_xref "GeneID:… 7 NC_016163.1 RefSeq gene 103 375 . + . gene_id "phiR1-37_gp001"; transcript_id ""; db_xref "GeneID:1… 11 NC_016163.1 RefSeq gene 326 577 . + . gene_id "phiR1-37_gp002"; transcript_id ""; db_xref "GeneID:1… 15 NC_016163.1 RefSeq gene 564 812 . + . gene_id "phiR1-37_gp003"; transcript_id ""; db_xref "GeneID:1… 19 NC_016163.1 RefSeq gene 784 1002 . + . gene_id "phiR1-37_gp004"; transcript_id ""; db_xref "GeneID:… 23 NC_016163.1 RefSeq gene 999 1187 . + . gene_id "phiR1-37_gp005"; transcript_id ""; db_xref "GeneID:… 27 NC_016163.1 RefSeq gene 1181 1534 . + . gene_id "phiR1-37_gp006"; transcript_id ""; db_xref "GeneID… 31 NC_016163.1 RefSeq gene 1531 1749 . + . gene_id "phiR1-37_gp007"; transcript_id ""; db_xref "GeneID… 35 NC_016163.1 RefSeq gene 1736 1924 . + . gene_id "phiR1-37_gp008"; transcript_id ""; db_xref "GeneID… 39 NC_016163.1 RefSeq gene 1918 2166 . + . gene_id "phiR1-37_gp009"; transcript_id ""; db_xref "GeneID… [all …]
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H A D | 2.entry.gtf | 2 U54469.1 Genbank gene 80 2881 . + . gene_id "eIF4E"; transcript_id ""; gbkey "Gene"; gene "eIF4E"; … 3 U54469.1 Genbank transcript 80 2881 . + . gene_id "eIF4E"; transcript_id "unassigned_transcript_1";… 4 U54469.1 Genbank exon 80 224 . + . gene_id "eIF4E"; transcript_id "unassigned_transcript_1"; gene "… 5 U54469.1 Genbank exon 892 1458 . + . gene_id "eIF4E"; transcript_id "unassigned_transcript_1"; gene… 6 U54469.1 Genbank exon 1550 1920 . + . gene_id "eIF4E"; transcript_id "unassigned_transcript_1"; gen… 7 U54469.1 Genbank exon 1986 2085 . + . gene_id "eIF4E"; transcript_id "unassigned_transcript_1"; gen… 8 U54469.1 Genbank exon 2317 2404 . + . gene_id "eIF4E"; transcript_id "unassigned_transcript_1"; gen… 9 U54469.1 Genbank exon 2466 2881 . + . gene_id "eIF4E"; transcript_id "unassigned_transcript_1"; gen… 10 U54469.1 Genbank transcript 80 2881 . + . gene_id "eIF4E"; transcript_id "unassigned_transcript_2";… 11 U54469.1 Genbank exon 80 224 . + . gene_id "eIF4E"; transcript_id "unassigned_transcript_2"; gene "… [all …]
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/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/PerlLib/ |
H A D | GTF_utils2.pm | 40 my $gene_id = $gene_obj->{TU_feat_name}; 43 if ($seen{$gene_id}) { 50 $seen{$gene_id} = $gene_obj; 62 push (@$gene_list, $gene_id); 94 my $gene_id = $1; 98 $gene_id = "$seqname" . "|" . "$gene_id"; # make unique per scaffold. 103 $gene_id_to_source{$gene_id} = $source; 135 $coding_genes{$gene_id}++; 168 if ($seen{$gene_id}) { 169 … print STDERR ("Error, already saw $gene_id,$seqname as $gene_id,$seen{$gene_id}\nSkipping."); [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/gffread/gffread-0.12.7/examples/ |
H A D | transcripts.gtf | 1 NT_187562.1 StringTie transcript 403 10275 . + . transcript_id "STRG.1.1"; gene_id "STRG.1"; 2 NT_187562.1 StringTie exon 403 495 . + . transcript_id "STRG.1.1"; gene_id "STRG.1"; 3 NT_187562.1 StringTie exon 1995 2726 . + . transcript_id "STRG.1.1"; gene_id "STRG.1"; 4 NT_187562.1 StringTie exon 9665 10275 . + . transcript_id "STRG.1.1"; gene_id "STRG.1"; 6 NT_187562.1 StringTie exon 214032 214270 . - . transcript_id "STRG.3.1"; gene_id "STRG.3"; 7 NT_187562.1 StringTie exon 214372 214511 . - . transcript_id "STRG.3.1"; gene_id "STRG.3"; 8 NT_187562.1 StringTie exon 216955 217211 . - . transcript_id "STRG.3.1"; gene_id "STRG.3"; 9 NT_187562.1 StringTie exon 217435 217573 . - . transcript_id "STRG.3.1"; gene_id "STRG.3"; 10 NT_187562.1 StringTie exon 219568 219648 . - . transcript_id "STRG.3.1"; gene_id "STRG.3"; 11 NT_187562.1 StringTie exon 219891 219967 . - . transcript_id "STRG.3.1"; gene_id "STRG.3"; [all …]
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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 | 1 140 Twinscan inter 5141 8522 . - . gene_id ""; transcript_id ""; 2 140 Twinscan inter_CNS 8523 9711 . - . gene_id ""; transcript_id ""; 3 140 Twinscan inter 9712 13182 . - . gene_id ""; transcript_id ""; 4 140 Twinscan 3UTR 65149 65487 . - . gene_id "140.000"; transcript_id "140.000.1"; 5 140 Twinscan 3UTR 66823 66992 . - . gene_id "140.000"; transcript_id "140.000.1"; 6 140 Twinscan stop_codon 66993 66995 . - 0 gene_id "140.000"; transcript_id "140.000.1"; 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"; [all …]
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H A D | gene-mrna-exon-cds.gtf | 1 Chr1 TAIR10 gene 3631 5899 . + . gene_id "AT1G01010" 2 Chr1 TAIR10 mRNA 3631 5899 . + . gene_id "AT1G01010"; transcript_id "AT1G01010.1" 3 Chr1 TAIR10 exon 3631 3913 . + . gene_id "AT1G01010"; transcript_id "AT1G01010.1" 4 Chr1 TAIR10 CDS 3760 3913 . + 0 gene_id "AT1G01010"; transcript_id "AT1G01010.1" 5 Chr1 TAIR10 exon 3996 4276 . + . gene_id "AT1G01010"; transcript_id "AT1G01010.1" 6 Chr1 TAIR10 CDS 3996 4276 . + 2 gene_id "AT1G01010"; transcript_id "AT1G01010.1" 7 Chr1 TAIR10 exon 4486 4605 . + . gene_id "AT1G01010"; transcript_id "AT1G01010.1" 8 Chr1 TAIR10 CDS 4486 4605 . + 0 gene_id "AT1G01010"; transcript_id "AT1G01010.1" 9 Chr1 TAIR10 exon 4706 5095 . + . gene_id "AT1G01010"; transcript_id "AT1G01010.1" 10 Chr1 TAIR10 CDS 4706 5095 . + 0 gene_id "AT1G01010"; transcript_id "AT1G01010.1" [all …]
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H A D | exon-cds.gtf | 2 381 Twinscan exon 300 401 . + . gene_id "381.000"; transcript_id "381.000.1"; amb… 3 381 Twinscan exon 800 851 . + . gene_id "381.000"; transcript_id "381.000.1"; amb… 4 381 Twinscan CDS 380 401 . + 0 gene_id "381.000"; transcript_id "381.000.1"; 5 381 Twinscan exon 501 650 . + . gene_id "381.000"; transcript_id "381.000.1"; rea… 6 381 Twinscan CDS 501 650 . + 2 gene_id "381.000"; transcript_id "381.000.1"; 7 381 Twinscan exon 700 800 . + . gene_id "381.000"; transcript_id "381.000.1"; rea… 8 381 Twinscan CDS 700 707 . + 2 gene_id "381.000"; transcript_id "381.000.1"; 9 381 Twinscan exon 900 1000 . + . gene_id "381.000"; transcript_id "381.000.1"; rea… 10 381 Twinscan exon 1100 1200 . + . gene_id "381.000"; transcript_id "381.000.1"; rea… 11 381 Twinscan start_codon 380 382 . + 0 gene_id "381.000"; transcript_id "381.000.1"; [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/manual/source/Tutorial/DataStructures/Store/ |
H A D | assignment_annotations.gtf | 1 381 Twinscan exon 150 200 . + . gene_id "381.000"; transcript_id "381.000.1"; 2 381 Twinscan exon 300 401 . + . gene_id "381.000"; transcript_id "381.000.1"; 3 381 Twinscan CDS 380 401 . + 0 gene_id "381.000"; transcript_id "381.000.1"; 4 381 Twinscan exon 501 650 . + . gene_id "381.000"; transcript_id "381.000.1"; 5 381 Twinscan CDS 501 650 . + 2 gene_id "381.000"; transcript_id "381.000.1"; 6 381 Twinscan exon 700 800 . + . gene_id "381.000"; transcript_id "381.000.1"; 7 381 Twinscan CDS 700 707 . + 2 gene_id "381.000"; transcript_id "381.000.1"; 8 381 Twinscan exon 900 1000 . + . gene_id "381.000"; transcript_id "381.000.1"; 10 381 Twinscan exon 160 210 . + . gene_id "381.000"; transcript_id "381.000.2"; 11 381 Twinscan exon 310 411 . + . gene_id "381.000"; transcript_id "381.000.2"; [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/genome_annotations/ |
H A D | assignment_annotations.gtf | 1 381 Twinscan exon 150 200 . + . gene_id "381.000"; transcript_id "381.000.1"; 2 381 Twinscan exon 300 401 . + . gene_id "381.000"; transcript_id "381.000.1"; 3 381 Twinscan CDS 380 401 . + 0 gene_id "381.000"; transcript_id "381.000.1"; 4 381 Twinscan exon 501 650 . + . gene_id "381.000"; transcript_id "381.000.1"; 5 381 Twinscan CDS 501 650 . + 2 gene_id "381.000"; transcript_id "381.000.1"; 6 381 Twinscan exon 700 800 . + . gene_id "381.000"; transcript_id "381.000.1"; 7 381 Twinscan CDS 700 707 . + 2 gene_id "381.000"; transcript_id "381.000.1"; 8 381 Twinscan exon 900 1000 . + . gene_id "381.000"; transcript_id "381.000.1"; 10 381 Twinscan exon 160 210 . + . gene_id "381.000"; transcript_id "381.000.2"; 11 381 Twinscan exon 310 411 . + . gene_id "381.000"; transcript_id "381.000.2"; [all …]
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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 | 6 KI270734.1 ENSEMBL gene 138082 161852 . - . gene_id "ENSG00000277196.4"; gene_type "protein_coding"… 7 KI270734.1 ENSEMBL transcript 138082 161750 . - . gene_id "ENSG00000277196.4"; transcript_id "ENST0… 8 KI270734.1 ENSEMBL exon 161689 161750 . - . gene_id "ENSG00000277196.4"; transcript_id "ENST0000061… 9 KI270734.1 ENSEMBL exon 156289 156497 . - . gene_id "ENSG00000277196.4"; transcript_id "ENST0000061… 10 KI270734.1 ENSEMBL CDS 156289 156446 . - 0 gene_id "ENSG00000277196.4"; transcript_id "ENST00000615… 12 KI270734.1 ENSEMBL exon 150987 151021 . - . gene_id "ENSG00000277196.4"; transcript_id "ENST0000061… 13 KI270734.1 ENSEMBL CDS 150987 151021 . - 1 gene_id "ENSG00000277196.4"; transcript_id "ENST00000615… 14 KI270734.1 ENSEMBL exon 150350 150499 . - . gene_id "ENSG00000277196.4"; transcript_id "ENST0000061… 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… [all …]
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