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/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/sample_data/supertranscripts_example/
H A Dsupertranscripts.gtf1 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 …]
/dports/biology/py-crossmap/CrossMap-0.5.4/test/
H A Dtest08_hg19.gtf1 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 …]
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/ngs_roi/example/
H A Ddmel.gtf1 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 …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/unit_test/gtfreader_test_cases/
H A Dgene-mrna-exon-cds.gtf1 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 …]
H A Dexon-cds.gtf2 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 …]
/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/sample_data/stringtie_example/
H A Dstringtie_merged.gtf3 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 …]
/dports/biology/gffread/gffread-0.12.7/examples/output/
H A Dannotation.gtf1 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 …]
/dports/biology/bcftools/bcftools-1.14/misc/
H A Dgff2gff.py24 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 …]
/dports/biology/bio-mocha/bcftools-1.14/misc/
H A Dgff2gff.py24 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 …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/unit_test/gtfwriter_test_cases/
H A Drw-836-3.entry.gtf2 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 …]
H A D1.annot.gtf16 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 …]
H A Drw-329.annot.gtf2 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 …]
H A Drw-836-2.entry.gtf50 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 …]
H A Drw-836-1.entry.gtf2 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 …]
H A D2.entry.gtf2 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 …]
/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/PerlLib/
H A DGTF_utils2.pm40 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 …]
/dports/biology/subread/subread-2.0.2-source/test/featureCounts/data/
H A Dtest-minimum.GTF1 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 …]
H A Dtest-chralias.GTF1 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 …]
/dports/biology/gffread/gffread-0.12.7/examples/
H A Dtranscripts.gtf1 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 …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/import/unit_test/data/input/
H A Dtest-classified-exons.gtf1 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 …]
H A Dgene-mrna-exon-cds.gtf1 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"
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H A Dexon-cds.gtf2 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";
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/manual/source/Tutorial/DataStructures/Store/
H A Dassignment_annotations.gtf1 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";
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/genome_annotations/
H A Dassignment_annotations.gtf1 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";
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/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/
H A Dgencode.and.this.is.a.valid.one.too.table.gtf6 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…
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