Mercurial > repos > iuc > length_and_gc_content
diff test-data/in.gtf @ 2:e3ba567abdf5 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit 7b6b07d22f3e6fed77b2c237de2b0d96fa939711"
| author | iuc |
|---|---|
| date | Fri, 11 Mar 2022 14:08:11 +0000 |
| parents | 2ca1baabdae0 |
| children |
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--- a/test-data/in.gtf Sun Jan 28 04:04:58 2018 -0500 +++ b/test-data/in.gtf Fri Mar 11 14:08:11 2022 +0000 @@ -1,6 +1,20 @@ -1 ensembl_havana gene 1 103 . + . gene_id "ENSG00000162526"; gene_version "4"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; -1 ensembl_havana transcript 1 103 . + . gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; tag "basic"; transcript_support_level "NA"; -1 ensembl_havana exon 1 103 . + . gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; exon_id "ENSE00002319515"; exon_version "1"; tag "basic"; transcript_support_level "NA"; -1 ensembl_havana CDS 1 100 . + 0 gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; protein_id "ENSP00000334393"; protein_version "3"; tag "basic"; transcript_support_level "NA"; -1 ensembl_havana start_codon 1 3 . + 0 gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; tag "basic"; transcript_support_level "NA"; -1 ensembl_havana stop_codon 101 103 . + 0 gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; tag "basic"; transcript_support_level "NA"; +fake_chr2 HAVANA gene 257 3416 . + . gene_id "ENSG00000128710.6"; gene_type "protein_coding"; gene_name "HOXD10"; level 1; hgnc_id "HGNC:5133"; tag "overlapping_locus"; havana_gene "OTTHUMG00000132511.5"; +fake_chr2 HAVANA transcript 257 3416 . + . gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA exon 257 1057 . + . gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 1; exon_id "ENSE00000882912.6"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA CDS 313 1057 . + 0 gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 1; exon_id "ENSE00000882912.6"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA start_codon 313 315 . + 0 gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 1; exon_id "ENSE00000882912.6"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA exon 2433 3416 . + . gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 2; exon_id "ENSE00001816717.3"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA CDS 2433 2707 . + 2 gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 2; exon_id "ENSE00001816717.3"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA stop_codon 2708 2710 . + 0 gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 2; exon_id "ENSE00001816717.3"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA UTR 257 312 . + . gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 1; exon_id "ENSE00000882912.6"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA UTR 2708 3416 . + . gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 2; exon_id "ENSE00001816717.3"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA gene 6198 8416 . + . gene_id "ENSG00000128709.13"; gene_type "protein_coding"; gene_name "HOXD9"; level 2; hgnc_id "HGNC:5140"; havana_gene "OTTHUMG00000132516.6"; +fake_chr2 HAVANA transcript 6198 8416 . + . gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA exon 6198 7064 . + . gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 1; exon_id "ENSE00000882914.5"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA CDS 6248 7064 . + 0 gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 1; exon_id "ENSE00000882914.5"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA start_codon 6248 6250 . + 0 gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 1; exon_id "ENSE00000882914.5"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA exon 7413 8416 . + . gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 2; exon_id "ENSE00001845001.4"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA CDS 7413 7651 . + 2 gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 2; exon_id "ENSE00001845001.4"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA stop_codon 7652 7654 . + 0 gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 2; exon_id "ENSE00001845001.4"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA UTR 6198 6247 . + . gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 1; exon_id "ENSE00000882914.5"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA UTR 7652 8416 . + . gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 2; exon_id "ENSE00001845001.4"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6";