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add: generate transcript structure

Closed add: generate transcript structure
gen_transc into main
Closed Timon Baltisberger requested to merge gen_transc into main
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tests/resources/test_transcript_structure/RP1_RIK.gtf 0 → 100644
+ 12
− 0
1 ensembl_havana gene 3999557 4409241 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding";
    • Alex Kanitz
      Alex Kanitz @kanitz
      Owner

      Better to put test files independent of the tool or functionally tested, becaus they may be used by multiple tests/tools. We have asked other to put test files in tests/test_files, so perhaps you could do the same

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1 havana transcript 4290846 4409241 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-204"; transcript_source "havana"; transcript_biotype "retained_intron"; transcript_support_level "1";
1 havana exon 4409170 4409241 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "1"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-204"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
1 havana exon 4352202 4352837 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "2"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-204"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001377400"; exon_version "1"; transcript_support_level "1";
1 havana exon 4351910 4352081 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "3"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-204"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001380148"; exon_version "1"; transcript_support_level "1";
1 havana exon 4290846 4293012 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "4"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-204"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001345123"; exon_version "1"; transcript_support_level "1";
1 havana gene 9747648 9791924 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA";
1 havana transcript 9747648 9791922 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-202"; transcript_source "havana"; transcript_biotype "lncRNA"; transcript_support_level "1";
1 havana exon 9747648 9748604 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "1"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001104564"; exon_version "1"; transcript_support_level "1";
1 havana exon 9752449 9752564 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "2"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001144804"; exon_version "1"; transcript_support_level "1";
1 havana exon 9789656 9789780 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "3"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001175967"; exon_version "1"; transcript_support_level "1";
1 havana exon 9791125 9791922 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "4"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001174858"; exon_version "1"; transcript_support_level "1";
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