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a-frantz merged 3 commits into from
Aug 25, 2026
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test: transcript sequences fixture #330

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4 changes: 4 additions & 0 deletions test/fixtures/reference/README.md
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Expand Up @@ -20,6 +20,10 @@ Unheadered 2 column TSV file containing genelengths with `gene_name` labels from

Gencode v31 release GTF (or GFFv2) file, subsetted to only contain annotations for `chrY` and `chrM`. Gzipped.

## gencode.v50.BCR_ABL1.transcripts.fa.gz

Gencode v50 release protein-coding transcript sequences FASTA, subsetted to only contain sequences from the genes BCR and ABL1. Gzipped.

@adthrasher adthrasher Aug 25, 2026

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I'm not fully familiar with the gencode transcript reference, but does it actually contain the gene labels (e.g. BCR, ABL1). If so did you just grep for those plus protein_coding or something?

Short version, is this enough information to recreate the file easily?

@a-frantz a-frantz Aug 25, 2026

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I created them "by hand": opened the whole file in my editor, searched for the gene labels, copy and pasted into a new file. It could be done with some Bash-Fu, but that is complicated by the released FASTA formatting being linebroken on nucleotide 80 (or something around that) of each line.

$  gunzip -c test/fixtures/reference/gencode.v50.BCR_ABL1.transcripts.fa.gz | head -n 50
>ENST00000928586.2|ENSG00000186716.23|OTTHUMG00000150655.5|-|BCR-216|BCR|6876|UTR5:1-596|CDS:597-4361|UTR3:4362-6876|
GGGGGGAGGGTGGCGGCTCGATGGGGGAGCCGCCTCCAGGGGGCCCCCCCGCCCTGTGCC
CACGGCGCGGCCCCTTTAAGAGGCCCGCCTGGCTCCGTCATCCGCGCCGCGGCCACCTCC
CCCCGGCCCTCCCCTTCCTGCGGCGCAGAGTGCGGGCCGGGCGGGAGTGCGGCGAGAGCC
GGCTGGCTGAGCTTAGCGTCCGAGGAGGCGGCGGCGGCGGCGGCGGCACGGCGGCGGCGG
GGCTGTGGGGCGGTGCGGAAGCGAGAGGCGAGGAGCGCGCGGGCCGTGGCCAGAGTCTGG
CGGCGGCCTGGCGGAGCGGAGAGCAGCGCCCGCGCCTCGCCGTGCGGAGGAGCCCCGCAC
ACAATAGCGGCGCGCGCAGCCCGCGCCCTTCCCCCCGGCGCGCCCCGCCCCGCGCGCCGA
GCGCCCCGCTCCGCCTCACCTGCCACCAGGGAGTGGGCGGGCATTGTTCGCCGCCGCCGC
CGCCGCGCGGGCCATGGGGGCCGCCCGGCGCCCGGGGCCGGGCTGGCGAGGCGCCGCGCC
GCCGCTGAGACGGGCCCCGCGCGCAGCCCGGCGGCGCAGGTAAGGCCGGCCGCGCCATGG
TGGACCCGGTGGGCTTCGCGGAGGCGTGGAAGGCGCAGTTCCCGGACTCAGAGCCCCCGC
GCATGGAGCTGCGCTCAGTGGGCGACATCGAGCAGGAGCTGGAGCGCTGCAAGGCCTCCA
TTCGGCGCCTGGAGCAGGAGGTGAACCAGGAGCGCTTCCGCATGATCTACCTGCAGACGT
TGCTGGCCAAGGAAAAGAAGAGCTATGACCGGCAGCGATGGGGCTTCCGGCGCGCGGCGC
AGGCCCCCGACGGCGCCTCCGAGCCCCGAGCGTCCGCGTCGCGCCCGCAGCCAGCGCCCG
CCGACGGAGCCGACCCGCCGCCCGCCGAGGAGCCCGAGGCCCGGCCCGACGGCGAGGGTT
CTCCGGGTAAGGCCAGGCCCGGGACCGCCCGCAGGCCCGGGGCAGCCGCGTCGGGGGAAC
GGGACGACCGGGGACCCCCCGCCAGCGTGGCGGCGCTCAGGTCCAACTTCGAGCGGATCC
GCAAGGGCCATGGCCAGCCCGGGGCGGACGCCGAGAAGCCCTTCTACGTGAACGTCGAGT
TTCACCACGAGCGCGGCCTGGTGAAGGTCAACGACAAAGAGGTGTCGGACCGCATCAGCT
CCCTGGGCAGCCAGGCCATGCAGATGGAGCGCAAAAAGTCCCAGCACGGCGCGGGCTCGA
GCGTGGGGGATGCATCCAGGCCCCCTTACCGGGGACGCTCCTCGGAGAGCAGCTGCGGCG
TCGACGGCGACTACGAGGACGCCGAGTTGAACCCCCGCTTCCTGAAGGACAACCTGATCG
ACGCCAATGGCGGTAGCAGGCCCCCTTGGCCGCCCCTGGAGTACCAGCCCTACCAGAGCA
TCTACGTCGGGGGCATGATGGAAGGGGAGGGCAAGGGCCCGCTCCTGCGCAGCCAGAGCA
CCTCTGAGCAGGAGAAGCGCCTTACCTGGCCCCGCAGGTCCTACTCCCCCCGGAGTTTTG
AGGATTGCGGAGGCGGCTATACCCCGGACTGCAGCTCCAATGAGAACCTCACCTCCAGCG
AGGAGGACTTCTCCTCTGGCCAGTCCAGCCGCGTGTCCCCAAGCCCCACCACCTACCGCA
TGTTCCGGGACAAAAGCCGCTCTCCCTCGCAGAACTCGCAACAGTCCTTCGACAGCAGCA
GTCCCCCCACGCCGCAGTGCCATAAGCGGCACCGGCACTGCCCGGTTGTCGTGTCCGAGG
CCACCATCGTGGGCGTCCGCAAGACCGGGCAGATCTGGCCCAACGATGGCGAGGGCGCCT
TCCATGGAGACGCAGATGGCTCGTTCGGAACACCACCTGGATACGGCTGCGCTGCAGACC
GGGCAGAGGAGCAGCGCCGGCACCAAGATGGGCTGCCCTACATTGATGACTCGCCCTCCT
CATCGCCCCACCTCAGCAGCAAGGGCAGGGGCAGCCGGGATGCGCTGGTCTCGGGAGCCC
TGGAGTCCACTAAAGCGAGTGAGCTGGACTTGGAAAAGGGCTTGGAGATGAGAAAATGGG
TCCTGTCGGGAATCCTGGCTAGCGAGGAGACTTACCTGAGCCACCTGGAGGCACTGCTGC
TGCCCATGAAGCCTTTGAAAGCCGCTGCCACCACCTCTCAGCCGGTGCTGACGAGTCAGC
AGATCGAGACCATCTTCTTCAAAGTGCCTGAGCTCTACGAGATCCACAAGGAGTTCTATG
ATGGGCTCTTCCCCCGCGTGCAGCAGTGGAGCCACCAGCAGCGGGTGGGCGACCTCTTCC
AGAAGCTGGCCAGCCAGCTGGGTGTGTACCGGGCCTTCGTGGACAACTACGGAGTTGCCA
TGGAAATGGCTGAGAAGTGCTGTCAGGCCAATGCTCAGTTTGCAGAAATCTCCGAGAACC
TGAGAGCCAGAAGCAACAAAGATGCCAAGGATCCAACGACCAAGAACTCTCTGGAAACTC
TGCTCTACAAGCCTGTGGACCGTGTGACGAGGAGCACGCTGGTCCTCCATGACTTGCTGA
AGCACACTCCTGCCAGCCACCCTGACCACCCCTTGCTGCAGGACGCCCTCCGCATCTCAC
AGAACTTCCTGTCCAGCATCAATGAGGAGATCACACCCCGACGGCAGTCCATGACGGTGA
AGAAGGGAGAGCACCGGCAGCTGCTGAAGGACAGCTTCATGGTGGAGCTGGTGGAGGGGG
CCCGCAAGCTGCGCCACGTCTTCCTGTTCACCGACCTGCTTCTCTGCACCAAGCTCAAGA
AGCAGAGCGGAGGCTTCCAGATGGTGGATGAACTGGAGGCAGTGCCCAACATCCCCCTGG
TGCCCGATGAGGAGCTGGACGCTTTGAAGATCAAGATCTCCCAGATCAAGAATGACATCC

@a-frantz a-frantz Aug 25, 2026

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as for the protein coding part, the gencode site hosts a subsetted transcriptome of just protein-coding transcripts, which was the file I started with


## GRCh38.chr1_chr19.dict

Sequence dictionary for GRCh38 reference containing `chr1` and `chr19` only
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3 changes: 3 additions & 0 deletions test/fixtures/reference/gencode.v50.BCR_ABL1.transcripts.fa.gz
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