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Issue #501: Add simple parsing function to explode on transcript #523

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@akotlar akotlar commented Jun 8, 2024

  • Adds function to take a Bystro annotation tsv and explode it on refSeq.name, segregating the refSeq annotations as necessary to make sure each field has only the values for that transcript

Before:
trio_trim_vep_vcf-20240524162149542.annotation.tsv.gz

After:
test_output.tsv.gz

Notice at loci like chrom:chr2 pos:207647981 type:SNP inputRef:C alt:T we no longer have FASTKD2;FASTKD2;FASTKD2;MIR3130-1;MIR3130-2 in the refSeq.name2 field (the gene name field) and NM_001136194;NM_014929;NM_001136193;NR_036077;NR_036078 in the refSeq.name field (the transcript name field). Instead we have 5 rows, with 1 transcript/gene per row (the same is true for all of the refSeq.* fields; they are exploded relative to the refSeq.name field).

@akotlar akotlar requested a review from cristinaetrv June 8, 2024 03:29
@akotlar akotlar mentioned this pull request Jun 10, 2024
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We discussed where this code should live and decided it makes more sense for this to be a cli tool rather than being in utils.

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