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mutation_sheet: Write script to write a mutation sheet automatically from covidCG lists #94

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vicfabienne opened this issue Sep 2, 2021 · 2 comments
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good first issue Good for newcomers prio:Low issues needs to be fixed in long term type:enhancement any enhancement that doesn't fit into aesthetics, bug or documentation

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@vicfabienne
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vicfabienne commented Sep 2, 2021

The mutation sheet needs to have the variants as columns listing the signature mutations (Amino acid seq location) but also the codon_number/location on the nt sequence.
Both is e.g derived by tables sourced from covidCG. For the first column some parsing has to be done, the other one is just the column "codon_num" .

It would be nice to have a script that parses together this mutation sheet from a given list of input files.

@vicfabienne vicfabienne added type:enhancement any enhancement that doesn't fit into aesthetics, bug or documentation good first issue Good for newcomers prio:Low issues needs to be fixed in long term labels Sep 2, 2021
@vicfabienne vicfabienne changed the title mutation_sheet: Write script to write a mutation sheet automatically from outbreak.info lists mutation_sheet: Write script to write a mutation sheet automatically from covidCG lists Apr 1, 2022
@jonasfreimuth
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Could you please clarify which data are downloaded from covidCG (e.g. the query) and the format the downloaded tables have?

@jonasfreimuth
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Also this is the same issue as in #68.

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Labels
good first issue Good for newcomers prio:Low issues needs to be fixed in long term type:enhancement any enhancement that doesn't fit into aesthetics, bug or documentation
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