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BIMSBbioinfo / pigx_sars-cov-2

PiGx SARS-CoV-2 wastewater sequencing pipeline
GNU General Public License v3.0
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mutation_sheet: Write script to write a mutation sheet automatically from covidCG lists #94

Open vicfabienne opened 3 years ago

vicfabienne commented 3 years ago

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.

jonasfreimuth commented 2 years ago

Could you please clarify which data are downloaded from covidCG (e.g. the query) and the format the downloaded tables have?

jonasfreimuth commented 2 years ago

Also this is the same issue as in #68.