Split records by serotype by using the virus-tax-id field in NCBI datasets. Historically, we obtained each serotype individually in this code, leading to redundant fetching and processing of each sequence. Now that we're using ncbi datasets, these numeric IDs are recorded in a virus-tax-id field, that we can use to separate the serotypes.
Changes in this PR include:
Pull virus-tax-id and virus-name from the dengue NCBI dataset
Use the virus-tax-id to infer the ncbi_serotype field of each record
Use the ncbi_serotype field to split sequences and metadata files into serotypes
Update target files in the Snakefile to reflect the new serotype split
Description of proposed changes
Split records by serotype by using the virus-tax-id field in NCBI datasets. Historically, we obtained each serotype individually in this code, leading to redundant fetching and processing of each sequence. Now that we're using ncbi datasets, these numeric IDs are recorded in a
virus-tax-idfield, that we can use to separate the serotypes.Changes in this PR include:
virus-tax-idandvirus-namefrom the dengue NCBI datasetvirus-tax-idto infer thencbi_serotypefield of each recordncbi_serotypefield to split sequences and metadata files into serotypesRelated issue(s)
Checklist