Function to map GCA_ID to TaxID, and TaxID to Lineage
Usage
GCA2lin(
prot_data,
assembly_path = "/data/research/jravilab/common_data/assembly_summary_genbank.txt",
lineagelookup_path = "/data/research/jravilab/common_data/lineage_lookup.tsv",
acc_col = "AccNum"
)Arguments
- prot_data
Dataframe containing a column
GCA_ID- assembly_path
String of the path to the assembly_summary path This file can be generated using the "DownloadAssemblySummary()" function
- lineagelookup_path
String of the path to the lineage lookup file (taxid to lineage mapping). This file can be generated using the "create_lineage_lookup()" function
- acc_col