acc2lin

This function combines 'efetch_ipg()' and 'ipg2lin()' to map a set of protein accessions to their assembly (GCA_ID), tax ID, and lineage.

Function to map protein accession numbers to lineage

This function combines 'efetch_ipg()' and 'ipg2lin()' to map a set of protein accessions to their assembly (GCA_ID), tax ID, and lineage.

Usage

acc2lin(
  accessions,
  assembly_path,
  lineagelookup_path,
  ipgout_path = NULL,
  plan = "multicore"
)

acc2lin(
  accessions,
  assembly_path,
  lineagelookup_path,
  ipgout_path = NULL,
  plan = "multicore"
)

Arguments

accessions

Character vector of protein accessions

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

ipgout_path

Path to write the results of the efetch run of the accessions on the ipg database. If NULL, the file will not be written. Defaults to NULL

plan

Value

Describe return, in detail

Author

Samuel Chen, Janani Ravi

Examples

if (FALSE) { # \dontrun{
acc2lin()
} # }