get_GB_sequence_data: Builds a curated data frame with sample details and sequence...

In EvolEcolGroup/mtDNAcombine: R package to download, combine, and curate sequences from public databases

Description

get_GB_sequence_data

Usage

get_GB_sequence_data(accessions_of_interest, gene, new_names_file = NULL)

Arguments

accessions_of_interest	user provided file which lists accession numbers. Should be a .csv or .txt file without a header.
gene	gene of interest written as character string.
new_names_file	csv file of species names that have been flagged as problematic and the replacement name to be used, needed for 'standardise_spp_name' function, default to NULL if not provided

Details

This function extracts and collates details of the sample, as well as the sequence data for a selected gene, from GenBank for each accession number given.

Function designed to construct a comprehensive reference data frame of sample and sequence data available for the gene of interest from each of the accession numbers given. Uses functions load_accession_list, get_sample_details, and get_gene_details to extract information from NCBI website. As well as standardise_gene_names and remove_duplicates to clean up data frame.

EvolEcolGroup/mtDNAcombine documentation built on July 8, 2021, 10:30 p.m.