get_GenBank_seqs_with_efecth: Quality check graphics for DNA Barcodes

In carvajalc/BarcoR: Quality Check Graphics for DNA Barcodes

Description

Obtain a full sequences, CDS sequence and protein files from a list of NCBI accession number

Usage

get_GenBank_seqs_with_efecth(
  seq_genbank_ids_user,
  is_nucleotide_user = TRUE,
  get_cds_user = TRUE,
  organize_name_user = c("species", "gene", "accession_number"),
  force_name_to_genes_user = NULL,
  file_out_user = NULL,
  out_directory_user = NULL
)

Arguments

seq_genbank_ids_user	A list of NCBI accession numbers
is_nucleotide_user	Logical. True indicates if the accession numbers are nucleotides data. False indicates if data are protein data
get_cds_user	Logical. Indicates if CDS information is obtain from NCBI
organize_name_user	A list of characters or names to include in the sequence header.
force_name_to_genes_user	Character to rename the gene name in a sequence. default is NULL.
file_out_user	character to add in the output file.
out_directory_user	Output directory.

Value

three fasta files: full sequence, CDS sequence and protein information. a data frame with sequences information in text format

Examples

get_genes <- list( c("KU494314",
                    "MK369820",
                    "KC520685",
                    "DQ502716",
                    "KM024310"))

file_out <- c("COX1")

for(i in 1:length(file_out)) {
 get_GenBank_seqs_with_efecth (seq_genbank_ids_user = get_genes[[i]],
                              is_nucleotide_user = TRUE,
                               get_cds_user = TRUE,
                               organize_name_user = c("species","gene","accession_number"),
                               force_name_to_genes_user = NULL,
                               file_out_user = file_out[i],
                               out_directory_user = NULL)
                             }
                              rm(i)

carvajalc/BarcoR documentation built on Dec. 19, 2021, 1:54 p.m.