genbank_parse_rentrez_xml: Download and parse sequences from GenBank using rentrez and...

In vaulot/dvutils: A set of utilities

Description

Does not write the GenBank file. Notes:

• Use only sequence_keep = TRUE for simple gene sequences, else it may crash

• Use acc_step = 1 if several accession numbers point to the same accession number (case of metagenomes). In this case the queries are sent one by one and the old accession number is kept.

Usage

genbank_parse_rentrez_xml(
  accession,
  acc_step = 50,
  seq_length_max = 15000,
  seq_length_discard = 3e+05
)

Arguments

accession	Character vector of accession numbers
acc_step	Integer, number of accession numbers for each query.
seq_length_max,	maximum length of sequences returned (set to zero to prevent returning sequence)
seq_length_discard,	if the sequence length is longer than this value, no information is returned.

Value

Data frame with the metadata information.

Examples

gb_metadata <- genbank_parse_rentrez_xml(accession = c("JX015376", "JQ768406", "LT621940"), seq_length_max = 15000)

vaulot/dvutils documentation built on Nov. 20, 2021, 11:01 a.m.