fetch_genbank: all [filter] Retrieves everthing Specified [property] Formal...

In alexpiper/taxreturn: An R package for retrieving and curating public DNA barcode reference data

all ⁠[filter]⁠ Retrieves everthing Specified ⁠[property]⁠ Formal binomial and trinomial at or below species level ⁠[property]⁠ family ⁠[rank]⁠ Rank-based query taxonomy genome ⁠[filter]⁠ Taxa with a direct link to a genome sequence 2009/10/21:2020 ⁠[date]⁠ Date-bounded query mammalia ⁠[subtree]⁠ All taxa within the Mammalia extinct ⁠[property]⁠ Extinct organisms Terminal ⁠[property]⁠ Terminal nodes in the tree loprovencyclife ⁠[filter]⁠ Entries with LinkOut links to the Encyclopedia of Life

Description

Fetch sequences from genbank

Usage

fetch_genbank(
  x,
  database = "nuccore",
  marker = c("COI[GENE]", "CO1[GENE]", "COX1[GENE]"),
  output = "h",
  min_length = 1,
  max_length = 2000,
  subsample = FALSE,
  chunk_size = 100,
  db = NULL,
  multithread = FALSE,
  quiet = FALSE,
  progress = FALSE,
  retry_attempt = 3,
  retry_wait = 5
)

Arguments

x	A taxon name or vector of taxa to download sequences for
database	The database to download from. For NCBI GenBank this currently onlt accepts the arguments 'nuccore' or 'genbank' which is an alias for nuccore.
marker	The barcode marker used as a search term for the database. If this is set to "mitochondria" or "mitochondrion" it will download full mitochondrial genomes. If set to "genome" it will download entire genomes only.
output	The output format for the taxonomy in fasta headers. Options include "h" for full heirarchial taxonomy (Accession;Domain;Phylum;Class;Order;Family;Genus;Species), "binom" for just genus species binomials (Accession;Genus_species), "bold" for BOLD taxonomic ID only (Accession;BoldTaxID), "gb" for genbank taxonomic ID (Accession|GBTaxID), "gb-binom" which outputs genbank taxonomic ID's and Genus species binomials, translating BOLD taxonomic ID's to genbank in the process (Accession|GBTaxID;Genus_species) or "standard" which outputs the default format for each database. For bold this is ⁠sampleid|species name|markercode|genbankid⁠
min_length	The minimum length of sequences to download
max_length	The maximum length of sequences to download
subsample	(Numeric) return a random subsample of sequences from the search.
chunk_size	Split up the query into chunks of this size to avoid overloading API servers. if left NULL, the default will be 300
db	a database file generated using taxreturn::get_ncbi_taxonomy(). Generated automatically if NULL.
multithread	Whether multithreading should be used, if TRUE the number of cores will be automatically detected, or provided a numeric vector to manually set the number of cores to use
quiet	Whether progress should be printed to the console.
progress	A logical, for whether or not to print a progress bar when multithread is true. Note, this will slow down processing.
retry_attempt	The number of query attempts in case of query failure due to poor internet connection.
retry_wait	How long to wait between query attempts.

alexpiper/taxreturn documentation built on Sept. 14, 2024, 7:56 p.m.