seqrec_get: seqrec_get

Description Usage Arguments Details Value See Also

View source: R/stage2-tools.R

Description

Downloads sequences from GenBank in batches.

Usage

1
seqrec_get(txid, ps, direct = FALSE, lvl = 0)

Arguments

txid

NCBI taxonomic ID

ps

Parameters list, generated with parameters()

direct

Node-level only or subtree as well? Default FALSE.

lvl

Integer, number of message indentations indicating code depth.

Details

If a restez database is available and the number of sequences to retrieve is less than 'btchsz', the function will look the sequences up from the database rather than download.

Value

Vector of sequence records

See Also

Other run-private: batcher, blast_clstr, blast_filter, blast_setup, blast_sqs, blastcache_load, blastcache_save, blastdb_gen, blastn_run, cache_rm, cache_setup, clade_select, clstr2_calc, clstr_all, clstr_direct, clstr_sqs, clstr_subtree, clstrarc_gen, clstrarc_join, clstrrec_gen, clstrs_calc, clstrs_join, clstrs_merge, clstrs_renumber, clstrs_save, cmdln, descendants_get, download_obj_check, error, gb_extract, hierarchic_download, info, ncbicache_load, ncbicache_save, obj_check, obj_load, obj_save, outfmt_get, parameters_load, parameters_setup, parent_get, progress_init, progress_read, progress_reset, progress_save, rank_get, rawseqrec_breakdown, safely_connect, search_and_cache, searchterm_gen, seeds_blast, seq_download, seqarc_gen, seqrec_augment, seqrec_convert, seqrec_gen, sids_check, sids_get, sids_load, sids_save, sqs_count, sqs_save, stage_args_check, stages_run, tax_download, taxdict_gen, taxtree_gen, txids_get, txnds_count, warn


ropensci/phylotaR documentation built on Jan. 16, 2020, 11:47 a.m.