seqrec_get: seqrec_get

In ropensci/phylotaR: Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

seqrec_get

Description

Downloads sequences from GenBank in batches.

Usage

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 July 9, 2023, 3:17 p.m.