hierarchic_download: Hierarchically get sequences for a txid

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

Hierarchically get sequences for a txid

Description

Looks up and downloads sequences for a taxonomic ID.

Usage

hierarchic_download(txid, txdct, ps, lvl = 0)

Arguments

txid	Taxonomic node ID, numeric
txdct	Taxonomic dictionary
ps	Parameters list, generated with parameters()
lvl	Integer, number of message indentations indicating code depth.

Value

Vector of SeqRecs

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(), 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(), seqrec_get(), 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 21, 2024, 1:01 a.m.