hierarchic_download: Hierarchically get sequences for a txid

View source: R/stage2-tools.R

hierarchic_downloadR Documentation

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.