sids_get: Return random set of sequence IDs

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

Return random set of sequence IDs

Description

For a given txid return a random set of sequences associated.

Usage

sids_get(txid, direct, ps, retmax = 100, hrdmx = 1e+05)

Arguments

txid	NCBI taxon identifier
direct	Node-level only or subtree as well? Default FALSE.
ps	Parameters list, generated with parameters()
retmax	Maximum number of sequences when querying model organisms. The smaller the more random, the larger the faster.
hrdmx	Absolute maximum number of sequence IDs to download in a single query.

Details

For model organisms downloading all IDs can a take long time or even cause an xml parsing error. For any search with more than hrdmx sequences, this function we will run multiple small searches downloading retmax seq IDs at a time with different retstart values to generate a semi-random vector of sequence IDs. For all other searches, all IDs will be retrieved. Note, it makes no sense for mdlthrs in parameters to be greater than hrdmx in this function.

Value

vector of IDs

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(), seqrec_get(), sids_check(), 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.