searchterm_gen: Construct GenBank Search Term

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

Description

Construct search term for searching GenBank's nucleotide database. Limits the maximum size of sequences, avoids whole genome shotguns, predicted, unverified and synthetic sequences.

Usage

searchterm_gen(txid, ps, direct = FALSE)

Arguments

txid	Taxonomic ID
ps	Parameters list, generated with parameters()
direct	Node-level only or subtree as well? Default FALSE.

Value

character, search term

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, hierarchic_download, info, ncbicache_load, ncbicache_save, obj_check, obj_load, obj_save, parameters_load, parameters_setup, parent_get, progress_init, progress_read, progress_reset, progress_save, rank_get, safely_connect, search_and_cache, 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_load, sqs_save, stage_args_check, stages_run, tax_download, taxdict_gen, taxtree_gen, txids_get, txnds_count, warn

phylotaR documentation built on May 1, 2019, 9:26 p.m.