blast_sqs: BLAST All vs All

View source: R/stage3-tools.R

blast_sqsR Documentation

BLAST All vs All

Description

Return BLAST results from BLASTing all vs all for given sequences. Returns NULL if no BLAST results generated.

Usage

blast_sqs(txid, typ, sqs, ps, lvl)

Arguments

txid

Taxonomic node ID, numeric

typ

Cluster type, 'direct' or 'subtree'

sqs

Sequences

ps

Parameters list, generated with parameters()

lvl

Integer, number of message indentations indicating code depth.

Value

blast_res data.frame or NULL

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), 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_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.