BLAST All vs All — blast_sqs • phylotaR

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()