blast_sqs: BLAST All vs All

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

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, 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, 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_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.