blast_filter: Filter BLAST results

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

Description

Given a BLAST output, filters query-subject pairs such that only HSPs with a coverage greater than mncvrg (specified in the pipeline parameters) remain. Filters both: query-subject and subject-query pairs, if one of the coverages is insufficient. HSP coverage is obtained from the BLAST column qcovs.

Usage

blast_filter(blast_res, ps)

Arguments

blast_res	BLAST results
ps	Parameters list, generated with parameters()

Value

data.frame blast res

See Also

Other run-private: batcher, blast_clstr, 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, 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.