Cluster sequences directly associated with txid

In GenBank certain sequences may only be associated with a higher level taxon (e.g. genus, family ...). This function generates clusters from these sequences, alone. This function identifies such sequences in the sequence object and generates a list of clusters of cl_type 'direct'.

Usage

clstr_direct(txid, sqs, txdct, ps, lvl)

Arguments

txid

Taxonomic ID

sqs

Sequence object of all downloaded sequences

txdct

Taxonomic dictionary

ps

Parameters list, generated with parameters()

lvl

Integer, number of message indentations indicating code depth.

Value

ClstrArc

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_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()