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'.
clstr_direct(txid, sqs, txdct, ps, lvl)Taxonomic ID
Sequence object of all downloaded sequences
Taxonomic dictionary
Parameters list, generated with parameters()
Integer, number of message indentations indicating code depth.
ClstrArc
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,
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