Downloads sequences from GenBank in batches.
Arguments
- txid
NCBI taxonomic ID
- ps
Parameters list, generated with parameters()
- direct
Node-level only or subtree as well? Default FALSE.
- lvl
Integer, number of message indentations indicating code depth.
Details
If a restez database is available and the number of sequences to retrieve is less than 'btchsz', the function will look the sequences up from the database rather than download.
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_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(),
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()