Check if sids are already downloaded for a txid.
Details
#' @name sqs_load
#' @title Load sequences from cache
#' @description Load sequences downloaded by dwnld function.
#' @param wd Working directory
#' @param txid Taxonomic ID, numeric
#' @family run-private
#' @return SeqArc
sqs_load <- function(wd, txid)
d <- file.path(wd, 'cache')
if (!file.exists(d))
stop('Cache does not exist.') d <- file.path(d, 'sqs')
if (!file.exists(d))
stop('`sqs` not in cache. Have you run the download stage?') fl <- file.path(d, paste0(txid, '.RData'))
if (!file.exists(fl))
stop(paste0('[', txid, '] not in `sqs` of cache.')) sqs <- try(readRDS(file = fl), silent = TRUE)
if (inherits(sqs, 'try-error'))
file.remove(fl) sqs
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(),
seqrec_get(),
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()