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()