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Made changes in assign_job_queue.R, cleanup.R, lineage.R, msa.R, tree.R #106

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Made changes in assign_job_queue.R, cleanup.R, lineage.R, msa.R, tree.R #106

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c8633bd
Made changes in assign_job_queue.R, cleanup.R, lineage.R, msa.R, tree.R
SunSummoner Oct 20, 2024
a3247de
Merge commit 'b758992729ba7310fb7dc553259ac5c9d5ae6fca'
the-mayer Oct 30, 2024
d1bedab
remove .data prefix from param
the-mayer Oct 31, 2024
1a68176
kalign seems to come from an external GitHub repo -- removing from na…
the-mayer Oct 31, 2024
1ba4da6
revert .data additions
the-mayer Nov 1, 2024
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2 changes: 2 additions & 0 deletions NAMESPACE
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Expand Up @@ -247,6 +247,7 @@ importFrom(shiny,showNotification)
importFrom(stats,as.formula)
importFrom(stats,complete.cases)
importFrom(stats,logLik)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stringi,stri_extract_all_regex)
importFrom(stringi,stri_replace_all_regex)
Expand Down Expand Up @@ -276,6 +277,7 @@ importFrom(tidyr,replace_na)
importFrom(tidyr,separate)
importFrom(tidyr,unite)
importFrom(utils,combn)
importFrom(utils,globalVariables)
importFrom(viridis,scale_fill_viridis)
importFrom(visNetwork,visEdges)
importFrom(visNetwork,visGroups)
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2 changes: 1 addition & 1 deletion R/msa.R
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Expand Up @@ -196,7 +196,7 @@ createMSA_PDF <- function(fasta_path, out_path = NULL,
#' will be saved.
#'
#' @importFrom Biostrings readAAStringSet
#' @importFrom stats kalign
#'
#' @return A list containing the alignment object and the output file path.
#' @export
#'
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5 changes: 1 addition & 4 deletions R/tree.R
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Expand Up @@ -57,11 +57,8 @@
#' here("src/FastTree")
#' }
convertFA2Tree <- function(fa_path = here("data/alns/pspa_snf7.fa"),
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If these default/example files don't exist, we could remove them. Otherwise, placeholders that work might be a good idea!

.data$tre_path = here("data/alns/pspa_snf7.tre"),
tre_path = here("data/alns/pspa_snf7.tre"),
fasttree_path = here("src/FastTree")) {
# fa_path=here("data/alns/pspa_snf7.fa")
# .data$tre_path=here("data/alns/pspa_snf7.tre")
# fasttree_path=here("src/FastTree")

# Check if the FASTA file exists
if (!file.exists(fa_path)) {
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