Skip to content

Commit

Permalink
trailing spaces
Browse files Browse the repository at this point in the history 
Signed-off-by: Awa Synthia <[email protected]>
  • Loading branch information
@awasyn
awasyn committed Nov 20, 2024
1 parent 424b0e8 commit 9ce780b
Show file tree
Hide file tree
Showing 2 changed files with 36 additions and 36 deletions.
66 changes: 33 additions & 33 deletions R/pre-msa-tree.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ api_key <- Sys.getenv("ENTREZ_API_KEY", unset = "YOUR_KEY_HERE")
#' @param y Delimitter. Default is space (" ").
#'
#' @importFrom rlang abort
#'
#'
#' @return A character vector in title case.
#' @export
#'
Expand Down Expand Up @@ -112,21 +112,21 @@ addLeaves2Alignment <- function(aln_file = "",
lin_file = "data/rawdata_tsv/all_semiclean.txt", # !! finally change to all_clean.txt!!
# lin_file="data/rawdata_tsv/PspA.txt",
reduced = FALSE) {

#Check if the alignment file is provided and exists
if (nchar(aln_file) == 0) {
abort("Error: Alignment file path must be provided.")
}

if (!file.exists(aln_file)) {
abort(paste("Error: The alignment file '", aln_file, "' does not exist."))
}

# Check if the lineage file exists
if (!file.exists(lin_file)) {
abort(paste("Error: The lineage file '", lin_file, "' does not exist."))
}

# Check that the 'reduced' parameter is logical
if (!is.logical(reduced) || length(reduced) != 1) {
abort("Error: 'reduced' must be a single logical value (TRUE or FALSE).")
Expand Down Expand Up @@ -249,15 +249,15 @@ addName <- function(data,
if (!is.data.frame(data)) {
abort("Error: The input 'data' must be a data frame")
}

# Check that the specified columns exist in the data
required_cols <- c(accnum_col, spec_col, lin_col)
missing_cols <- setdiff(required_cols, names(data))
if (length(missing_cols) > 0) {
abort(paste("Error: The following columns are missing from the data:",
abort(paste("Error: The following columns are missing from the data:",
paste(missing_cols, collapse = ", ")))
}

cols <- c(accnum_col, "Kingdom", "Phylum", "Genus", "Spp")
split_data <- data %>%
separate(
Expand Down Expand Up @@ -347,16 +347,16 @@ convertAlignment2FA <- function(aln_file = "",
if (nchar(aln_file) == 0) {
abort("Error: Alignment file path must be provided.")
}

if (!file.exists(aln_file)) {
abort(paste("Error: The alignment file '", aln_file, "' does not exist."))
}

# Check if the lineage file exists
if (!file.exists(lin_file)) {
abort(paste("Error: The lineage file '", lin_file, "' does not exist."))
}

# Check that the 'reduced' parameter is logical
if (!is.logical(reduced) || length(reduced) != 1) {
abort("Error: 'reduced' must be a single logical value (TRUE or FALSE).")
Expand Down Expand Up @@ -424,14 +424,14 @@ mapAcc2Name <- function(line, acc2name, acc_col = "AccNum", name_col = "Name") {
if (!is.data.frame(acc2name)) {
abort("Error: acc2name must be a data frame.")
}

# Check if the specified columns exist in the data frame
if (!(acc_col %in% colnames(acc2name))) {
abort("Error: The specified acc_col '", acc_col, "' does not exist in
abort("Error: The specified acc_col '", acc_col, "' does not exist in
acc2name.")
}
if (!(name_col %in% colnames(acc2name))) {
abort("Error: The specified name_col '", name_col, "' does not exist in
abort("Error: The specified name_col '", name_col, "' does not exist in
acc2name.")
}

Expand Down Expand Up @@ -475,7 +475,7 @@ rename_fasta <- function(fa_path, outpath,
abort("Error: The input FASTA file does not exist at the specified
path: ", fa_path)
}

# Check if the output path is writable
outdir <- dirname(outpath)
if (!dir.exists(outdir)) {
Expand Down Expand Up @@ -541,20 +541,20 @@ generateAllAlignments2FA <- function(aln_path = here("data/rawdata_aln/"),
reduced = F) {
# Check if the alignment path exists
if (!dir.exists(aln_path)) {
abort("Error: The alignment directory does not exist at the specified
abort("Error: The alignment directory does not exist at the specified
path: ", aln_path)
}

# Check if the output path exists; if not, attempt to create it
if (!dir.exists(fa_outpath)) {
dir.create(fa_outpath, recursive = TRUE)
message("Note: The output directory did not exist and has been created: ",
message("Note: The output directory did not exist and has been created: ",
fa_outpath)
}

# Check if the linear file exists
if (!file.exists(lin_file)) {
abort("Error: The linear file does not exist at the specified path: ",
abort("Error: The linear file does not exist at the specified path: ",
lin_file)
}
# library(here)
Expand Down Expand Up @@ -626,7 +626,7 @@ acc2FA <- function(accessions, outpath, plan = "sequential") {
if (!is.character(accessions) || length(accessions) == 0) {
abort("Error: 'accessions' must be a non-empty character vector.")
}

if (!dir.exists(dirname(outpath))) {
abort("Error: The output directory does not exist: ", dirname(outpath))
}
Expand Down Expand Up @@ -676,7 +676,7 @@ acc2FA <- function(accessions, outpath, plan = "sequential") {
id = accessions_partitioned[[x]],
db = "protein",
rettype = "fasta",
#api_key = Sys.getenv("ENTREZ_API_KEY")
# api_key = Sys.getenv("ENTREZ_API_KEY")
)
)
})
Expand Down Expand Up @@ -732,21 +732,21 @@ acc2FA <- function(accessions, outpath, plan = "sequential") {
createRepresentativeAccNum <- function(prot_data,
reduced = "Lineage",
accnum_col = "AccNum") {

# Validate input
if (!is.data.frame(prot_data)) {
abort("Error: 'prot_data' must be a data frame.")
}

# Check if the reduced column exists in prot_data
if (!(reduced %in% colnames(prot_data))) {
abort("Error: The specified reduced column '", reduced, "' does not
abort("Error: The specified reduced column '", reduced, "' does not
exist in the data frame.")
}

# Check if the accnum_col exists in prot_data
if (!(accnum_col %in% colnames(prot_data))) {
abort("Error: The specified accession number column '", accnum_col, "'
abort("Error: The specified accession number column '", accnum_col, "'
does not exist in the data frame.")
}
# Get Unique reduced column and then bind the AccNums back to get one AccNum per reduced column
Expand Down Expand Up @@ -808,7 +808,7 @@ alignFasta <- function(fasta_file, tool = "Muscle", outpath = NULL) {
if (!file.exists(fasta_file)) {
abort("Error: The FASTA file does not exist: ", fasta_file)
}

# if (file_ext(fasta_file) != "fasta" && file_ext(fasta_file) != "fa") {
# abort("Error: The specified file is not a valid FASTA file: ", fasta_file)
# }
Expand Down Expand Up @@ -857,23 +857,23 @@ writeMSA_AA2FA <- function(alignment, outpath) {
if (!inherits(alignment, "AAMultipleAlignment")) {
abort("Error: The alignment must be of type 'AAMultipleAlignment'.")
}

# Check the output path is a character string
if (!is.character(outpath) || nchar(outpath) == 0) {
abort("Error: Invalid output path specified.")
}

# Check if the output directory exists
outdir <- dirname(outpath)
if (!dir.exists(outdir)) {
abort("Error: The output directory does not exist: ", outdir)
}

l <- length(names(unmasked(alignment)))
l <- length(names(unmasked((alignment))))
fasta <- ""
for (i in 1:l)
{
fasta <- paste0(fasta, paste(">", names(unmasked(alignment)[i])), "\n")
fasta <- paste0(fasta, paste(">", names(unmasked((alignment)))[i]), "\n")
seq <- toString(unmasked(alignment)[[i]])
fasta <- paste0(fasta, seq, "\n")
}
Expand Down Expand Up @@ -955,4 +955,4 @@ getAccNumFromFA <- function(fasta_file) {
# cfile <- read_delim("data/alignments/pspc.gismo.aln", delim=" ")
# cfile <- as.data.frame(map(cfile,function(x) gsub("\\s+", "",x)))
# colnames(cfile) <- c("AccNum", "Alignment")
# }
# }
6 changes: 3 additions & 3 deletions R/summarize.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -690,18 +690,18 @@ totalGenContextOrDomArchCounts <- function(prot, column = "DomArch", lineage_col
abort("Error: 'digits' must be a non-negative integer.")
}

column <- sym(column)
# column <- sym(column)

prot <- select(prot, {{ column }}, {{ lineage_col }}) %>%
filter(!is.na({{ column }}) & !is.na({{ lineage_col }})) %>%
filter({{ column }} != "")

prot <- summarizeByLineage(prot, column, by = lineage_col, query = "all")
col_count <- prot %>%
group_by({{ column }}) %>%
group_by(!!sym(column)) %>%
summarise(totalcount = sum(count))

total <- left_join(prot, col_count, by = as_string(column))
total <- left_join(prot, col_count, by = column)

sum_count <- sum(total$count)
total <- total %>%
Expand Down

0 comments on commit 9ce780b

Please sign in to comment.