Merge branch 'master' of https://github.com/rsa-tools/rsat-code

R-scripts/motif_databases/RSAT_motif_DB_table.R

@@ -0,0 +1,111 @@
+#############################
+## Load required libraries ##
+#############################
+
+## List of packages to install from CRAN
+required.packages = c("dplyr",
+                      "gt", 
+                      "lubridate",
+                      "optparse")
+
+for (lib in required.packages) {
+  suppressPackageStartupMessages(library(lib, character.only = TRUE, quietly = TRUE))
+}
+
+
+option_list = list(
+
+  make_option(c("-m", "--motif_table"), type = "character", default = NULL, 
+              help = "RSAT motif DB table: $RSAT/public_html/motif_databases/db_matrix_files.tab (Mandatory). ", metavar = "character"),
+
+  make_option(c("-o", "--output_folder"), type = "character", default = NULL, 
+              help = "Folder to save the results (Mandatory)", metavar = "character")
+);
+
+message("; Reading arguments from command-line")
+opt_parser = OptionParser(option_list = option_list);
+opt = parse_args(opt_parser);
+
+
+## Output file prefix
+rsat.motif.db.file <- opt$motif_table
+output.folder      <- opt$output_folder
+
+dir.create(output.folder, recursive = TRUE, showWarnings = FALSE)
+
+## Example: Rscript $RSAT/R-scripts/motif_databases/RSAT_motif_DB_table.R -m /home/rsat/packages/rsat-2021/rsat/public_html/motif_databases/db_matrix_files.tab -o $RSAT/public_html/motif_databases
+# rsat.motif.db.file <- "db_matrix_files.tab"
+# output.folder      <- "."
+
+
+###############
+## Functions ##
+###############
+
+count.motifs.in.db <- function(motif.collection.lines = NULL) {
+
+  ## All motifs are in transfac, se we count the number of separators
+  return(sum(grepl(motif.collection.lines, pattern = "^//\\s*$")))
+}
+
+
+##########
+## Main ##
+##########
+message("; Reading RSAT DB table: ", rsat.motif.db.file)
+rsat.motif.db.tab <- read.table(rsat.motif.db.file, header = TRUE, comment.char = ";", sep = "\t") %>%
+  rename(Collection  = X.COLLECTION,
+         Format      = FORMAT,
+         File        = FILE,
+         Description = DESCR,
+         Version     = VERSION,
+         Category    = CATEGORY,
+         DataBase    = DATABASE)
+
+
+## Read the tf files
+rsat.motif.db.content <- purrr::map(.x = as.vector(rsat.motif.db.tab$File),
+                                    .f = ~readLines(con = .x))
+
+## Count the number of motifs per collection
+## We count the number of separators '//' in each file
+message("; Counting motifs in each collection")
+rsat.motif.db.nb.motifs <- purrr::map_dbl(.x = rsat.motif.db.content,
+                                          .f = ~count.motifs.in.db(motif.collection.lines = .x))
+
+rsat.motif.db.tab$Nb_motifs <- rsat.motif.db.nb.motifs
+
+rsat.motif.db.tab <- rsat.motif.db.tab %>% 
+                      arrange(Category, desc(Nb_motifs))
+
+## Export table as a text file
+write.table(rsat.motif.db.tab, file = file.path(output.folder, "RSAT_motif_DB_table.tab"), quote = FALSE, sep = "\t", row.names = FALSE, col.names = TRUE)
+
+
+## Export html document
+message("; Generating html file")
+rsat.motif.db.tab %>%
+  select(Category, DataBase, Collection, Version, Description, Nb_motifs, URL) %>% 
+  group_by(Category) %>% 
+  gt(rowname_col = "DataBase") %>%
+  tab_header(
+    title    = md(paste0("Motif collections in RSAT by ", today())),
+    subtitle = md(paste0("List of the ", nrow(rsat.motif.db.tab), " motif collections integrated in RSAT."))) %>% 
+  data_color(
+    columns = Nb_motifs,
+    colors = scales::col_numeric(palette = c("white", "yellow", "darkred"),
+                                 domain = range(Nb_motifs))) %>% 
+  # tab_spanner_delim(delim = ".") %>% 
+  cols_align(align = "center") %>%
+  tab_options(
+    table.width = pct(100),
+    row_group.as_column = TRUE
+  ) %>% 
+  grand_summary_rows(
+    columns = c(Nb_motifs),
+    fns = list(Total = ~sum(.)),
+    formatter = fmt_number,
+    decimal = 0,
+    use_seps  = TRUE
+  ) %>% 
+  gtsave(file.path(output.folder, "RSAT_motif_DB_table.html"))

contrib/matrix-scan-quick/main.cpp

@@ -25,14 +25,6 @@ using namespace std;
 #include "seq.h"
 #include "dist.h"
 #include "pval.h"
-#include "dist.cpp"
-#include "markov.cpp"
-#include "matrix.cpp"
-#include "pval.cpp"
-#include "scan.cpp"
-#include "seq.cpp"
-#include "utils.cpp"
-#include "cfasta.cpp"
 
 int VERSION = 20160208;
 char *COMMAND_LINE;