Merge pull request #42 from josschavezf/devel

fix issue with database link

Author: josschavezf

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: regutools
 Title: regutools: an R package for data extraction from RegulonDB
 Version: 1.23.0
-Date: 2021-11-15
+Date: 2026-04-01
 Authors@R: c(
     person ("Joselyn", "Chavez", email =  "joselynchavezf@gmail.com",
         role = c("aut", "cre"), comment = c(ORCID = "0000-0002-4974-4591")),
@@ -35,7 +35,7 @@ Description: RegulonDB has collected, harmonized and centralized data
     to further our understanding of gene regulatory networks.
 License: Artistic-2.0
 Encoding: UTF-8
-Depends: R (>= 4.0)
+Depends: R (>= 4.5.0)
 Imports:
     AnnotationDbi,
     AnnotationHub,
@@ -51,8 +51,8 @@ Imports:
     stats,
     utils,
     BiocFileCache
-LazyData: true
-RoxygenNote: 7.1.1
+LazyData: false
+RoxygenNote: 7.3.3
 Suggests: 
     BiocStyle,
     knitr,

NEWS.md

@@ -1,3 +1,9 @@
+# regutools 1.23.0
+
+BUG FIXES
+
+* Fixed URL for the database
+
 # regutools 1.3.2
 
 SIGNIFICANT USER-VISIBLE CHANGES

R/build_condition.R

@@ -47,12 +47,14 @@
 #' @export
 
 build_condition <-
-    function(regulondb,
-    dataset,
-    filters,
-    operator,
-    interval,
-    partialmatch) {
+    function(
+      regulondb,
+      dataset,
+      filters,
+      operator,
+      interval,
+      partialmatch
+    ) {
         if (is(filters, "list")) {
             if (!all(names(filters) %in% list_attributes(regulondb, dataset))) {
                 non.existing.attrs.index <-

R/connect_database.R

@@ -26,8 +26,9 @@
 #' regulondb_conn_noAH <- connect_database(ah = NULL)
 connect_database <-
     function(
-    ah = AnnotationHub::AnnotationHub(),
-    bfc = BiocFileCache::BiocFileCache()) {
+      ah = AnnotationHub::AnnotationHub(),
+      bfc = BiocFileCache::BiocFileCache()
+    ) {
         if (!is.null(ah)) {
             ## Check input
             stopifnot(methods::is(ah, "AnnotationHub"))
@@ -50,13 +51,8 @@ connect_database <-
             }
         }
 
-
         ## Otherwise, use the Dropbox version and cache it with BiocFileCache
-        url <-
-            paste0(
-                "https://www.dropbox.com/s/ufp6wqcv5211v1w/",
-                "regulondb_v10.8_sqlite.db?dl=1"
-            )
+        url <- "https://github.com/ComunidadBioInfo/regutoolsData/raw/refs/heads/main/regulondb_v10.8_sqlite.db"
         destfile <- BiocFileCache::bfcrpath(bfc, url)
         AnnotationDbi::dbFileConnect(destfile)
     }

R/get_binding_sites.R

@@ -25,8 +25,10 @@
 #' ## Get the binding sites for AraC
 #' get_binding_sites(e_coli_regulondb, transcription_factor = "AraC")
 #' @export
-get_binding_sites <- function(regulondb, transcription_factor,
-    output_format = "GRanges") {
+get_binding_sites <- function(
+      regulondb, transcription_factor,
+      output_format = "GRanges"
+) {
     ## For a BiocCheck NOTE
     left <- right <- NULL
     if (!output_format %in% c("GRanges", "Biostrings")) {
@@ -49,7 +51,7 @@ get_binding_sites <- function(regulondb, transcription_factor,
         )
     tfbs_table <- strsplit(
         as.character(tfbs_table$res),
-        split =  "\t"
+        split = "\t"
     )
     tfbs_table <- as.data.frame(do.call(rbind, tfbs_table))
     colnames(tfbs_table) <-

R/get_dataset.R

@@ -63,14 +63,16 @@
 #' @importFrom S4Vectors DataFrame
 #' @importFrom Biostrings DNAStringSet BStringSet
 get_dataset <-
-    function(regulondb,
-    dataset = NULL,
-    attributes = NULL,
-    filters = NULL,
-    and = TRUE,
-    interval = NULL,
-    partialmatch = NULL,
-    output_format = "regulondb_result") {
+    function(
+      regulondb,
+      dataset = NULL,
+      attributes = NULL,
+      filters = NULL,
+      and = TRUE,
+      interval = NULL,
+      partialmatch = NULL,
+      output_format = "regulondb_result"
+    ) {
         # Check if format specification is valid
         if (!output_format %in% c(
             "regulondb_result",
@@ -244,8 +246,8 @@ get_dataset <-
 #' convert_to_granges(get_dataset(e_coli_regulondb, dataset = "GENE"))
 convert_to_granges <- function(regulondb_result) {
     if (!is(regulondb_result, "regulondb_result")) {
-          stop("The input is not a 'regulondb_result' object.")
-      }
+        stop("The input is not a 'regulondb_result' object.")
+    }
     dataset <- regulondb_result@dataset
     if (dataset %in% c("GENE", "DNA_OBJECTS")) {
         posLeft <- "posleft"
@@ -292,11 +294,11 @@ convert_to_granges <- function(regulondb_result) {
             DataFrame(regulondb_result[keep, !colnames(regulondb_result) %in%
                 c(posLeft, posRight, "strand"), drop = FALSE])
         if (sum(!keep) > 0) {
-              warning(sprintf(
-                  "Dropped %s entries where genomic coordinates were NAs",
-                  sum(!keep)
-              ))
-          }
+            warning(sprintf(
+                "Dropped %s entries where genomic coordinates were NAs",
+                sum(!keep)
+            ))
+        }
         grdata
     } else {
         stop(
@@ -349,11 +351,11 @@ convert_to_granges <- function(regulondb_result) {
 convert_to_biostrings <-
     function(regulondb_result, seq_type = "DNA") {
         if (!is(regulondb_result, "regulondb_result")) {
-              stop("The input is not a 'regulondb_result' object.")
-          }
+            stop("The input is not a 'regulondb_result' object.")
+        }
         if (!seq_type %in% c("DNA", "product")) {
-              stop("'seq_type' must be either 'DNA' or 'product'")
-          }
+            stop("'seq_type' must be either 'DNA' or 'product'")
+        }
         dataset <- regulondb_result@dataset
         if (dataset == "GENE") {
             if (seq_type == "DNA") {

R/get_dna_objects.R

@@ -16,8 +16,8 @@
 #' @examples
 #' ## Connect to the RegulonDB database if necessary
 #' if (!exists("regulondb_conn")) {
-#'       regulondb_conn <- connect_database()
-#'   }
+#'     regulondb_conn <- connect_database()
+#' }
 #'
 #' ## Build the regulondb object
 #' e_coli_regulondb <-
@@ -45,10 +45,12 @@
 #' )
 #' @export
 get_dna_objects <-
-    function(regulondb,
-    genome = "eschColi_K12",
-    grange = GRanges("chr", IRanges(1, 5000)),
-    elements = "gene") {
+    function(
+      regulondb,
+      genome = "eschColi_K12",
+      grange = GRanges("chr", IRanges(1, 5000)),
+      elements = "gene"
+    ) {
         valid_elements <- c(
             "-10 promoter box",
             "-35 promoter box",

R/get_gene_regulators.R

@@ -42,10 +42,12 @@
 #' @export
 
 get_gene_regulators <-
-    function(regulondb,
-    genes,
-    format = "multirow",
-    output.type = "TF") {
+    function(
+      regulondb,
+      genes,
+      format = "multirow",
+      output.type = "TF"
+    ) {
         stopifnot(validObject(regulondb))
         # Check genes parameter class
         ##        if (!class(genes) %in% c("vector", "list", "character")) {

R/get_gene_synonyms.R

@@ -32,10 +32,12 @@
 #' @export
 
 get_gene_synonyms <-
-    function(regulondb,
-    genes,
-    from = "name",
-    to = c("id", "name", "bnumber", "gi")) {
+    function(
+      regulondb,
+      genes,
+      from = "name",
+      to = c("id", "name", "bnumber", "gi")
+    ) {
         # Function checks
         stopifnot(validObject(regulondb))
 

R/get_regulatory_network.R

@@ -52,10 +52,12 @@
 #' setEdgeColorMapping setVisualStyle
 
 get_regulatory_network <-
-    function(regulondb,
-    regulator = NULL,
-    type = "TF-GENE",
-    cytograph = FALSE) {
+    function(
+      regulondb,
+      regulator = NULL,
+      type = "TF-GENE",
+      cytograph = FALSE
+    ) {
         # Check type parameter
         if (!type %in% c("GENE-GENE", "TF-GENE", "TF-TF")) {
             stop("Parameter 'type' must be TF-GENE, TF-TF, or GENE-GENE.",