Upload folder using huggingface_hub

scripts/create_promoter_regions.Rmd

@@ -0,0 +1,122 @@
+```{r setup}
+library(rtracklayer)
+library(GenomicRanges)
+library(BSgenome.Scerevisiae.UCSC.sacCer3)
+```
+
+```{r}
+# note that GRanges objects are 1 based closed intervals. The bed files are 0 based
+# half open. GRanges parses and represents the interval differently than what is
+# in the actual file
+tss_list = list(
+  gal = rtracklayer::import("~/code/hf/yeast_genome_resources/gal_tss_sgd-5-1_verified_orf.bed"),
+  ypd = rtracklayer::import("~/code/hf/yeast_genome_resources/ypd_tss_sgd-5-1_verified_orf.bed"),
+  median = rtracklayer::import("~/code/hf/yeast_genome_resources/median_across_conds_tss_sgd-5-1_verified_orf.bed")
+)
+
+# Fix: need to assign the result back and return the modified object
+tss_list = map(tss_list, ~{
+  seqinfo(.x) <- seqinfo(BSgenome.Scerevisiae.UCSC.sacCer3)
+  .x  # Return the modified GRanges object
+})
+
+intergenic_regions_sgd = rtracklayer::import("~/code/hf/yeast_genome_resources/intergenic_regions_5_1.bed")
+seqinfo(intergenic_regions_sgd) <- seqinfo(BSgenome.Scerevisiae.UCSC.sacCer3)
+```
+
+```{r}
+#' Create promoter regions from transcription start sites
+#'
+#' Generates promoter regions by extending upstream and downstream from TSS
+#' positions. Regions are trimmed to chromosome boundaries and can optionally be
+#' intersected with intergenic regions to ensure promoters are entirely within
+#' intergenic space.
+#'
+#' @param tss_gr A GRanges object containing transcription start site positions.
+#'   Must have seqinfo set for proper trimming.
+#' @param intergenic_gr Optional GRanges object containing intergenic regions.
+#'   If provided, promoters will be intersected with these regions, truncating
+#'   any portions that extend into annotated features. This is assumed to be
+#'   unstranded and the intersection ignores strand information while preserving
+#'   the original strand from the TSS/promoter regions.
+#' @param upstream Integer specifying the number of base pairs upstream of the TSS
+#'   to include in the promoter region. Default is 500.
+#' @param downstream Integer specifying the number of base pairs downstream of the TSS
+#'   to include in the promoter region. Default is 50.
+#'
+#' @return A GRanges object containing the promoter regions with preserved strand
+#'   information. If \code{intergenic_gr} is provided, promoters are truncated to 
+#'   only the portions overlapping intergenic regions. Promoters with no intergenic 
+#'   overlap are excluded.
+#'
+#' @details
+#' The function respects strand information: for positive strand features, upstream
+#' is towards lower coordinates; for negative strand features, upstream is towards
+#' higher coordinates. Promoter regions are trimmed to prevent extension beyond
+#' chromosome boundaries. When intersecting with intergenic regions, strand information
+#' from the original TSS is preserved in the output.
+#'
+#' @examples
+#' \dontrun{
+#' # Get all promoters
+#' tss_gr = rtracklayer::import("path/to/tss.bed")
+#' # for example, if these are yeast TSS
+#' seqinfo(tss_gr) = seqinfo(BSgenome.Scerevisiae.UCSC.sacCer3)
+#' promoters_all <- get_promoter_regions(tss_gr, upstream = 500, downstream = 50)
+#'
+#' # Get only intergenic promoters
+#' promoters_intergenic <- get_promoter_regions(
+#'   tss_gr, 
+#'   intergenic_gr = intergenic_regions,
+#'   upstream = 500, 
+#'   downstream = 50
+#' )
+#' }
+get_promoter_regions = function(tss_gr, intergenic_gr, upstream = 500, downstream = 50){
+  # Validate inputs
+  stopifnot(
+    "upstream must be a positive number" = upstream > 0,
+    "downstream must be a positive number" = downstream > 0,
+    "tss_gr must have seqinfo set for trimming" = 
+      !is.null(seqinfo(tss_gr)) && length(seqinfo(tss_gr)) > 0
+  )
+  
+  pr_regions = GenomicRanges::trim(
+    GenomicRanges::promoters(
+      tss_gr,
+      upstream = upstream,
+      downstream = downstream,
+      use.names = TRUE))
+  
+  # Optionally restrict to intergenic regions
+  if (!missing(intergenic_gr)) {
+    # Find which intergenic region contains each TSS
+    tss_to_intergenic <- GenomicRanges::findOverlaps(tss_gr, intergenic_gr, 
+                                       type = "within",
+                                       ignore.strand = TRUE,
+                                       select = "first")
+    
+    # Keep only promoters whose TSS is in an intergenic region
+    has_intergenic <- !is.na(tss_to_intergenic)
+    pr_regions <- pr_regions[has_intergenic]
+    intergenic_match <- intergenic_gr[tss_to_intergenic[has_intergenic]]
+    
+    # Manually clip to intergenic boundaries
+    new_starts <- IRanges::pmax(GenomicRanges::start(pr_regions),
+                                GenomicRanges::start(intergenic_match))
+    new_ends <- IRanges::pmin(GenomicRanges::end(pr_regions),
+                              GenomicRanges::end(intergenic_match))
+    
+    GenomicRanges::ranges(pr_regions) <- IRanges::IRanges(start = new_starts, end = new_ends)
+  }
+  
+  pr_regions
+}
+
+# example, the first truncating by intergenic regions, the second not
+promoters_500_50_intergenic = map(tss_list, get_promoter_regions, intergenic_regions_sgd)
+promoters_500_50 = map(tss_list, get_promoter_regions)
+
+
+```
+

scripts/parse_intergenic_regions.R

@@ -0,0 +1,81 @@
+# This code will:
+#
+#   1. **Create a BED file** (`intergenic_regions.bed`) with columns:
+#   - chromosome
+# - start (converted to 0-based for BED format)
+# - end
+# - name (ir_1, ir_2, ...)
+# - score (.)
+# - strand (.)
+#
+# 2. **Create a renamed FASTA** (`intergenic_regions_renamed.fasta`) where headers look like:
+#   ```
+# NOTE: the coordinate in the fasta are 1-based. Bed files are 0-based
+# >ir_1 A:802-1806, Chr I from 802-1806, Genome Release 64-5-1, between TEL01L and YAL068C
+
+library(tidyverse)
+library(Biostrings)
+
+# Read the FASTA file
+fasta_file <- "~/ref/sacCer3/S288C_reference_genome_R64-5-1_20240529/NotFeature.fasta.gz"
+seqs <- readDNAStringSet(fasta_file)
+
+# Parse the headers
+headers <- names(seqs)
+
+# Create a tibble with parsed information
+parsed_data <- tibble(header = headers) %>%
+  mutate(
+    # Extract chromosome - now includes Mito
+    chr = str_extract(header, "Chr ([IVX]+|Mito)", group = 1),
+    # Standardize to use "chrM" for mitochondrial for BED format convention
+    chr = if_else(chr == "Mito", "chrM", paste0("chr", chr)),
+
+    # Extract the coordinate range (the part after "from")
+    coords = str_extract(header, "from (\\d+)-(\\d+)", group = 0),
+    start = as.integer(str_extract(coords, "from (\\d+)", group = 1)),
+    end = as.integer(str_extract(coords, "-(\\d+)", group = 1)),
+
+    # Extract features (between X and Y)
+    between = str_extract(header, "between (.+)$", group = 1),
+    feature_left = str_extract(between, "^([^ ]+)", group = 1),
+    feature_right = str_extract(between, "and (.+)$", group = 1),
+
+    # Extract genome release
+    genome_release = str_extract(header, "Genome Release ([^,]+)", group = 1),
+
+    # Create IR names
+    ir_name = paste0("ir_", row_number())
+  )
+
+# Create GRanges object (keeping 1-based coordinates)
+gr <- GRanges(
+  seqnames = parsed_data$chr,
+  ranges = IRanges(start = parsed_data$start, end = parsed_data$end),
+  strand = "*",
+  name = parsed_data$ir_name
+)
+
+# Export to BED. rtracklayer converts to 0-based half open intervals
+# export(gr, "~/code/hf/yeast_genome_resources/intergenic_regions_5_1.bed", format = "bed")
+
+# 2. Create modified FASTA with ir_X prefix
+new_headers <- paste(parsed_data$ir_name, headers)
+names(seqs) <- new_headers
+# writeXStringSet(seqs, "~/code/hf/yeast_genome_resources/intergenic_regions_5_1.fasta.gz")
+
+# 3. Create metadata file
+# NOTE: this is 1 based, closed intervals in the metadata
+metadata <- parsed_data %>%
+  select(
+    ir_name,
+    chr,
+    start,
+    end,
+    feature_left,
+    feature_right,
+    genome_release,
+    original_header = header
+  )
+
+# write_csv(metadata, "~/code/hf/yeast_genome_resources/intergenic_regions_metadata_5_1.csv")