scripts/parse_intergenic_regions.R

# 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")