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# 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")
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