adding additional promoters

README.md

@@ -57,7 +57,40 @@ You can find these by clicking on the [files and versions](https://huggingface.c
 - **chrmap** (csv): This file provides a mapping between chromosome names between, eg
   UCSC, ensembl, etc.
 
-## Usage
+## Accessing Data
 
-Currently, we expect that this will be used for its raw files, eg by downloading a given
-file and opening it in your favorite program.
+The examples below require the
+[HuggingFace Hub client](https://huggingface.co/docs/huggingface_hub/installation)
+(`pip install huggingface_hub`).
+
+Currently, we expect that this will be used for its raw files. Download
+individual files and open them in your preferred tool.
+
+### Direct parquet access
+
+```python
+from huggingface_hub import snapshot_download
+import duckdb
+
+repo_path = snapshot_download(
+    repo_id="BrentLab/yeast_genome_resources",
+    repo_type="dataset",
+    allow_patterns="brentlab_features.parquet",
+)
+conn = duckdb.connect()
+# returns a pandas DataFrame with the first 5 rows
+conn.execute(
+    "SELECT * FROM read_parquet(?) LIMIT 5",
+    [f"{repo_path}/brentlab_features.parquet"],
+).df()
+```
+
+### Accessing using R
+
+Clone the repository and read parquet files directly with
+[arrow](https://arrow.apache.org/docs/r/):
+
+```r
+# install.packages("arrow")
+arrow::read_parquet("brentlab_features.parquet")
+```

scripts/create_promoter_bed_from_mindel.R

@@ -154,4 +154,4 @@ promoter_coordinates_final = promoter_coordinates_df %>%
            strand, promoter_sequence,
            in_mahendrawada_features, promoter_exact_aligns)
 
-write_csv(promoter_coordinates_final, "~/code/hf/yeast_genome_resources/mindel_promoters.csv.gz")
+# write_csv(promoter_coordinates_final, "~/code/hf/yeast_genome_resources/mindel_promoters.csv.gz")

scripts/create_promoter_regions.R

@@ -6,6 +6,7 @@ library(BSgenome.Scerevisiae.UCSC.sacCer3)
 # half open. GRanges parses and represents the interval differently than what is
 # in the actual file
 tss_list = list(
+  start_codon = rtracklayer::import("~/code/hf/yeast_genome_resources/start_codon_verified_orf.bed"),
   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")
@@ -13,6 +14,7 @@ tss_list = list(
 
 # Fix: need to assign the result back and return the modified object
 tss_list = map(tss_list, ~{
+  seqlevels(.x) <- seqlevels(BSgenome.Scerevisiae.UCSC.sacCer3)
   seqinfo(.x) <- seqinfo(BSgenome.Scerevisiae.UCSC.sacCer3)
   .x  # Return the modified GRanges object
 })
@@ -40,8 +42,8 @@ seqinfo(intergenic_regions_sgd) <- seqinfo(BSgenome.Scerevisiae.UCSC.sacCer3)
 #'   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 
+#'   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
@@ -61,56 +63,59 @@ seqinfo(intergenic_regions_sgd) <- seqinfo(BSgenome.Scerevisiae.UCSC.sacCer3)
 #'
 #' # Get only intergenic promoters
 #' promoters_intergenic <- get_promoter_regions(
-#'   tss_gr, 
+#'   tss_gr,
 #'   intergenic_gr = intergenic_regions,
-#'   upstream = 500, 
+#'   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" = 
+    "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, 
+    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)
-
+# promoters_500_50_intergenic = map(tss_list, get_promoter_regions, intergenic_regions_sgd)
+# promoters_500_50 = map(tss_list, get_promoter_regions)
 
+# promoters_start_codons_500bp = get_promoter_regions(tss_list$start_codon, upstream=500, downstream=0)
+# promoters_start_codons_500bp <- promoters_start_codons_500bp[width(promoters_start_codons_500bp) == 500]
+# rtracklayer::export(promoters_start_codons_500bp,
+#                     "~/code/hf/yeast_genome_resources/start_codon_500bp_upstream_promoters.bed")
 

scripts/create_tss_files.R

@@ -3,12 +3,12 @@ library(BSgenome.Scerevisiae.UCSC.sacCer3)
 library(rtracklayer)
 
 gff = rtracklayer::import("~/ref/sacCer3/S288C_reference_genome_R64-5-1_20240529/saccharomyces_cerevisiae_R64-5-1_20240529_chr_normalized.gtf")
- 
-gff_with_conditions = gff %>% 
-  as_tibble() %>% 
-  select(seqnames, start, end, strand, type, Name, conditions) %>% 
-  filter(type %in% c("gene", "mRNA", "CDS")) %>% 
-  mutate(locus_tag = str_remove(Name, "_.*")) %>% 
+
+gff_with_conditions = gff %>%
+  as_tibble() %>%
+  select(seqnames, start, end, strand, type, Name, conditions) %>%
+  filter(type %in% c("gene", "mRNA", "CDS")) %>%
+  mutate(locus_tag = str_remove(Name, "_.*")) %>%
   replace_na(list(conditions = "none"))
 
 gff_with_conditions_tss <- gff_with_conditions %>%
@@ -53,12 +53,12 @@ gff_with_conditions_tss <- gff_with_conditions %>%
   mutate(five_utr_width = abs(cds_start-tss)) %>%
   mutate(source = "sgd-5-1")
 
-orf_classifications_tmp = gff %>% 
-  as_tibble() %>% 
+orf_classifications_tmp = gff %>%
+  as_tibble() %>%
   filter(type == "gene", !is.na(orf_classification)) %>%
   select(Name, orf_classification) %>%
   dplyr::rename(locus_tag = Name)
-  
+
 orf_classifications_complete = orf_classifications_tmp %>%
   bind_rows(
     # the na orf_classifications
@@ -77,7 +77,7 @@ orf_classifications_complete = orf_classifications_tmp %>%
 
 gff_with_conditions_tss_complete_orf_classification = gff_with_conditions_tss %>%
   left_join(orf_classifications_complete)
-  
+
 
 create_condition_specific_tss = function(df, sel_cond){
   gr = makeGRangesFromDataFrame(
@@ -89,7 +89,7 @@ create_condition_specific_tss = function(df, sel_cond){
       start.field = "tss",
       end.field = "tss",
       strand.field = "strand")
-  
+
   suppressWarnings(seqinfo(gr) <- seqinfo(BSgenome.Scerevisiae.UCSC.sacCer3))
   message("trimming in order to avoid out of bounds locations on inferred TSS")
   trim(gr)
@@ -111,12 +111,22 @@ tss_gr_list = list(
                                                            "median_utr_across_conds")
 )
 
-rtracklayer::export(tss_gr_list$ypd, "~/code/hf/yeast_genome_resources/ypd_tss_sgd-5-1.bed")
-rtracklayer::export(tss_gr_list$gal, "~/code/hf/yeast_genome_resources/gal_tss_sgd-5-1.bed")
-rtracklayer::export(tss_gr_list$median_across_conds_tss_gr, "~/code/hf/yeast_genome_resources/median_across_conds_tss_sgd-5-1.bed")
-
-rtracklayer::export(tss_gr_list$ypd[tss_gr_list$ypd$orf_classification=="Verified"], "~/code/hf/yeast_genome_resources/ypd_tss_sgd-5-1_verified_orf.bed")
-
-rtracklayer::export(tss_gr_list$gal[tss_gr_list$gal$orf_classification=="Verified"], "~/code/hf/yeast_genome_resources/gal_tss_sgd-5-1_verified_orf.bed")
-
-rtracklayer::export(tss_gr_list$median_across_conds_tss_gr[tss_gr_list$median_across_conds_tss_gr$orf_classification=="Verified"], "~/code/hf/yeast_genome_resources/median_across_conds_tss_sgd-5-1_verified_orf.bed")
+# create the ORF start cocon locations
+# read_csv("~/code/hf/yeast_genome_resources/brentlab_features.csv.gz") |>
+#     filter(type == 'gene', str_detect(note, regex("dubious", ignore_case=TRUE), negate=TRUE)) |>
+#     mutate(orf = ifelse(strand == "-", end, start)) |>
+#     mutate(score = 100) |>
+#     dplyr::select(seqnames=chr, start=orf, end = orf, name=locus_tag, score, strand) |>
+#     GenomicRanges::GRanges() |>
+#     rtracklayer::export("~/code/hf/yeast_genome_resources/start_codon_verified_orf.bed")
+#
+#
+# rtracklayer::export(tss_gr_list$ypd, "~/code/hf/yeast_genome_resources/ypd_tss_sgd-5-1.bed")
+# rtracklayer::export(tss_gr_list$gal, "~/code/hf/yeast_genome_resources/gal_tss_sgd-5-1.bed")
+# rtracklayer::export(tss_gr_list$median_across_conds_tss_gr, "~/code/hf/yeast_genome_resources/median_across_conds_tss_sgd-5-1.bed")
+#
+# rtracklayer::export(tss_gr_list$ypd[tss_gr_list$ypd$orf_classification=="Verified"], "~/code/hf/yeast_genome_resources/ypd_tss_sgd-5-1_verified_orf.bed")
+#
+# rtracklayer::export(tss_gr_list$gal[tss_gr_list$gal$orf_classification=="Verified"], "~/code/hf/yeast_genome_resources/gal_tss_sgd-5-1_verified_orf.bed")
+#
+# rtracklayer::export(tss_gr_list$median_across_conds_tss_gr[tss_gr_list$median_across_conds_tss_gr$orf_classification=="Verified"], "~/code/hf/yeast_genome_resources/median_across_conds_tss_sgd-5-1_verified_orf.bed")

scripts/get_promoter_seqs.R

@@ -0,0 +1,42 @@
+library(GenomicRanges)
+library(rtracklayer)
+library(BSgenome)
+library(BSgenome.Scerevisiae.UCSC.sacCer3)
+library(tidyverse)
+
+saccer3 <- BSgenome.Scerevisiae.UCSC.sacCer3
+
+promoters <- rtracklayer::import("~/code/hf/yeast_genome_resources/yiming_promoters.bed")
+promoters_unique <- promoters[!duplicated(paste(seqnames(promoters), start(promoters), end(promoters), strand(promoters)))]
+promoter_seqs <- BSgenome::getSeq(saccer3, promoters_unique)
+
+# Genome-wide base frequencies (all nuclear chromosomes, both strands balanced so +/- cancel)
+genome_seqs <- BSgenome::getSeq(saccer3, seqnames(saccer3))
+genome_freq <- Biostrings::alphabetFrequency(genome_seqs, as.prob = FALSE)
+genome_freq_acgt <- colSums(genome_freq[, c("A", "C", "G", "T")])
+genome_prop <- genome_freq_acgt / sum(genome_freq_acgt)
+
+genome_df <- tibble(
+    basepair = names(genome_prop),
+    freq = genome_prop
+)
+
+# Promoter position frequency matrix
+cm <- Biostrings::consensusMatrix(promoter_seqs)
+pm <- prop.table(cm, margin = 2)
+pm_acgt <- pm[c("A", "C", "G", "T"), ]
+
+pm_acgt %>%
+    as_tibble(rownames = "basepair") %>%
+    pivot_longer(-basepair) %>%
+    mutate(name = as.numeric(str_remove(name, "V"))) %>%
+    filter(name <= 700) %>%
+    left_join(genome_df, by = "basepair") %>%
+    ggplot(aes(color = basepair)) +
+    geom_line(aes(name, value)) +
+    geom_hline(
+        data = genome_df,
+        aes(yintercept = freq, color = basepair),
+        linetype = "dashed"
+    ) +
+    labs(x = "position", y = "proportion")