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library(tidyverse)
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, "_.*")) %>%
replace_na(list(conditions = "none"))
gff_with_conditions_tss <- gff_with_conditions %>%
filter(seqnames != "chrM") %>%
mutate(fiveprime_loc = ifelse(strand == "+", start, end)) %>%
group_by(locus_tag) %>%
reframe(
seqnames = unique(seqnames),
strand = unique(strand),
cds_start = ifelse(
any(type == "CDS"),
ifelse(
unique(strand) == "+",
min(start[type == "CDS"], na.rm = TRUE),
max(end[type == "CDS"], na.rm = TRUE)
),
NA_integer_
),
tss_ypd = ifelse(
any(type == "mRNA" & conditions == "YPD"),
fiveprime_loc[type == "mRNA" & conditions == "YPD"][1],
NA_integer_
),
tss_gal = ifelse(
any(type == "mRNA" & conditions == "GAL"),
fiveprime_loc[type == "mRNA" & conditions == "GAL"][1],
NA_integer_
)
) %>%
pivot_longer(-c(locus_tag, seqnames, strand, cds_start), names_to = "conditions", values_to = "tss") %>%
mutate(inferred = is.na(tss),
five_utr_width = abs(cds_start-tss)) %>%
mutate(avg_5utr_width_across_conds = median(five_utr_width, na.rm=TRUE)) %>%
group_by(conditions) %>%
mutate(avg_5utr_width_in_conds = median(five_utr_width, na.rm=TRUE)) %>%
mutate(tss = case_when(
is.na(tss) & strand == "+" ~ cds_start - avg_5utr_width_in_conds,
is.na(tss) & strand == "-" ~ cds_start + avg_5utr_width_in_conds,
.default = tss
)) %>%
ungroup() %>%
mutate(five_utr_width = abs(cds_start-tss)) %>%
mutate(source = "sgd-5-1")
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
gff_with_conditions_tss %>%
select(locus_tag) %>%
distinct() %>%
filter(!locus_tag %in% orf_classifications_tmp$locus_tag) %>%
select(locus_tag) %>%
left_join(
gff %>%
as_tibble() %>%
filter(type %in% c("transposable_element_gene", "blocked_reading_frame")) %>%
select(ID, type, display), by = c("locus_tag" = "ID")) %>%
select(locus_tag, type) %>% dplyr::rename(orf_classification = type)
)
gff_with_conditions_tss_complete_orf_classification = gff_with_conditions_tss %>%
left_join(orf_classifications_complete)
create_condition_specific_tss = function(df, sel_cond){
gr = makeGRangesFromDataFrame(
df %>%
filter(conditions == sel_cond) %>%
dplyr::rename(name = locus_tag),
keep.extra.columns = TRUE,
seqnames.field = "seqnames",
start.field = "tss",
end.field = "tss",
strand.field = "strand")
suppressWarnings(seqinfo(gr) <- seqinfo(BSgenome.Scerevisiae.UCSC.sacCer3))
message("trimming in order to avoid out of bounds locations on inferred TSS")
trim(gr)
}
median_across_conds_tss = gff_with_conditions_tss_complete_orf_classification %>%
select(locus_tag, seqnames, orf_classification,
strand, cds_start, avg_5utr_width_across_conds) %>%
distinct() %>%
mutate(tss = ifelse(strand == "+",
cds_start - avg_5utr_width_across_conds,
cds_start + avg_5utr_width_across_conds)) %>%
mutate(conditions = "median_utr_across_conds")
tss_gr_list = list(
ypd = create_condition_specific_tss(gff_with_conditions_tss_complete_orf_classification, "tss_ypd"),
gal = create_condition_specific_tss(gff_with_conditions_tss_complete_orf_classification, "tss_gal"),
median_across_conds_tss_gr = create_condition_specific_tss(median_across_conds_tss,
"median_utr_across_conds")
)
rtracklayer::export(tss_gr_list$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")
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