| library(tidyverse) |
| library(arrow) |
| library(here) |
| library(yaml) |
|
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| |
| |
| multiqc_chec_config = yaml::read_yaml("data/mahendrawada_multiqc_config.yml") |
| chec_meta <- map_dfr(multiqc_chec_config$sample_names_rename, |
| ~tibble(!!!setNames(., multiqc_chec_config$sample_names_rename_buttons))) |
|
|
| genetable = arrow::read_parquet("~/code/hf/yeast_genome_resources/brentlab_features.parquet") |
|
|
| parsed_chec_meta = chec_meta %>% |
| mutate(mahendrawada_symbol = str_remove(`sample_description"`, "_\\w_ChEC-seq"), |
| replicate = str_remove_all(str_extract(`sample_description"`, "_(A|B|C)"), "_")) %>% |
| select(sample, mahendrawada_symbol, replicate) %>% |
| mutate(mahendrawada_symbol = str_remove(mahendrawada_symbol, "_(A|B|C)$")) %>% |
| mutate( |
| condition = str_remove(str_extract(mahendrawada_symbol, "_.*"), "^_"), |
| mahendrawada_symbol = toupper(str_remove(mahendrawada_symbol, "_.*"))) %>% |
| replace_na(list(condition = "standard")) %>% |
| mutate(condition = str_remove(condition, "_(A|B|C)_S\\d+_L001")) %>% |
| mutate(tmp_m_symbol = case_when( |
| mahendrawada_symbol == "MED15" ~ "GAL11", |
| mahendrawada_symbol == "YNR063W" ~ "PUL4", |
| .default = mahendrawada_symbol |
| )) %>% |
| left_join( |
| select(genetable, locus_tag, symbol) %>% |
| dplyr::rename(tmp_m_symbol = symbol, |
| regulator_locus_tag = locus_tag)) %>% |
| dplyr::rename(regulator_symbol = tmp_m_symbol) %>% |
| mutate(regulator_locus_tag = case_when( |
| regulator_symbol == "FREEMNASE" ~ "FREEMNASE", |
| .default = regulator_locus_tag)) %>% |
| dplyr::rename(sra_accession = sample) |
|
|
| parsed_chec_meta_with_ids = parsed_chec_meta %>% |
| filter(regulator_symbol != "FREEMNASE") %>% |
| mutate(replicate = factor(replicate, levels = c("A", "B", "C"))) %>% |
| arrange(regulator_locus_tag, condition, replicate) %>% |
| group_by(regulator_locus_tag, condition) %>% |
| mutate(sample_id = cur_group_id()) %>% |
| ungroup() %>% |
| mutate(replicate = as.character(replicate)) |
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| |
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| annotated_feature_meta = parsed_chec_meta_with_ids %>% |
| select(regulator_locus_tag, regulator_symbol, condition, sample_id) %>% |
| distinct() |
|
|
| freemnase_meta = parsed_chec_meta %>% |
| filter(regulator_symbol == "FREEMNASE") %>% |
| mutate(replicate = factor(replicate, levels = c("A", "B", "C"))) %>% |
| arrange(regulator_locus_tag, condition, replicate) %>% |
| group_by(regulator_locus_tag, condition) %>% |
| mutate(sample_id = cur_group_id() + max(parsed_chec_meta_with_ids$sample_id)) %>% |
| ungroup() %>% |
| mutate(replicate = as.character(replicate)) %>% |
| select(sra_accession, replicate, condition) |
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| |
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|
| mahendrawada_genome_map_bed = list.files("~/code/hf/mahendrawada_2025/chec_genome_map_bed", ".bed$") |
|
|
| mahendrawada_genome_map = map( |
| mahendrawada_genome_map_bed, |
| ~read_tsv(file.path("~/code/hf/mahendrawada_2025/chec_genome_map_bed", .), |
| col_names = c("chr", "start", "end", "name", "score", "strand")) |
| ) |
|
|
| names(mahendrawada_genome_map) = str_remove(mahendrawada_genome_map_bed, "_REP1.mLb.mkD.sorted_5p.bed") |
|
|
| mahendrawada_genome_map_df = bind_rows( |
| mahendrawada_genome_map, |
| .id = 'sra_accession') |
|
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| rm(mahendrawada_genome_map) |
| gc() |
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