| | library(tidyverse) |
| | library(arrow) |
| | library(here) |
| | library(yaml) |
| |
|
| | |
| | |
| | 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)$")) %>% |
| | mutate( |
| | condition = str_remove(str_extract(mahendrawada_symbol, "_.*"), "^_"), |
| | mahendrawada_symbol = toupper(str_remove(mahendrawada_symbol, "_.*"))) %>% |
| | replace_na(list(condition = "standard")) %>% |
| | mutate(condition = str_remove(condition, "_(A|B|C)_S\\d+_L001")) %>% |
| | mutate(tmp_m_symbol = case_when( |
| | mahendrawada_symbol == "MED15" ~ "GAL11", |
| | mahendrawada_symbol == "YNR063W" ~ "PUL4", |
| | .default = mahendrawada_symbol |
| | )) %>% |
| | left_join( |
| | select(genetable, locus_tag, symbol) %>% |
| | dplyr::rename(tmp_m_symbol = symbol, |
| | regulator_locus_tag = locus_tag)) %>% |
| | dplyr::rename(regulator_symbol = tmp_m_symbol) %>% |
| | mutate(regulator_locus_tag = case_when( |
| | regulator_symbol == "FREEMNASE" ~ "FREEMNASE", |
| | .default = regulator_locus_tag)) %>% |
| | dplyr::rename(sra_accession = sample) |
| |
|
| | parsed_chec_meta_with_ids = parsed_chec_meta %>% |
| | filter(regulator_symbol != "FREEMNASE") %>% |
| | mutate(replicate = factor(replicate, levels = c("A", "B", "C"))) %>% |
| | arrange(regulator_locus_tag, condition, replicate) %>% |
| | group_by(regulator_locus_tag, condition) %>% |
| | mutate(sample_id = cur_group_id()) %>% |
| | ungroup() %>% |
| | mutate(replicate = as.character(replicate)) |
| |
|
| | |
| |
|
| | annotated_feature_meta = parsed_chec_meta_with_ids %>% |
| | select(regulator_locus_tag, regulator_symbol, condition, sample_id) %>% |
| | distinct() |
| |
|
| | freemnase_meta = parsed_chec_meta %>% |
| | filter(regulator_symbol == "FREEMNASE") %>% |
| | mutate(replicate = factor(replicate, levels = c("A", "B", "C"))) %>% |
| | arrange(regulator_locus_tag, condition, replicate) %>% |
| | group_by(regulator_locus_tag, condition) %>% |
| | mutate(sample_id = cur_group_id() + max(parsed_chec_meta_with_ids$sample_id)) %>% |
| | ungroup() %>% |
| | mutate(replicate = as.character(replicate)) %>% |
| | select(sra_accession, replicate, condition) |
| |
|
| | |
| |
|
| | 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') |
| |
|
| | rm(mahendrawada_genome_map) |
| | gc() |
| |
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