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