| library(httr) | |
| library(jsonlite) | |
| library(tidyverse) | |
| ## TODO: this uses the rossi metadata that already existed. That will eventually | |
| ## be removed. This needs to be created from the yeastepigenome pull below, | |
| ## and the data from the getGEO directly | |
| # Fetch all samples from the API | |
| response <- GET("https://odin.cac.cornell.edu/yep_api/reviewSamples") | |
| # Parse the JSON response | |
| samples_data <- content(response, "text", encoding = "UTF-8") %>% | |
| fromJSON(flatten = TRUE) | |
| # Convert to tibble | |
| # The data comes as a named list with numeric indices as names | |
| yeastepigenome_sample_df <- samples_data %>% | |
| map_df(~as_tibble(.), .id = "index") %>% | |
| select(sampleId, assayType, treatments, growthMedia, antibody) %>% | |
| dplyr::rename(yeastepigenome_id = sampleId, | |
| assay_type = assayType, | |
| treatment = treatments, | |
| growth_media = growthMedia) | |
| rossi_meta = arrow::read_parquet("~/code/hf/rossi_2021/deprecated_rossi_2021_metadata.parquet") | |
| rossi_meta_with_addtl = rossi_meta %>% | |
| left_join(yeastepigenome_sample_df) %>% | |
| filter(!run_accession %in% c('SRR11466887', 'SRR11466891')) %>% | |
| bind_rows( | |
| tibble( | |
| regulator_locus_tag = c("YNL076W", "YGL244W"), | |
| regulator_symbol = c("MKS1", "RTF1"), | |
| run_accession = c("SRR11466887", "SRR11466891"), | |
| yeastepigenome_id = c(14846, 12031), | |
| assay_type = "ChIP-exo", | |
| treatment = "Normal", | |
| growth_media = "YPD", | |
| antibody = c("HA-tag: Santa Cruz sc-7392", "TAP-tag: Sigma i5006"))) %>% | |
| arrange(regulator_locus_tag) %>% | |
| select(-assay_type) %>% | |
| group_by(regulator_locus_tag, treatment, growth_media) %>% | |
| mutate(sample_id = cur_group_id()) %>% | |
| ungroup() | |
| # arrow::write_parquet( | |
| # rossi_meta_with_addtl, | |
| # "~/code/hf/rossi_2021/rossi_2021_metadata.parquet", | |
| # compression = "zstd", | |
| # write_statistics = TRUE, | |
| # use_dictionary = c( | |
| # sample_id = TRUE, | |
| # regulator_locus_tag=TRUE, | |
| # regulator_symbol = TRUE, | |
| # treatment = TRUE, | |
| # growth_media = TRUE)) | |
| # NOTE: the following works, but is currently unused | |
| # | |
| # library(GEOquery) | |
| # library(tidyverse) | |
| # | |
| # # Get the GEO series data | |
| # gse <- getGEO("GSE147927", GSEMatrix = FALSE) | |
| # sample_list <- GSMList(gse) | |
| # | |
| # # Helper function for NULL coalescing | |
| # `%||%` <- function(x, y) if (is.null(x)) y else x | |
| # | |
| # # Extract sample metadata | |
| # extract_sample_metadata_robust <- function(gsm) { | |
| # meta <- Meta(gsm) | |
| # | |
| # # Start with basic info | |
| # result <- tibble( | |
| # gsm_id = meta$geo_accession %||% NA, | |
| # title = meta$title %||% NA, | |
| # source_name = meta$source_name_ch1 %||% NA, | |
| # organism = meta$organism_ch1 %||% NA | |
| # ) | |
| # | |
| # # Extract characteristics from the 'characteristics_ch1' field | |
| # if (!is.null(meta$characteristics_ch1)) { | |
| # for (char in meta$characteristics_ch1) { | |
| # # Split on first colon | |
| # parts <- str_split(char, ":\\s*", n = 2)[[1]] | |
| # if (length(parts) == 2) { | |
| # char_name <- parts[1] | |
| # char_value <- parts[2] | |
| # result[[char_name]] <- char_value | |
| # } | |
| # } | |
| # } | |
| # | |
| # # Add protocols | |
| # result$treatment_protocol <- paste(meta$treatment_protocol_ch1, collapse = " ") %||% NA | |
| # result$growth_protocol <- paste(meta$growth_protocol_ch1, collapse = " ") %||% NA | |
| # result$extract_protocol <- paste(meta$extract_protocol_ch1, collapse = " ") %||% NA | |
| # | |
| # # Add library info | |
| # result$library_strategy <- meta$library_strategy %||% NA | |
| # result$library_source <- meta$library_source %||% NA | |
| # result$library_selection <- meta$library_selection %||% NA | |
| # result$instrument_model <- meta$instrument_model %||% NA | |
| # | |
| # # Add data processing | |
| # result$data_processing <- paste(meta$data_processing, collapse = " | ") %||% NA | |
| # | |
| # # Extract SRA accession | |
| # relations <- meta$relation | |
| # sra_relation <- relations[grepl("SRA", relations)] | |
| # if (length(sra_relation) > 0) { | |
| # result$sra_accession <- str_extract(sra_relation, "SR[XR]\\d+") | |
| # } else { | |
| # result$sra_accession <- NA | |
| # } | |
| # | |
| # return(result) | |
| # } | |
| # | |
| # # Apply to all samples | |
| # all_samples_metadata <- map_df(sample_list, extract_sample_metadata_robust) | |
| # | |
| # # View results | |
| # glimpse(all_samples_metadata) | |