# This script processes data.
# gene Ids
library("readr")
library("dplyr")
library("devtools")
# Download
# url <- "ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/annotation/geneIDs/c_elegans.PRJNA13758.current.geneIDs.txt.gz"
# tmp <- tempfile()
# download.file(url,tmp)
# gene_info <- readr::read_csv(gzfile(tmp), col_names = c("taxon","WBID","name","protein","live")) %>%
# dplyr::select(-taxon)
#
# gene_ids <- as.list(gene_info$name)
# names(gene_ids) <- gene_info$WBID
#
# save(gene_info, file = "data/gene_info.rda")
# save(gene_ids, file = "data/gene_ids.rda")
load("R/sysdata.rda")
# Strain Isotype File
strain_isotype <- data.table::fread("https://docs.google.com/spreadsheets/d/1V6YHzblaDph01sFDI8YK_fP0H7sVebHQTXypGdiQIjI/pub?output=tsv") %>%
dplyr::arrange(strain, isotype)
# Create Strain --> Isotype Table
strain_isotype_mapping <- dplyr::bind_rows(strain_isotype %>%
dplyr::select(previous_names, isotype) %>%
dplyr::filter(complete.cases(.), isotype != "") %>%
dplyr::mutate(previous_names = stringr::str_split(previous_names, "\\|")) %>%
tidyr::unnest(previous_names) %>%
dplyr::rename(strain = previous_names),
strain_isotype %>%
dplyr::select(strain, isotype) %>%
dplyr::filter(complete.cases(.), isotype != ""),
strain_isotype %>%
dplyr::select(strain, isotype) %>%
dplyr::mutate(strain = isotype)
) %>%
dplyr::distinct() %>%
dplyr::select(strain, isotype)
vcf_version <- 20180527
vcf_version_d <- "2018-05-27"
wb_build <- 245
vcf_path <- paste0("~/Dropbox/Andersenlab/Reagents/WormReagents/_SEQ/WI/WI-", vcf_version_d, "/vcf/impute.", vcf_version, ".vcf.gz")
kinship <- generate_kinship(vcf_path)
snps <- generate_mapping(vcf_path)
# Save Datasets
devtools::use_data(kinship, snps, strain_isotype, mapping_snps, gene_ids, wb_build, strain_isotype_mapping, internal = F, overwrite = T)
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