R/old_functions/studies_to_db.R

In pedrostrusso/cemitooldb3:

library(GEOquery)
library(Biobase)
library(CEMiTool)
library(data.table)
library(RMySQL)
library(pool)
library(plyr)
library(rentrez)
library(XML)

gpl_ids <- get_gds_gpl_ids()
gpl_ids2 <- unique(gpl_ids)
gpl_id <- gpl_ids[1]
#gpl_id <- "GPL13158"
user_data <- get_user_data("prusso", "cemitooldb2", "127.0.0.1")
gmt_fname <- system.file("extdata", "pathways.gmt", package = "CEMiTool")
gmt_in <- CEMiTool::read_gmt(gmt_fname)
## Get example interactions file
int_df <- read.delim(system.file("extdata", "interactions.tsv", package = "CEMiTool"))
#gds_id <- "GDS651"
gds_studies <- c("GDS6177", "GDS651")
p <- list()
p$interactions <- int_df
p$gmt <- gmt_in

#gds_studies0 <- gds_studies
gds_studies <- gds_studies0
remove_studies <- dir(results_dir)
keep <- setdiff(gds_studies, remove_studies)
gds_studies <- keep

studies_to_db <- function(user_data,
                          gpl_id,
                          min_sample_num=18, max_sample_num=200,
                          results_dir="/home/prusso/Documents/CSBL/new_database/intermediate/CEMiTool",
                          verbose=TRUE, force=FALSE, ...){
    p <- list(...)
    p$verbose <- verbose
    results_dir <- file.path(results_dir, gpl_id)

    if(dir.exists(results_dir)){
        if(!force){
            stop("Stopping analysis: ", results_dir, " already exists! Use force=TRUE to overwrite")
        }
    }else{
        dir.create(results_dir, recursive=TRUE)
    }

    message("Getting studies for ", gpl_id)
    gds_studies <- get_gpl_related_gds(gpl_id, min_sample_num=min_sample_num,
                                       max_sample_num=max_sample_num, verbose=TRUE)
    if(identical(gds_studies, "GDS")){
        unlink(results_dir, recursive=TRUE)
        return(NULL)
    }
    if(verbose) message("Creating database link...")
    pool <- pool::dbPool(drv=RMySQL::MySQL(),
                         dbname=user_data$dbname,
                         host=user_data$host,
                         user=user_data$user,
                         password=user_data$password)

    for(gds_id in gds_studies){

        if(verbose) message("Study ", which(gds_studies == gds_id), " of ", length(gds_studies))
        if(verbose) message("Getting data from GEO for study ", gds_id)
        possible_error <- tryCatch(gds <- get_gds(gds_id),
                                   error=function(e) e)
        if(inherits(possible_error, "error")){
            message("Error in GEOquery")
            next
        }else{
            gds <- possible_error
        }
        if(verbose) message("Getting and processing expression and annotation data")
        expr <- get_expr_from_gds(gds)

        sample_num <- ncol(expr) - 1
        if(sample_num > max_sample_num | sample_num < min_sample_num){
            message(paste("Sample size for study", gds_id,
                          "is out of the range defined by max_sample_num and min_sample_num"))
            next
        }

        expr <- process_and_collapse(expr)
        annot <- make_gds_annot(gds)
        #names_list[[gds_id]] <- annot

        run_date <- lubridate::now()
        if(verbose) message("Running CEMiTool")
        cem <- run_cemitool(gds_id, expr, annot, results_dir, p)

        if(!is.null(cem)){
            if(verbose) message("Populating MySQL database")
            populate_sql(pool=pool, gds_id=gds_id, user_data=user_data, run_date=run_date, cem=cem)
        }
    }
    poolClose(pool)
}

for(gpl_id in gpl_ids2){
    studies_to_db(user_data=user_data,
                  gpl_id=gpl_id,
                  min_sample_num=18, 
                  max_sample_num=200,
                  results_dir="/home/prusso/Documents/CSBL/new_database/intermediate/test",
                  verbose=TRUE, force=FALSE)
}


# mapply(studies_to_db, gpl_id=gpl_ids2, 
#        MoreArgs = list(user_data=user_data,
#        min_sample_num=18, max_sample_num=200, 
#        results_dir="/home/prusso/Documents/CSBL/new_database/intermediate/test",
#        verbose=TRUE, force=FALSE))