comparison create_sqlite_db.R @ 22:c8b34df46dae draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 04023134d8f28e85927ca293373c506484149ead-dirty

21:e8291b9d129b

                           rtrawColumns = rtrawColumns)
}

con <- DBI::dbConnect(RSQLite::SQLite(), db_pth)

add_extra_table_elucidation <- function(name, pth, db_con, filter_Score=NA, filter_Rank=NA){
    if (is.null(pth)){
        return(0)
    }
    DBI::dbWriteTable(conn=db_con, name=name, value=pth, sep='\t', header=T)


}

        colnames(df_ids) <- c('grp_id', 'file_id', 'pid')
        df <- cbind(df_ids, df)
        DBI::dbWriteTable(db_con, name=name, value=df, row.names=FALSE, append=append)
}

add_probmetab <- function(pth, con){
  if (!is.null(pth)){

      df <- read.table(pth,  header = TRUE, sep='\t', stringsAsFactors = FALSE,  comment.char = "")
      df$grp_id <- 1:nrow(df)
      start <- T 
      for (i in 1:nrow(df)){

         x <- df[i,]

}

add_extra_table_elucidation('metfrag_results', opt$metfrag_result, con, filter_Score=0.6, filter_Rank=NA)
add_extra_table_elucidation('sirius_csifingerid_results', opt$sirius_csifingerid_result, con, filter_Score=NA, filter_Rank=5)
add_probmetab(opt$probmetab_result, con)

if (is.null(xset)){
  DBI::dbWriteTable(con, name='xset_classes', value=xa@xcmsSet@phenoData, row.names=TRUE)
}else{

  DBI::dbWriteTable(con, name='xset_classes', value=xset@phenoData, row.names=TRUE)

}

cmd <- paste('SELECT cpg.grpid, cpg.mz, cpg.mzmin, cpg.mzmax, cpg.rt, cpg.rtmin, cpg.rtmax, c_peaks.cid, ',
             'c_peaks.mzmin AS c_peak_mzmin, c_peaks.mzmax AS c_peak_mzmax, ',

22:c8b34df46dae

                           rtrawColumns = rtrawColumns)
}

con <- DBI::dbConnect(RSQLite::SQLite(), db_pth)

add_extra_table_elucidation <- function(name, pth, db_con){
    if (is.null(pth)){
        return(0)
    } 

    
    DBI::dbWriteTable(conn=db_con, name=name, value=pth, sep='\t', header=T)


}

        colnames(df_ids) <- c('grp_id', 'file_id', 'pid')
        df <- cbind(df_ids, df)
        DBI::dbWriteTable(db_con, name=name, value=df, row.names=FALSE, append=append)
}

add_probmetab <- function(pth, xset, con){
  if (!is.null(pth)){

      df <- read.table(pth,  header = TRUE, sep='\t', stringsAsFactors = FALSE,  comment.char = "")
      df$grp_id <- match(df$name, xcms::groupnames(xset))
      start <- T 
      for (i in 1:nrow(df)){

         x <- df[i,]

}

add_extra_table_elucidation('metfrag_results', opt$metfrag_result, con, filter_Score=0.6, filter_Rank=NA)
add_extra_table_elucidation('sirius_csifingerid_results', opt$sirius_csifingerid_result, con, filter_Score=NA, filter_Rank=5)


if (is.null(xset)){
  DBI::dbWriteTable(con, name='xset_classes', value=xa@xcmsSet@phenoData, row.names=TRUE)
  add_probmetab(opt$probmetab_result, xset,  con)
}else{

  DBI::dbWriteTable(con, name='xset_classes', value=xset@phenoData, row.names=TRUE)
  add_probmetab(opt$probmetab_result, xset,  con)

}

cmd <- paste('SELECT cpg.grpid, cpg.mz, cpg.mzmin, cpg.mzmax, cpg.rt, cpg.rtmin, cpg.rtmax, c_peaks.cid, ',
             'c_peaks.mzmin AS c_peak_mzmin, c_peaks.mzmax AS c_peak_mzmax, ',