R/filterSQMASSdb.R

In Roestlab/mstools: OpenSWATH Mass Spectrometry Data Exploration

#// **********************************************************************************************
#//                         filterSQMASSdb.R
#// **********************************************************************************************
#//
#// 
#// **********************************************************************************************
#// @Maintainer: Justin Sing
#// @Author: Justin Sing

#' @export
#' @title Filter and sqMass db file 
#' @description This function can be used to filter an sqMass db file given a list of unmodified sequences
#' 
#' @param sqmass_file A character vector of the absolute path and filename of the sqMass file. (Must be .osw format)
#' @param unmodified_sequence_filter A character vector for extraction of specific peptide(s). I.e. c('ANSSPTTNIDHLK', 'ESTAEPDSLSR', 'NLSPTKQNGKATHPR', 'KDSNTNIVLLK', 'NKESPTKAIVR')
#' @return A data.table containing spectral library information
#' 
#' @author Justin Sing \url{https://github.com/singjc}
#' 
#' @importFrom DBI dbConnect dbDisconnect dbExecute
#' @importFrom RSQLite SQLite 
#' @importFrom dplyr collect tbl
#' @importFrom dbplyr sql 
#' @importFrom MazamaCoreUtils logger.isInitialized logger.info logger.error logger.warn logger.trace
#' @importFrom tools file_ext
filterSQMASSdb <- function( sqmass_file, unmodified_sequence_filter) {
  ## TODO add controls tatements for check tables being present
  DEBUG=FALSE
  if ( DEBUG ){
    sqmass_file <- "/media/justincsing/ExtraDrive1/Documents2/Roest_Lab/Github/DrawAlignR/inst/extdata/Synthetic_Dilution_Phosphoproteomics/sqmass/test.sqMass"
    unmodified_sequence_filter <- c('ANSSPTTNIDHLK', 'ESTAEPDSLSR', 'NLSPTKQNGKATHPR', 'KDSNTNIVLLK', 'NKESPTKAIVR')
  }
  
  tryCatch(
    expr = {
      
      ## Check if logging has been initialized
      if( MazamaCoreUtils::logger.isInitialized() ){
        log_setup()
      }
      
      ## Get and Evaluate File Extension Type to ensure an osw file was supplied
      fileType <- tools::file_ext(sqmass_file)
      if( tolower(fileType)!='sqmass' ){
        MazamaCoreUtils::logger.error( "[mstools::filterSQMASSdb] The supplied file was not a valid OSW database file!\n You provided a file of type: %s", fileType)
      }
      
      ##************************************************
      ##    Establiash Connection to DB
      ##************************************************
      MazamaCoreUtils::logger.trace( "[mstools::filterSQMASSdb] Connecting to Database: %s", sqmass_file)
      db <- DBI::dbConnect( RSQLite::SQLite(), sqmass_file )
      
      ##************************************************
      ##    Filter Precursor Table
      ##************************************************
      ## query statement to get a table of non desired peptide sequences to delete
      precursor_filter_stmt <- sprintf( "SELECT * FROM PRECURSOR
WHERE PRECURSOR.PEPTIDE_SEQUENCE NOT IN ('%s')", paste(unmodified_sequence_filter, collapse="','") )
      
      ## Send query to database
      MazamaCoreUtils::logger.trace( "[mstools::filterSQMASSdb] Querying Database: %s", precursor_filter_stmt)
      precursor_table <- dplyr::collect( dplyr::tbl( db, dbplyr::sql( precursor_filter_stmt )) )
      
      ## Split chromatogram ids into partitions of 100. Large queries don't work well in sqlite
      chromatogram_ids_list <- split(precursor_table$CHROMATOGRAM_ID, ceiling(seq_along(precursor_table$CHROMATOGRAM_ID)/10000))
      
      for ( chromatogram_ids_sub_list in chromatogram_ids_list ){
        
        ## Delete Query
        precursor_delete_stmt <- sprintf( "DELETE FROM PRECURSOR WHERE PRECURSOR.CHROMATOGRAM_ID IN (%s)", paste(chromatogram_ids_sub_list, collapse = ","))
        ## Execute delete query
        MazamaCoreUtils::logger.trace( "[mstools::filterSQMASSdb] Querying Database: %s", precursor_delete_stmt)
        DBI::dbExecute( db, precursor_delete_stmt )
        
        ##************************************************
        ##    Filter Chromatogram Table
        ##************************************************
        ## chromatogram table delte query
        chromatogram_table_delete_stmt <- sprintf( "DELETE FROM CHROMATOGRAM WHERE CHROMATOGRAM.ID IN (%s)", paste(chromatogram_ids_sub_list, collapse = ","))
        ## Execute delete query
        MazamaCoreUtils::logger.trace( "[mstools::filterSQMASSdb] Querying Database: %s", chromatogram_table_delete_stmt)
        DBI::dbExecute( db, chromatogram_table_delete_stmt )
        
        ##************************************************
        ##    Filter Data Table
        ##************************************************
        ## chromatogram table delte query
        data_table_delete_stmt <- sprintf( "DELETE FROM DATA WHERE DATA.CHROMATOGRAM_ID IN (%s)", paste(chromatogram_ids_sub_list, collapse = ","))
        ## Execute delete query
        MazamaCoreUtils::logger.trace( "[mstools::filterSQMASSdb] Querying Database: %s", data_table_delete_stmt)
        DBI::dbExecute( db, data_table_delete_stmt )
        
        ##************************************************
        ##    Filter Product Table
        ##************************************************
        ## chromatogram table delte query
        product_table_delete_stmt <- sprintf( "DELETE FROM PRODUCT WHERE PRODUCT.CHROMATOGRAM_ID IN (%s)", paste(chromatogram_ids_sub_list, collapse = ","))
        ## Execute delete query
        MazamaCoreUtils::logger.trace( "[mstools::filterSQMASSdb] Querying Database: %s", product_table_delete_stmt)
        DBI::dbExecute( db, product_table_delete_stmt )
      }
      ##***********************************************
      ##    Clear unused space in db
      ##***********************************************
      MazamaCoreUtils::logger.trace( "[mstools::filterSQMASSdb] Vacuuming Database")
      DBI::dbExecute(db, "VACUUM")
      
      ##***********************************************
      ##    Disconnect fom DB 
      ##***********************************************
      MazamaCoreUtils::logger.trace( "[mstools::filterSQMASSdb] Disconnecting From Database: %s", sqmass_file)
      DBI::dbDisconnect( db )
    },
    error = function(e){
      MazamaCoreUtils::logger.error("[mstools::filterSQMASSdb] There was the following error that occured during function call...\n", e$message)
    }
  ) # End tryCatch
}# End functin