Utilities for interacting with PNNL DMS

Source: R/PNNL_DMS_utils.R

Fetches results of different data analysis tools. Not useful outside of PNNL unless connected through VPN. Works on windows out of the box. To make it work on Mac/Linux FreeTDS needs to be installed. Mac/Linux functionality is not well tested.

  • get_dms_job_records(): returns job records given variety keyword patterns

  • get_tool_output_files_for_job_number(): returns the output of the tool given tool name and file pattern

  • get_output_folder_for_job_and_tool(): returns the path given job id and tool name

  • get_AScore_results(): returns Ascore results given data package number

  • get_job_records_by_dataset_package(): returns job records given data package number

  • get_results_for_multiple_jobs(): returns concatenated results given job numbers

  • get_results_for_multiple_jobs.dt(): returns results as concatenated data.table given job numbers

  • get_results_for_single_job(): returns results given job number

  • get_results_for_single_job.dt(): returns results as data.table given job number

  • get_datasets_by_data_package(): returns table with datasets info

  • download_datasets_by_data_package(): downloads datasets into provided location

tool2suffix

is_PNNL_DMS_connection_successful()

get_dms_job_records(
  jobs = NULL,
  datasetPttrn = "",
  experimentPttrn = "",
  toolPttrn = "",
  parPttrn = "",
  settingsPttrn = "",
  fastaPttrn = "",
  proteinOptionsPttrn = "",
  instrumentPttrn = ""
)

get_tool_output_files_for_job_number(
  jobNumber,
  toolName = NULL,
  fileNamePttrn,
  mostRecent = TRUE
)

get_output_folder_for_job_and_tool(jobNumber, toolName, mostRecent = TRUE)

get_job_records_by_dataset_package(data_package_num)

get_datasets_by_data_package(data_package_num)

download_datasets_by_data_package(
  data_package_num,
  copy_to = ".",
  fileNamePttrn = ".raw",
  ncores = 2
)

get_results_for_multiple_jobs(jobRecords)

get_results_for_multiple_jobs.dt(jobRecords, expected_multiple_files = FALSE)

get_results_for_single_job(pathToFile, fileNamePttrn)

get_url_from_dir_and_file(dir, file_name_segment)

get_results_for_single_job.dt(
  pathToFile,
  fileNamePttrn,
  expected_multiple_files = FALSE
)

path_to_FASTA_used_by_DMS(data_package_num, organism_db = NULL)

Format

An object of class list of length 7.

Arguments

jobs

(integer) DMS job ID

datasetPttrn
experimentPttrn
toolPttrn
parPttrn
settingsPttrn
fastaPttrn
proteinOptionsPttrn
instrumentPttrn
jobNumber
toolName
fileNamePttrn
mostRecent

(logical) only most recent or all output files

data_package_num

(integer) data package ID number.

copy_to

folder path to copy files into

ncores

number of cores to use in cluster

jobRecords
expected_multiple_files

do we expect multiple files for a single job or not. Default is FALSE.

pathToFile
dir
file_name_segment
organism_db

(character) FASTA file. This is the same as the Organism DB column. No need to specify this if there is only one FASTA file associated with the jobs.

Examples

if (is_PNNL_DMS_connection_successful()) {
  get_output_folder_for_job_and_tool(863951, "DTA_Refinery")
}