pnnl_dms_utils | R Documentation |
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)
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
|
An object of class list
of length 8.
if (is_PNNL_DMS_connection_successful()) {
get_output_folder_for_job_and_tool(863951, "DTA_Refinery")
}
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