python/xptcleaner/README.md

In phuse-org/sendigR: Enable Cross-Study Analysis of 'CDISC' 'SEND' Datasets

xptcleaner

• xptcleaner package provides functions for creating json file for vocabulary mappings and for Standardizing SEND xpt files (SAS v5 Transport format) using CDISC controlled terminologies.

Installation

Using pip

Probably the easiest way: from your conda, virtualenv or just base installation do:

pip install xptcleaner

If you are running on a machine without admin rights, and you want to install against your base installation you can do:

pip install xptcleaner --user

Using source archive or using wheel file

You can choose to install xptcleaner using source archive or using wheel file.

• Using source archive: Using the below shell command to install the xptcleaner package, assume that the source archive is under 'dist' sub folder. Replace {version} with the correct version number, e.g. 1.0.0.

$ py -m pip install ./dist/xptcleaner-{version}.tar.gz

• Using wheel: Using the below shell command to install the xptcleaner package, assume that the wheel file is under 'dist' sub folder. Replace {version} with the correct version number, e.g. 1.0.0.

$ py -m pip install ./dist/xptcleaner-{version}-py3-none-any.whl

The following required python packages will be installed during the xptcleaner package installation:

* pandas

* pyreadstat

Functions

gen_vocab(in_file, out_path)

    Create json file for vocabulary mappings.
    Keys are synonyms and values are the CDISC Controlled Terminology Submission values.
    Vocabularies are defined by column values from the tab-delimited files.

    Parameters
    ----------
    in_file : str
        List of tab-delimited files with synonyms and preferred terms.
    out_path : str
        output json filename.

standardize_file(input_xpt_dir, output_xpt_dir, json_file)

    Standardizes SEND xpt files using CDISC controlled terminologies.
    Here is the list of CDISC codelist supported.
    - Sex
    - Strain/Substrain
    - Species
    - SEND Severity
    - Route of Administration Response
    - Standardized Disposition Term
    - Specimen
    - Non-Neoplastic Finding Type
    - SEND Control Type

     Parameters
    ----------
    input_xpt_dir : str
        input folder name with xpt files under the folder.
    output_xpt_dir : str
        output folder name for writing the cleaned xpt files.
    json_file : str
        json filename used for mapping.

How to use

xptcleaner can be used from python script and from R script.

Use xptcleaner from python script

# xptcleaner and module xptclean import
import xptcleaner
from xptcleaner import xptclean

#input CDISC and Extensible CT files.
infile1="{path to CT file}/SEND_Terminology_EXTENSIBLE.txt"
infile2="{path to CT file}/SEND Terminology_2021_12_17.txt"
#output JSON file
jsonfile="{path to CT file to be created}/SENDct.json"

#Call the gen_vocab function with the input and output files
xptclean.gen_vocab([infile1,infile2],jsonfile)

#Call the standardize_file function to clean the xpt file
rawXptFolder = "{path to xpt files}/96298/"
cleanXptFolder = "{path to cleaned xpt files}/96298/"
xptclean.standardize_file(rawXptFolder, cleanXptFolder, jsonfile)

Use xptcleaner from R script

xptcleaner is integrated with sendigR package. refer to installation and usage on sendigR.

phuse-org/sendigR documentation built on April 5, 2025, 1:29 a.m.