Skip to main content

A toolkit for ETL curation for the tranSMART data warehouse.

Project description

A toolkit for ETL curation for the tranSMART data warehouse. The TranSMART curation toolkit (tmtk) can be used to edit and validate studies prior to loading them with transmart-batch.

Some features:
  • create a transmart-batch ready study from clinical data files.

  • load an existing study and validate its contents.

  • edit the transmart concept tree in The Arborist graphical editor.

  • create chromosomal region annotation files.

Disclaimer

tmtk is a python3 package meant to be run in Jupyter notebooks. Results for other setups may vary.

Usage

Step 1: Opening a notebook

First open a Jupyter Notebook, open a shell and change directory to some place where your data is. Then start the notebook server:

cd /path/to/studies/
jupyter notebook

This should open your browser to Jupyters file browser, create a new notebook for here.

Step 2: Using tmtk

# First import the toolkit into your environment
import tmtk

# Then create a <tmtk.Study> object by pointing to study.params of a transmart-batch study
study = tmtk.Study('~/studies/a_tm_batch_ready_study/study.params')
# Or, by using the study wizard on a directory with correctly structured, clinical data files.
# (Visit the transmart-batch documentation to find out what is expected.)
study = tmtk.wizard.create_study('~/studies/dir_with_some_clinical_data_files/')

Now we have loaded the study as a tmtk.Study object we have some interesting functions available:

# Check whether transmart-batch will find any issues with the way your study is setup
study.validate_all()

# Graphically manipulate the concept tree in this study by using The Arborist
study.call_boris()

For more, see the examples.

Installation

To install tmtk, and all dependencies, into your Python environment run:

$   python3 setup.py install

or if you want to run the tool from code:

$   python3 setup.py develop

Requirements

These dependencies will have to be installed:
  • pandas

  • jupyter

  • flask

  • ipython

  • tqdm

  • requests

  • rpy2

Licence

GPLv3

Authors

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

tmtk-0.1.4.tar.gz (446.2 kB view hashes)

Uploaded Source

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page