OpenGDC.py

This is the Python implementation of the original OpenGDC Java software https://github.com/cumbof/OpenGDC

Usage

python OpenGDC.py [--tumor          [GDC_TUMOR]             ]
                  [--datatype       [GDC_DATATYPE]          ]
                  [--after          [AFTER_DATETIME]        ]
                  [--download       [DOWNLOAD_FLAG]         ]
                  [--download_dir   [DOWNLOAD_DIRECTORY]    ]
                  [--convert        [CONVERT_FLAG]          ]
                  [--convert_dir    [CONVERT_DIRECTORY]     ]
                  [--matrix         [EXPORT_TO_MATRIX]      ]
                  [--settings       [SETTINGS_FILE]         ]
                  [--verbose        [VERBOSE_FLAG]          ]

Optional arguments:
    --after       [AFTER_DATETIME]
    --matrix      [EXPORT_TO_MATRIX]

Notes:
    - both --tumor and --datatype are case sensitive;
    - flags --download and --convert activate the download and conversion of the GDC data;
    - at least one flag between --download and --convert must be specified;
    - the convertion procedure requires both the --download_dir and --convert-dir, 
      additionally to the --convert flag enabled.

WARNING:
    --matrix still must be implemented
    --datatype supports only
        - "Methylation Beta Value"
        - "Clinical and Biospecimen Supplements"

Credits

Please credit our work in your manuscript by citing:

Eleonora Cappelli, Fabio Cumbo, Anna Bernasconi, Arif Canakoglu, Stefano Ceri, Marco Masseroli, and Emanuel Weitschek. "OpenGDC: unifying, modeling, integrating cancer genomic data and clinical metadata" Appl. Sci. 2020, 10(18), 6367. https://doi.org/10.3390/app10186367