biopy-isatab

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We are currently maintaining the ISA-Tab python parser in the ISA-API code base. Please, refer to that repository for the latest parser.

Python Parser for ISA-Tab

This is a python parser for extracting information from ISA-Tab formatted metadata. Usage is:

      from bcbio import isatab
      rec = isatab.parse(isatab_metadata_directory)

The returned record matches the general Investigation/Study/Assay structure of ISATab. The top level ISATabRecord object contains information about the investigation, along with study information as ISATabStudyRecord objects. Each record has assay information in ISATabAssayRecord sub-objects.

The output is described in more detail in the parser module:

https://github.com/ISA-tools/biopy-isatab/blob/master/bcbio/isatab/parser.py

and the test directory contains example of use and information extraction:

https://github.com/ISA-tools/biopy-isatab/blob/master/test/test_isatab.py

You can also display the structure of an object by printing it:

>>> print isatab_rec

* ISATab Record
 metadata: {}
 studies:
  * Study
   metadata: {'Study Description': 'C2C12 mouse skeletal muscle cells',
      'Study Identifier': 'SB-S-1',
      'Study Submission Date': '2010-10-04'}
   nodes:
       * Node C2C12 sample3 rep3 Sample Name
         metadata: {'Sample Name': ['C2C12 sample3 rep3'],
          'organism': [Attrs(organism='Mus musculus (Mouse)',
                       Term_Source_REF='NEWT',
                       Term_Accession_Number='10090')]}

More information about ISATab:

• General info: http://isa-tools.org
• Twitter: @isatools
• IRC: irc://irc.freenode.net/#isatab
• Development blog: http://isatools.wordpress.com

License

The code is freely available under the MIT license_.

.. _MIT license: http://www.opensource.org/licenses/mit-license.html