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
The code is freely available under the MIT license
_.
.. _MIT license: http://www.opensource.org/licenses/mit-license.html