Creating ISA content¶
The ISA API provides a set of Python classes that you can use to create ISA content with.
The three main objects that you need to create ISA content are:
As a pre-requisite to using ISA model classes, please make sure you have read and understood the ISA Abstract Model that the ISA formats are based on.
isatools.model.v1, the class
Investigation is used as the top level container for all other ISA content.
Investigation Python class corresponds to the
Investigation as defined in the
ISA Model Specification. For example, to create an empty
ISA structure consisting of an investigation with one study, you might use the following code:
>>> from isatools.model.v1 import * >>> investigation = Investigation() >>> investigation.studies.append(Study()) # adds a new default Study object to investigation
This code simply creates one
Investigation object, and adds a single
Study object to it. The constructor of
each of these objects creates empty structures for each of these. We can then inspect the structure by accessing
its instance variables as follows:
>>> investigation.studies [<isatools.model.v1.Study object>] >>> investigation.studies.assays  >>> investigation.title ''
Since we have not set any data in our ISA objects, these are by default mostly empty at the moment. We can set some instance variables with data as follows:
>>> investigation.title = "My ISA Investigation" >>> investigation.title 'My ISA Investigation' >>> investigation.studies.title = "My ISA Study" >>> investigation.studies.title 'My ISA Study' >>> investigation.studies.assays.append(Assay()) # adds a new default Assay object to study >>> i.studies.assays [<isatools.model.v1.Assay object>]
If you then write these out to ISA-Tab, we can inspect the output written into an
i_investigation.txt file. We
do this using the
isatab module to
Investigation object we created, as follows:
>>> from isatools import isatab >>> isatab.dump(investigation, 'tmp/') # dump out ISA-Tab to tmp/ <isatools.model.v1.Investigation object>
If all went as expected, you should find an
i_investigation.txt file with the standard Investigation sections,
one Study section structured as defined by the
Remember that when you
dump() ISA content, you do it on the
Investigation object. This means any
Assay objects and content must be attached to the
Investigation for it to be serialized out.
Different classes in
isatools.model.v1 have class constructors and instance variables that roughly map to the
ISA Abstract Model. For full details of how to instantiate model classes, access and manipulate ISA data as objects,
please inspect the module’s docstrings.
Obviously this isn’t enough to create a fully populated ISA investigation, but we would recommend that you have a look
isatools.model.v1 package to inspect all the docstring documentation that is included with each of the ISA