Gene Parser AST

A rule expression in genetics can be found like this relation of AND+OR:

rule = '(9045_AT1 and (B0783 and B0088)) or (3705_AT1 or (91012_AT1 and 55304_AT1))'

This module enables a a parser that convert an string expression that relates the genes in a object structure like this:

Or(
    left=And(left=Gene(name='9045_AT1'), right=And(left=Gene(name='B0783'), right=Gene(name='B0088'))),
    right=Or(
        left=Gene(name='3705_AT1'),
        right=And(left=Gene(name='91012_AT1'), right=Gene(name='55304_AT1'))
    )
)

To process this and obtain the representative value first is necessary use the parser method and then call tree_analysis. This last function reads recursively all the tree and obtain, given this rules, the final value:

• or : sum([a,b])
• and : min([a,b])

And, for UNKNOWN value:

• Expression(UNKNOWN) :: mean([Expression(G_i)])

With this is possible to have the representative value for the gene rule expression.

Take a look on the examples on the tests directory.

How install this.

Call poetry

poetry install

Run the tests:

Basic example:

poetry run python tests/test_basic.py 

General Example:

poetry run python tests/test_parser_general.py 

Check then the parser.

Once installed you can check the for gene rule expressions using the command rule_parser.

rule_parser "1321A and 123123B and (123123B or 32312C)"