iggy 0.3

Installation
============


You can install iggy by running::

$ pip install --user iggy

The executable scripts can then be found in ~/.local/bin.


Usage
-----

Typical usage is::

$ iggy.py network.sif observation.obs --show_colorings 10 --show_predictions

For more options you can ask for help as follows::

$ iggy.py -h
usage: iggy.py [-h] [--no_zero_constraints]
[--propagate_unambigious_influences] [--no_founded_constraint]
[--autoinputs] [--scenfit] [--show_colorings SHOW_COLORINGS]
[--show_predictions]
networkfile observationfile

positional arguments:
networkfile influence graph in SIF format
observationfile observations in bioquali format

optional arguments:
-h, --help show this help message and exit
--no_zero_constraints
turn constraints on zero variations OFF, default is ON
--propagate_unambigious_influences
turn constraints ON that if all predecessor of a node
have the same influence this must have an effect,
default is ON
--no_founded_constraint
turn constraints OFF that every variation must be
explained by an input, default is ON
--autoinputs compute possible inputs of the network (nodes with
indegree 0)
--scenfit compute scenfit of the data, default is mcos
--show_colorings SHOW_COLORINGS
number of colorings to print, default is OFF, 0=all
--show_predictions show predictions


The second script contained is opt_graph.py
Typical usage is::

$ opt_graph.py network.sif observations_dir/ --show_repairs 10

For more options you can ask for help as follows::

$ opt_graph.py -h
usage: opt_graph.py [-h] [--no_zero_constraints]
[--propagate_unambigious_influences]
[--no_founded_constraint] [--autoinputs]
[--show_repairs SHOW_REPAIRS] [--opt_graph]
networkfile observationfiles

positional arguments:
networkfile influence graph in SIF format
observationfiles directory of observations in bioquali format

optional arguments:
-h, --help show this help message and exit
--no_zero_constraints
turn constraints on zero variations OFF, default is ON
--propagate_unambigious_influences
turn constraints ON that if all predecessor of a node
have the same influence this must have an effect,
default is ON
--no_founded_constraint
turn constraints OFF that every variation must be
explained by an input, default is ON
--autoinputs compute possible inputs of the network (nodes with
indegree 0)
--show_repairs SHOW_REPAIRS
number of repairs to show, default is OFF, 0=all
--opt_graph compute opt-graph repairs (allows also adding edges),
default is only removing edges


Samples
=======

Sample files available here:: iggy_demo_data.tar.gz_

.. _iggy_demo_data.tar.gz: http://www.cs.uni-potsdam.de/~sthiele/bioasp/downloads/samples/iggy_demo_data.tar.gz