Here is the ProCARs API, describing all modules and their functions.
procars package contains one module, procars_steps, and two subpackages: steps_modules and utils.
Copyright © Bonsai - LIFL (Université Lille 1, CNRS UMR 8022) and Inria-Lille Nord Europe
contact: aida.ouangraoua@inria.fr, amandine.perrin@inria.fr
This software is a computer program whose purpose is to progressively reconstruct ancestral gene orders.
This software is governed by the CeCILL-B license under French law and abiding by the rules of distribution of free software. You can use, modify and/or redistribute the software under the terms of the CeCILL-B license as circulated by CEA, CNRS and Inria at the following URL http://www.cecill.info, or in the LICENCE file at the root directory of this program.
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procars_steps module description:
This module contains all steps of the whole ProCARs pipeline, which are:
- step a) : Adding non-conflicting adjacencies
- step b) : Resolving conflicts between adjacencies
- step c) : Detecting DCJ-reliable adjacencies
These steps are called from the whole pipeline, in the main script : bin/procars_main
Module author: Aïda Ouangraoua, Amandine PERRIN
June 2014
Run step a) : Adding non-conflicting adjacencies
Parameters: | pqtree_file : string
adjacency_file : string
step : int
tree_bin : string
blocks_bin : string
car_bin : string
car_neigh_bin : string
nb_blocks : int
last_pqtree : string
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Returns: | tuple
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Run step b): Resolving conflicts between adjacencies.
Occurs after a step a) where the set of non-conflicting conserved adjacencies was empty, but the set of conflicting conserved adjacencies was not empty.
Parameters: | pqtree_file : string
adjacency_file : string
step : int
tree_bin : string
nb_blocks : int
|
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Returns: | tuple
|
Run step c): Detecting DCJ-reliable adjacencies
This step comes after a step a) that ended up with empty sets of conflicting and non-conflicting conserved adjacencies.
Parameters: | pqtree_file : string
adjacency_file : string
step : int
tree_bin : string
blocks_bin : string
car_bin : string
car_neigh_bin : string
nb_blocks : int
last_pqtree : string
donextstep : boolean
|
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Returns: | tuple
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