ProCARs API

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.

procars_steps module

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

procars.procars_steps.run_step_a(pqtree_file, adjacency_file, step, tree_bin, blocks_bin, car_bin, car_neigh_bin, nb_blocks, last_pqtree)[source]

Run step a) : Adding non-conflicting adjacencies

Parameters:

pqtree_file : string

Prefix of PQtree file name

adjacency_file : string

Prefix of adjacencies file name

step : int

Current step of ProCARs method

tree_bin : string

Name of binary file in which information about species tree is saved

blocks_bin : string

Name of binary file in which information about blocks is saved

car_bin : string

Name of binary file in which information about cars is saved

car_neigh_bin : string

Name of binary file in which information about car neighbors is saved

nb_blocks : int

Total number of blocks

last_pqtree : string

Name of the last PQtree file saved

Returns:

tuple

step: current step of ProCARs method

donextstep: boolean to indicate if we must run a new step a) or go to a step b) or c)

nb_discarded: number of discarded adjacencies found in this step a)

last_pqtree: name of last PQtree file saved (changed if we found non-conflicting adjacencies in this step)

procars.procars_steps.run_step_b(pqtree_file, adjacency_file, step, tree_bin, nb_blocks)[source]

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

Prefix of PQtree file name

adjacency_file : string

Prefix of adjacencies file name

step : int

Current step of ProCARs method

tree_bin : string

Name of binary file in which information about species tree is saved

nb_blocks : int

Total number of blocks

Returns:

tuple

donextstep: boolean to indicate if a new step a) must be run or not

last_pqtree: name of last PQtree file saved

procars.procars_steps.run_step_c(pqtree_file, adjacency_file, step, tree_bin, blocks_bin, car_bin, car_neigh_bin, nb_blocks, last_pqtree, donextstep)[source]

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

Prefix of PQtree file name

adjacency_file : string

Prefix of adjacencies file name

step : int

Current step of ProCARs method

tree_bin : string

Name of binary file in which information about species tree is saved

blocks_bin : string

Name of binary file in which information about blocks is saved

car_bin : string

Name of binary file in which information about cars is saved

car_neigh_bin : string

Name of binary file in which information about car neighbors is saved

nb_blocks : int

Total number of blocks

last_pqtree : string

Name of the last PQtree file saved

donextstep : boolean

If a next step must be run after this one or not

Returns:

tuple

donextstep: boolean to indicate if we must run a new step a) (if we added new adjs) or not

last_pqtree: name of last PQtree file saved (changed if we found DCJ-reliable adjacencies to add in this step)

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