---
title: padmet package - Documentation
author: Meziane AITE
date: 2018-07-12
version: 3.0.1
---
################################################################################
## Description
@padmet Version: 3.0.1
author: meziane aite (meziane.aite@inria.fr)
Python 3
Description:
The PADMet package allows conciliating genomics and metabolic network information used to produce a genome-scale constraint-based metabolic model within a database that traces all the reconstruction process steps. It allows representing the metabolic model in the form of a Wiki containing all the used/traced information. Other standard outputs are made available with the package.
The main concept underlying PADMet-Package is to provide solutions that ensure the consistency, the internal standardization and the reconciliation of the information used within any workflow that combines several tools involving metabolic networks reconstruction or analysis. The PADMet package is at the core of the AuReMe workflow, dedicated to the primary reconstruction of genome-scale metabolic networks from raw data. It allows the study of organisms for which few experimental data are available. Its main feature is to undergo the reconstruction of the metabolic network by combining several heterogeneous knowledge and data sources, including the information reported by several scaffold metabolic networks for cousin species.
## Installation
From pip:
pip install padmet
From git:
git clone https://gitlab.inria.fr/maite/padmet.git
make install (from git/padmet)
## Architecture
.
├── LICENSE
├── Makefile
├── MANIFEST.in
├── README.md
├── setup.cfg
├── setup.py
└── padmet
├── __init__.py
├── aspGenerator.py
├── node.py
├── padmetRef.py
├── padmetSpec.py
├── policy.py
├── README.md
├── relation.py
├── sbmlGenerator.py
├── sbmlPlugin.py
└── wikiGenerator.py
## Documentation
node.py:
Description:
Define the class Node used in padmet.
class Node:
"""
A Node represent an element in a metabolic network (eg: compound, reaction)
A Node contains 3 attributs:
_type: The type of the node (eg: 'reaction' or 'pathway')
_id: the identifier of the node (eg: 'rxn-45)
_misc: A dictionnary of miscellaneous data, k = tag of the data, v = list of values
(eg: {'DIRECTION':[REVERSIBLE]})
"""
__init__(self, _type, _id, misc = None):
"""
@param _type: The type of the node ('reaction','pathway')
@param _id: the identifier of the node ('rxn-45)
@param _misc: A dictionnary of miscellaneous data ({'DIRECTION':[REVERSIBLE]})
@type _type, _id: str
@type misc: dict
@return: _
@rtype: None
"""
toString(self):
"""
This function is used to stock the information relative to the node
in a padmet file.
@return: string with all data sep by tab' ex: reaction\tRXN0..
@rtype: str
"""
relation.py
Description:
Define the class Relation used in padmet.
class Relation:
"""
A Relation represent an link between two elements (node) in a metabolic network
eg: RXN-1 consumes CPD-1
A Relation contains 4 attributs:
_type: The type of the relation (eg: 'consumes' or 'produces')
id_in: the identifier of the node corresponding to the subject of the relation (eg: 'RXN-1)
id_out: the identifier of the node corresponding to the object of the relation (eg: 'CPD-1)
_misc: A dictionnary of miscellaneous data, k = tag of the data, v = list of values
(eg: {'STOICHIOMETRY':[1.0]})
"""
__init__(self, id_in, _type, id_out, misc = None):
"""
@param _type: The type of the relation (eg: 'consumes' or 'produces')
@param id_in: the identifier of the node corresponding to the subject of the relation ('RXN-1)
@param id_out: the identifier of the node corresponding to the object of the relation ('CPD-1)
@param _misc: A dictionnary of miscellaneous data (eg: {'STOICHIOMETRY':[1.0]})
@type _type, _id: str
@type misc: dict
@return: _
@rtype: None
"""
toString(self):
"""
This function is used to stock the information relative to the node
in a padmet file.
@return: string with all data sep by tab' ex: reaction\tRXN0..
@rtype: str
"""
compare(self,relation):
"""
compare 2 relations. return True or False
@param relation: the relation to compare
@type relation: Relation
@return: True,False
@rtype: bool
"""
policy.py
Description:
Define a policy in padmet object.
class Policy:
"""
A Policy define the types of relations, nodes in a network.
A policy contains 3 attributs:
policy_in_array: Is a list of list of arcs (eg: [['reaction','consumes','compounds'],['reaction','produces','compounds']])
class_of_node: Is a set of all the type of nodes represented in the network (eg: set(reaction, compound))
type_of_arc: Is a dictionnary of all the types of arcs represented in the network (eg: {reaction:[consumes,compounds]})
"""
__init__(self,policy_in_array = None):
"""
@param policy_in_array: Is a list of list of arcs (eg: [['reaction','consumes','compounds'],['reaction','produces','compounds']])
@type policy_in_array: list
@return: _
@rtype: None
"""
setPolicyInArray(self,policy_in_array):
"""
From policy_in_array, set class_of_node and type_of_arc
@param policy_in_array: Is a list of list of arcs (eg: [['reaction','consumes','compounds'],['reaction','produces','compounds']])
@type policy_in_array: list
@return: _
@rtype: None
"""
getPolicyInArray(self):
"""
return policy_in_array
@return: self.policy_in_array
@rtype: list
"""
_setClassOfNode(self):
"""
From self.policy_in_array set class_of_node
@return: _
@rtype: None
"""
getClassOfNode(self):
"""
return class_of_node
@return: self.class_of_node
@rtype: set
"""
_setTypeOfArc(self):
"""
From self.policy_in_array and self.class_of_node set type_of_arc
@return: _
@rtype: None
"""
getTypeOfArc(self):
"""
return class_of_node
@return: self.class_of_node
@rtype: set
"""
padmetRef.py
Description:
PadmetRef is an object representing a DATABASE of metabolic network.
class PadmetRef:
"""
PadmetRef is an object representing a DATABASE of metabolic network.
Contains <Policy>, <Node> and <Relation>
The policy defines the way Node and Relation are associated
A node is an Object that contains information about an element of the network
(can be a pathway, reaction...).
A realtion defines how two nodes are connected. In a relation there is
a node "in" and a node "out". (reactionX'in' consumes metaboliteX'out')
PadmetRef contains 3 attributs:
dicOfNode: a dictionary of node: key=Node's unique id / value = <Node>
dicOfRelationIn: a dictionnary of relation with: key= nodeIN id / value = list of <relation>
dicOfRelationOut: a dictionnary of relation with: key= nodeOut id / value = list of <relation>
policy: a <policy>
info: a dictionnary of informations about the network, the database used...
This dictionnary is always represented in the header of a padmet file
"""
#==============================================================================
# Constructor / getter
#==============================================================================
setInfo(self,source):
"""
All the information printed in the header of a padmet stocked in a dict.
{"metacyc":{version:XX,...},"ecocyc":{...}...}
set Info from a dictionnary or copying from an other padmet
@param source: may be a dict or an other padmet from where will be copied the info
@tyme source: dict or Padmet
"""
setPolicy(self,source):
"""
Set policy from a list or copying from an other padmet
@param sour
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资源分类:Python库 所属语言:Python 资源全名:padmet-3.1.1.tar.gz 资源来源:官方 安装方法:https://lanzao.blog.csdn.net/article/details/101784059
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