Metadata-Version: 1.1
Name: mpwt
Version: 0.2.9.9.1a1
Summary: Multiprocessing for Pathway-Tools
Home-page: https://gitlab.inria.fr/abelcour/mpwt
Author: A. Belcour
Author-email: arnaud.belcour@gmail.com
License: UNKNOWN
Description: .. image:: https://img.shields.io/pypi/v/mpwt.svg
        	:target: https://pypi.python.org/pypi/mpwt
        
        Pathway-tools multiprocessing script
        ====================================
        
        mpwt is a python package for running Pathway-Tools on multiple genomes using multiprocessing.
        
        There is no guarantee that this script will work, it is a Work In Progress in early state.
        
        .. contents:: Table of contents
           :backlinks: top
           :local:
        
        Installation
        ------------
        
        Requirements
        ~~~~~~~~~~~~
        
        You must have an environment where Pathway-Tools is installed. Pathway-Tools can be obtained `here <http://bioinformatics.ai.sri.com/ptools/>`__.
        For some versions you need to have Blast installed on you system, for further informations look at `this page <http://bioinformatics.ai.sri.com/ptools/installation-guide/released/blast.html>`__.
        
        If your OS doesn't support Pathway-Tools, you can use a docker. If it's your case, look at `Pathway-Tools Multiprocessing Docker <https://github.com/ArnaudBelcour/pathway-tools-multiprocessing-docker>`__.
        It is a dockerfile that will create container with Pathway-Tools, its dependancies and this package. You just need to give a Pathway-Tools installer as input.
        
        Using pip
        ~~~~~~~~~
        
        .. code:: sh
        
        	pip install mpwt
        
        Use
        ---
        
        Input data
        ~~~~~~~~~~
        
        The script takes a folder containing sub-folders as input. Each sub-folder contains a genbank file.
        
        .. code-block:: text
        
            Folder_input
            ├── Folder_for_species_1
            │   └── Genbank_species_1
            ├── Folder_for_species_2
            │   └── Genbank_species_2
            ├── Folder_for_species_3
            │   └── Genbank_species_3
            │
        
        Pathway-Tools will run on each genbank file. It will create an output folder containing all the result files from the PathoLogic inference for each species.
        
        Example
        ~~~~~~~
        
        .. code:: python
        
            import mpwt
        
            folder_input = "path/to/folder/input"
            folder_output = "path/to/folder/output"
        
            mpwt.multiprocess_pwt(folder_input, folder_output)
        
        Useful functions
        ~~~~~~~~~~~~~~~~
        
        1. multiprocess_pwt(folder_input, folder_output)
        
        folder_input: folder containing sub-folders with Genbank file inside.
        
        folder_output: output folder where all the result of Pathway-Tools will be moved. This argument is optional
        If you don't enter an argument, results will be stored in a folder named output inside the sub-folders containg Genbank file.
        
        2. cleaning()
        
        Delete all the previous PGDB and the metadata files.
        
        Errors
        ~~~~~~
        
        If you encounter errors (and it is highly possible) there is some tips that can help you resolved them.
        
        For error during PathoLogic inference, a log is created where you launch the command.
        The log contains the summary of the build and the error for each species.
        There is also a pathologic.log in each sub-folders.
        
        For others errors, currently nothing is made to help you.
        Maybe in the future.
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 2
