mpwt 0.2.9.12a1

Multiprocessing for Pathway-Tools

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.

Table of contents

• Installation

  • Requirements

  • Using pip

• Use

  • Input data

  • Example

  • Useful functions

  • Errors

Installation

Requirements

You must have an environment where Pathway-Tools is installed. Pathway-Tools can be obtained here. For some versions you need to have Blast installed on you system, for further informations look at this page.

If your OS doesn’t support Pathway-Tools, you can use a docker. If it’s your case, look at 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

pip install mpwt

Use

Input data

The script takes a folder containing sub-folders as input. Each sub-folder contains a genbank file.

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

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.