COBRApy Compatible Genome Scale Metabolic Network Reconstruction Tool: Reconstructor
Project description
Reconstructor - Current Version: 1.1.2
This repository contains all source code in the Reconstructor
Python package,
important file dependencies, and benchmarking scores for Reconstructor
models. Reconstructor
is a COBRApy compatible, automated GENRE building tool
from annotated aminoa acid .fasta files based on KEGG annotations.
[!NOTE]
Reconstructor
is currently only compatible on MacOSX and Windows machines
Quick Installation Guide
MacOSX pre-installation steps
In a terminal....
Install homebrew if you do not already have it installed by copying/pasting the following line into the terminal (further instructions here):
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
Download the DIAMOND sequence aligner (version >= 2.0.15) using homebrew:
brew install diamond
Now continue to the instructions for all platforms.
Installation (all platforms)
Install Reconstructor
using pip:
pip install reconstructor
Use following command to download additional dependencies/run final installation checks (should take ~1hr to complete depending on your system):
python -m reconstructor --test yes
See the documentation for additional details about installation.
Usage
Use reconstructor via COMMAND LINE
Now that Reconstructor
and all dependency databases are installed, you can
proceed to use Reconstructor
via the command line. An example would be:
python -m reconstructor --input_file <input fasta file> --file_type <1,2,3> --gram <negative, positive> --media rich
All possible command line arguments are described in a later section.
Type 1: Build GENRE from annotated amino acid .fasta file
python -m reconstructor --input_file Osplanchnicus.aa.fasta --file_type 1 --gram negative --media rich
Type 2: Build GENRE from BLASTp hits
python -m reconstructor --input_file Osplanchnicus.hits.out --file_type 2 --gram negative --media rich
Type 3: Additional gap-filling (if necessary)
python -m reconstructor --input Osplanchnicus.sbml --type 3 --media rich
Use Reconstructor directly in PYTHON
Reconstructor can be imported and used directly in Python for easy integration with COBRApy analysis tools:
from reconstructor import reconstruct
Here is an example of how to generate a GENRE from an annotated amino acid fasta file (.fa, type 1 input) directly in your python script.
model = reconstruct('218496.4.fa', file_type=1, gram='negative')
All arguments for this function are described in the next section.
Required and optional arguments
--input_file <REQUIRED input file, required, str>
--file_type <REQUIRED input file type, .fasta = 1, diamond blastp output = 2, .sbml = 3, Required, Default = 1, int>
--gram <REQUIRED Type of Gram classificiation (positive or negative), default = positive, str>`
--media <REQUIRED 'rich' is the default and can be used to generate model based on a rich media. List of strings of metabolites in modelseed namespace composing the media condition, comma separated. Must end with _e. For example: 'cpd00001_e'.>`
--org <KEGG organism code. Not required, str>
--min_frac <Minimum objective fraction required during gapfilling, default = 0.01, float>
--max_frac <Maximum objective fraction allowed during gapfilling, default = 0.5 ,float>
--out <Name of output GENRE file, default = default, str>
--name <ID of output GENRE, default = default, str>
--cpu <Number of processors to use, default = 1, int>
--test <run installation tests, default = no, str>
Git Repository Structure
reconstructor
Contains the source code for Reconstructor
.
reference
Contains a variety of zipped reference files related to Receonstructor
:
- RepresentativeGENRES.zip (comparison of models created by
Reconstructor
, ModelSeed, and CarveME) - MEMOTE.zip (MEMOTE benchmarking scores for 10 representative
Reconstructor
models) - C_difficile_media.zip (C. Difficile models made with 5 different media)
See the reference folder README for more details about its contents.
docs
Contains documentation files for Reconstructor
.
[!WARNING] The documentation is still very much under development.
Additional Information
Thank you for your interest in Reconstructor
. If you have any additional
questions please open an issue.
If you encounter any problems, please file an issue along with a detailed description.
Distributed under the terms of the MIT license, Reconstructor
is
free and open source software.
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