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.
Install Reconstructor using pip:
pip install reconstructorUse following command to download additional dependencies/run final installation checks (should take ~1hr to complete depending on your system):
python -m reconstructor --test yesNote
Running the test suite will automatically download a DIAMOND database and a
DIAMOND binary for blasting. If you do not want it to automatically download
the DIAMOND binary, then you can use the --skip-diamond option. See the
documentation for details.
See the documentation for additional details about installation.
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 richAll possible command line arguments are described in a later section.
python -m reconstructor --input_file Osplanchnicus.aa.fasta --file_type 1 --gram negative --media richpython -m reconstructor --input_file Osplanchnicus.hits.out --file_type 2 --gram negative --media richpython -m reconstructor --input Osplanchnicus.sbml --type 3 --media richReconstructor can be imported and used directly in Python for easy integration with COBRApy analysis tools:
from reconstructor import reconstructHere 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.
--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>If you use Reconstructor in your work, please cite the following publication:
Jenior ML, Glass EM, Papin JA. Reconstructor: a COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling. Bioinformatics. 2023;39: btad367. doi:10.1093/bioinformatics/btad367
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.