Important

Maintenance and updates for this project have moved to the csbl/reconstructor repository. Consequently this repository is no longer being updated. Please visit the csbl/reconstructor repository to view the most up-to-date version of the project, report bugs, provide feedback, and/or contribute to the project.

Reconstructor - Current Version: 1.2.0

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.

Installation

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

Note

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.

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.