jonls / psamm-import

Import tool for PSAMM containing importers for SBML format and a number of published Excel formats

PSAMM model importers

PSAMM is an open source software that is designed for the curation and analysis of metabolic models. It supports model version tracking, model annotation, data integration, data parsing and formatting, consistency checking, automatic gap filling, and model simulations.

The PSAMM model importers in this repository is collection of tools that allow metabolic models to be converted from various formats to the internal YAML-based format used by PSAMM.

The master branch tracks the latest release while the develop branch is the latest version in development. Please apply any pull requests to the develop branch when creating the pull request.

Overview

This package provides two additional commands, psamm-import and psamm-import-bigg. The psamm-import command allows the user to convert various model files to YAML format. The conversion of SBML, COBRA JSON and a number of Excel model formats are supported. The Excel format importers are manually designed to load a specific model correctly, so only a limited set of Excel models can be loaded. The SBML and COBRA JSON importers can be used with any valid model in those formats. To see a list of all the supported importers, use the following command:

$ psamm-import list

To import an SBML model from the file ecoli_sbml_file.xml and extract it as a YAML model in the directory ecoli_yaml:

$ psamm-import sbml --source ecoli_sbml_file.xml \
    --dest ecoli_yaml

The psamm-import-bigg command can be used to automatically download a model from the BiGG online model database and convert it to YAML format. This requires internet connection while running the command. To see a list of all the available models in the database, use the following command:

$ psamm-import-bigg list

To import the e_coli_core model and extract it as a YAML model in the directory e_coli_core:

$ psamm-import-bigg e_coli_core --dest e_coli_core

Install and documentation

Please see the main documentation for PSAMM that is available at Read the Docs.

Software license

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.

See LICENSE.