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Requirements

In order to function, the CoMetGeNe pipeline requires Python 2.7 and the following libraries: lxml (version >=3.5.0) and NetworkX (version >=1.10 and <=2.2). CoMetGeNe is not compatible with Python 3. In order to automatically extract metabolic pathway maps and genomic information from KEGG, CoMetGeNe needs an active internet connection. A multi-core CPU is recommended for faster (multi-threaded) trail finding.

CoMetGeNe has only been tested on GNU/Linux (although it should work under other operating systems).

Stable version

You can download the stable CoMetGeNe version (November 2018) from here: CoMetGeNe_v1.2.tar.gz (52 kb). See also the associated changelog.

Extract CoMetGeNe from the archive as follows:
tar xfz CoMetGeNe_v1.1.tar.gz

Latest version

The latest CoMetGeNe version can be obtained from GitHub.

Older versions

CoMetGeNe version 1.0 (June 2018): CoMetGeNe_v1.0.tar.gz (46 kb)

Optional data files

It is possible to perform trail finding on the 50 bacterial species in Table 2 of the accompanying publication without having to wait for data retrieval from KEGG and/or for computationally expensive pathways to get blacklisted.

  • You can download metabolic pathway maps in KGML format and genomic information (retrieved from KEGG on June 1, 2018) for the 50 bacterial species in Table 2 of our publication from here: data.tar.gz (15.1 Mb). Simply extract the archive to the CoMetGeNe/ project root. Upon extraction, a directory data/ (with subdirectories for all species in Table 2 in our publication) is added to the CoMetGeNe/ project root. In addition, the file kegg_genome_info.pickle is added to the pickle/ directory.
  • You can download the exclusions list (corresponding to blacklisted pathways) from here: excluded_pathways.txt (2 kb). Simply download this file to the CoMetGeNe/ project root.

Results

Results for trail finding for the 50 bacterial species in Table 2 of our accompanying publication, for gap parameters δD and δG ranging from 0 to 3, can be retrieved here: results.tar.gz (5.7 Mb). Execution times for the 50 species are available here.

License

The CoMetGeNe software is available under the MIT license:

MIT License

Copyright (c) 2018 Alexandra Zaharia

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Created by Alexandra Zaharia. Maintained by Alain Denise.
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