Metagenomix is a Python module for analyzing species composition of a sequenced sample of DNA or RNA.
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To install Metagenomix, either clone or download this repository and run:
python setup.py build install
After you've built Metagenomix, you need to download the information on taxa names, ranks and relationships:
wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdmp.zip
unzip taxdmp.zip
dmp2taxtree nodes.dmp names.dmp ./metagenomix/
python setup.py build install
After the build step, you need to setup the gi to taxonomy mapping database which will enable Metagenomix to map particular organism names to your GI identifiers.
This project is being developed my Ana Bulović. If you have any questions, or wish to leave a comment, you can contact me on https://twitter.com/praxaton, or using a contact form on http://metagen.zesoi.fer.hr.
Copyright (c) 2015 Ana Bulović metagen.zesoi.fer.hr
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.