CathPy - Python Bioinformatics Toolkit for CATH (Protein Classification).
cathpy is a Bioinformatics toolkit written in Python. It is developed and maintained by the
[http://orengogroup.info/](Orengo Group) at https://www.ucl.ac.uk/orengo-group/ and is used for maintaining the [http://www.cathdb.info](CATH protein structure database) (and associated research).
The easiest way to use this code is by installing the latest version into a virtual environment via
$ python3 -m venv venv $ source venv/bin/activate $ pip install cathpy
If everything is installed and working properly then the following should work:
$ cath-align-summary -d tests/data/funfams/ file aln_len seq_count dops gap_per tests/data/funfams/188.8.131.52-ff-14534.reduced.sto 69 51 61.53 12.53 tests/data/funfams/184.108.40.206-ff-15516.reduced.sto 66 429 100.00 13.04 tests/data/funfams/220.127.116.11-ff-5069.reduced.sto 59 14 7.81 3.15 tests/data/funfams/18.104.22.168-ff-15593.reduced.sto 63 203 95.88 17.70
If you are developing the code, then get access to the latest code and create a new branch:
$ git clone firstname.lastname@example.org:UCL/cathpy.git $ cd cathpy $ git checkout -b my-awesome-new-feature
Install the code (as editable package) into virtual environment
$ python3 -m venv venv $ source venv/bin/activate $ pip install -e .
Write your tests, make your changes then make sure all the tests still pass:
Then push your changes back to GitHub and raise a pull request.
$ git push
What is cathpy?
cathpy is a python package that contains bioinformatics tools and libraries
used in CATH (protein structure classification resource at UCL).
Hmmm.. that sounds like Yet Another Python Bioinformatics Toolkit?
Well it is... sort of.
Should I be using it?
If you are looking for a general Bioinformatics toolkit, you should look at BioPython first.
cathpy project does contain some generic functionality that may overlap with BioPython,
however we are definitely not trying to rewrite that library. It has been published mainly for
internal use (within CATH), however it has been released as open source in case others find the tools helpful.
This code base contains external tools that are not written and maintained by the authors of this project. If you use the results of these tools, please reference the relevant papers.
Capra JA and Singh M. Characterization and Prediction of Residues Determining Protein Functional Specificity. Bioinformatics, 24(13): 1473-1480, 2008.
Valdar WSJ (2002). Scoring residue conservation. Proteins: Structure, Function, and Genetics. 43(2): 227-241.
The most recent paper describing the CATH protein structure database:
Ian Sillitoe, et al (2018) CATH: expanding the horizons of structure-based functional annotations for genome sequences. Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D280–D284, https://doi.org/10.1093/nar/gky1097
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