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"description": "# cathpy\n\n[](https://cathpy.readthedocs.io/en/latest/?badge=latest)\n[](https://travis-ci.com/UCL/cathpy)\n[](https://codecov.io/gh/UCL/cathpy)\n\n`cathpy` is a Bioinformatics toolkit written in Python. It is developed and maintained by the\n[Orengo Group](http://orengogroup.info/) at [UCL](https://www.ucl.ac.uk/orengo-group/) and is used for maintaining the [CATH protein structure database](http://www.cathdb.info) (and associated research).\n\n\n## Getting Started\n\nThe easiest way to use this code is by installing the latest version into a virtual environment via `pip`:\n\n```sh\n$ python3 -m venv venv\n$ source venv/bin/activate\n$ pip install cathpy\n```\n\nIf everything is installed and working properly then the following should work:\n\n```sh\n$ cath-align-summary -d tests/data/funfams/\nfile aln_len seq_count dops gap_per\ntests/data/funfams/1.10.8.10-ff-14534.reduced.sto 69 51 61.53 12.53\ntests/data/funfams/1.10.8.10-ff-15516.reduced.sto 66 429 100.00 13.04\ntests/data/funfams/1.10.8.10-ff-5069.reduced.sto 59 14 7.81 3.15\ntests/data/funfams/1.10.8.10-ff-15593.reduced.sto 63 203 95.88 17.70\n```\n\nNow go and [have a look at the documentation](https://cathpy.readthedocs.io/en/latest/).\n\n## Contributing\n\nThere are many ways to contribute, all of which are most welcome.\n\n * If something is not clear then you have identified a gap in the documentation, please let us know by [raising a new issue](https://github.com/UCL/cathpy/issues/new) \n * If it looks like you should be able to do something that you can't then you've either identified a new feature request or a documentation gap - please let us know by [raising a new issue](https://github.com/UCL/cathpy/issues/new)\n * If you have noticed some unexpected behaviour, you may have found a bug - please let us know by [raising a new issue](https://github.com/UCL/cathpy/issues/new)\n\nWhen you do raise an issue, it is extremely helpful if you first check that a similar issue has not already been registered. It would also be great if you can be as clear, concise and specific as possible. If you are reporting a potential bug, please try to provide steps that will allow us to reproduce the unexpected behaviour.\n\nIf you accompany your issue with a Pull Request that actually solves the documentation / feature request / bug fix then you may well be eligible for doughnuts.\n\n## Development\n\nIf you are developing, then this is the general recommended flow:\n\nGet access to the latest version of the code and create a new branch (with a descriptive summary of your new feature/bugfix):\n\n```sh\n$ git clone git@github.com:UCL/cathpy.git\n$ cd cathpy\n$ git checkout -b my-awesome-new-feature\n```\n\nInstall the code (as editable package) into virtual environment\n\n```sh\n$ python3 -m venv venv\n$ source venv/bin/activate\n$ pip install -e .\n```\n\nWrite your tests, make your changes then make sure your tests (and all the other tests) still pass:\n\n```sh\n$ vim tests/my_new_feature_test.py\n$ vim cathpy/my_new_feature.py\n$ pytest\n```\n\nThen push your changes back to GitHub and raise a pull request through the web pages.\n\n```sh\n$ git push\n```\n\n## FAQ\n\n**What is cathpy?**\n\n`cathpy` is a python package that contains bioinformatics tools and libraries\nused in [CATH](http://cathdb.info) (protein structure classification resource at UCL).\n\n**Hmmm.. that sounds like Yet Another Python Bioinformatics Toolkit?**\n\nWell it is... sort of.\n\n**Should I be using it?**\n\nIf you are looking for a general Bioinformatics toolkit, you should look at [BioPython](https://biopython.org/) first.\n\nThe `cathpy` project does contain some generic functionality that may overlap with BioPython,\nhowever we are definitely not trying to rewrite that library. It has been published mainly for \ninternal use (within CATH), however it has been released as open source in case others find the tools helpful.\n\n## External software\n\nThis code base contains external tools that are not written and maintained by the authors\nof this project. If you use the results of these tools, please reference the relevant papers.\n\n#### GroupSim\n\nCharacterization and Prediction of Residues Determining Protein Functional Specificity.\n**Capra JA and Singh M (2008).**
\n*Bioinformatics, 24(13): 1473-1480, 2008.*\n\n#### Scorecons\n\nScoring residue conservation.\n**Valdar WSJ (2002)**
\n*Proteins: Structure, Function, and Genetics. 43(2): 227-241, 2002.*\n\n## References\n\nThe most recent paper describing the CATH protein structure database:\n\nCATH: expanding the horizons of structure-based functional annotations for genome sequences.\n**Sillitoe I, et al (2018)**
\n*Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D280\u2013D284, https://doi.org/10.1093/nar/gky1097*\n\n\n\n",
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