diff options
| author | CoprDistGit <infra@openeuler.org> | 2023-05-31 04:46:35 +0000 |
|---|---|---|
| committer | CoprDistGit <infra@openeuler.org> | 2023-05-31 04:46:35 +0000 |
| commit | 789614fea94762c228c5ffd9ada29c50f3efc7a8 (patch) | |
| tree | aecdb7267af931a55f7ded8cf24e15f7149dc4c0 | |
| parent | bf5fb1adfccd73e0eb3f5b8c13593ce37fae1113 (diff) | |
automatic import of python-cathpy
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | python-cathpy.spec | 455 | ||||
| -rw-r--r-- | sources | 1 |
3 files changed, 457 insertions, 0 deletions
@@ -0,0 +1 @@ +/cathpy-0.4.1.tar.gz diff --git a/python-cathpy.spec b/python-cathpy.spec new file mode 100644 index 0000000..2be3afa --- /dev/null +++ b/python-cathpy.spec @@ -0,0 +1,455 @@ +%global _empty_manifest_terminate_build 0 +Name: python-cathpy +Version: 0.4.1 +Release: 1 +Summary: CathPy - Python Bioinformatics Toolkit for CATH (Protein Classification). +License: MIT License +URL: https://github.com/UCL/cathpy +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/17/a3/9e828da752ffbd1923502e6268eb66f6442b2572fcde722b06e933acef27/cathpy-0.4.1.tar.gz +BuildArch: noarch + +Requires: python3-Click +Requires: python3-requests +Requires: python3-jsonpickle +Requires: python3-tqdm +Requires: python3-dendropy +Requires: python3-redis +Requires: python3-celery +Requires: python3-pymongo + +%description +# cathpy + +[](https://cathpy.readthedocs.io/en/latest/?badge=latest) +[](https://travis-ci.com/UCL/cathpy) +[](https://codecov.io/gh/UCL/cathpy) + +`cathpy` is a Bioinformatics toolkit written in Python. It is developed and maintained by the +[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). + + +## Getting Started + +The easiest way to use this code is by installing the latest version into a virtual environment via `pip`: + +```sh +$ python3 -m venv venv +$ source venv/bin/activate +$ pip install cathpy +``` + +If everything is installed and working properly then the following should work: + +```sh +$ cath-align-summary -d tests/data/funfams/ +file aln_len seq_count dops gap_per +tests/data/funfams/1.10.8.10-ff-14534.reduced.sto 69 51 61.53 12.53 +tests/data/funfams/1.10.8.10-ff-15516.reduced.sto 66 429 100.00 13.04 +tests/data/funfams/1.10.8.10-ff-5069.reduced.sto 59 14 7.81 3.15 +tests/data/funfams/1.10.8.10-ff-15593.reduced.sto 63 203 95.88 17.70 +``` + +Now go and [have a look at the documentation](https://cathpy.readthedocs.io/en/latest/). + +## Contributing + +There are many ways to contribute, all of which are most welcome. + + * 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) + * 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) + * 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) + +When 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. + +If 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. + +## Development + +If you are developing, then this is the general recommended flow: + +Get access to the latest version of the code and create a new branch (with a descriptive summary of your new feature/bugfix): + +```sh +$ git clone git@github.com:UCL/cathpy.git +$ cd cathpy +$ git checkout -b my-awesome-new-feature +``` + +Install the code (as editable package) into virtual environment + +```sh +$ python3 -m venv venv +$ source venv/bin/activate +$ pip install -e . +``` + +Write your tests, make your changes then make sure your tests (and all the other tests) still pass: + +```sh +$ vim tests/my_new_feature_test.py +$ vim cathpy/my_new_feature.py +$ pytest +``` + +Then push your changes back to GitHub and raise a pull request through the web pages. + +```sh +$ git push +``` + +## FAQ + +**What is cathpy?** + +`cathpy` is a python package that contains bioinformatics tools and libraries +used in [CATH](http://cathdb.info) (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](https://biopython.org/) first. + +The `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. + +## External software + +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. + +#### GroupSim + +Characterization and Prediction of Residues Determining Protein Functional Specificity. +**Capra JA and Singh M (2008).**<br> +*Bioinformatics, 24(13): 1473-1480, 2008.* + +#### Scorecons + +Scoring residue conservation. +**Valdar WSJ (2002)**<br> +*Proteins: Structure, Function, and Genetics. 43(2): 227-241, 2002.* + +## References + +The most recent paper describing the CATH protein structure database: + +CATH: expanding the horizons of structure-based functional annotations for genome sequences. +**Sillitoe I, et al (2018)**<br> +*Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D280–D284, https://doi.org/10.1093/nar/gky1097* + + + + + +%package -n python3-cathpy +Summary: CathPy - Python Bioinformatics Toolkit for CATH (Protein Classification). +Provides: python-cathpy +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-cathpy +# cathpy + +[](https://cathpy.readthedocs.io/en/latest/?badge=latest) +[](https://travis-ci.com/UCL/cathpy) +[](https://codecov.io/gh/UCL/cathpy) + +`cathpy` is a Bioinformatics toolkit written in Python. It is developed and maintained by the +[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). + + +## Getting Started + +The easiest way to use this code is by installing the latest version into a virtual environment via `pip`: + +```sh +$ python3 -m venv venv +$ source venv/bin/activate +$ pip install cathpy +``` + +If everything is installed and working properly then the following should work: + +```sh +$ cath-align-summary -d tests/data/funfams/ +file aln_len seq_count dops gap_per +tests/data/funfams/1.10.8.10-ff-14534.reduced.sto 69 51 61.53 12.53 +tests/data/funfams/1.10.8.10-ff-15516.reduced.sto 66 429 100.00 13.04 +tests/data/funfams/1.10.8.10-ff-5069.reduced.sto 59 14 7.81 3.15 +tests/data/funfams/1.10.8.10-ff-15593.reduced.sto 63 203 95.88 17.70 +``` + +Now go and [have a look at the documentation](https://cathpy.readthedocs.io/en/latest/). + +## Contributing + +There are many ways to contribute, all of which are most welcome. + + * 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) + * 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) + * 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) + +When 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. + +If 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. + +## Development + +If you are developing, then this is the general recommended flow: + +Get access to the latest version of the code and create a new branch (with a descriptive summary of your new feature/bugfix): + +```sh +$ git clone git@github.com:UCL/cathpy.git +$ cd cathpy +$ git checkout -b my-awesome-new-feature +``` + +Install the code (as editable package) into virtual environment + +```sh +$ python3 -m venv venv +$ source venv/bin/activate +$ pip install -e . +``` + +Write your tests, make your changes then make sure your tests (and all the other tests) still pass: + +```sh +$ vim tests/my_new_feature_test.py +$ vim cathpy/my_new_feature.py +$ pytest +``` + +Then push your changes back to GitHub and raise a pull request through the web pages. + +```sh +$ git push +``` + +## FAQ + +**What is cathpy?** + +`cathpy` is a python package that contains bioinformatics tools and libraries +used in [CATH](http://cathdb.info) (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](https://biopython.org/) first. + +The `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. + +## External software + +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. + +#### GroupSim + +Characterization and Prediction of Residues Determining Protein Functional Specificity. +**Capra JA and Singh M (2008).**<br> +*Bioinformatics, 24(13): 1473-1480, 2008.* + +#### Scorecons + +Scoring residue conservation. +**Valdar WSJ (2002)**<br> +*Proteins: Structure, Function, and Genetics. 43(2): 227-241, 2002.* + +## References + +The most recent paper describing the CATH protein structure database: + +CATH: expanding the horizons of structure-based functional annotations for genome sequences. +**Sillitoe I, et al (2018)**<br> +*Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D280–D284, https://doi.org/10.1093/nar/gky1097* + + + + + +%package help +Summary: Development documents and examples for cathpy +Provides: python3-cathpy-doc +%description help +# cathpy + +[](https://cathpy.readthedocs.io/en/latest/?badge=latest) +[](https://travis-ci.com/UCL/cathpy) +[](https://codecov.io/gh/UCL/cathpy) + +`cathpy` is a Bioinformatics toolkit written in Python. It is developed and maintained by the +[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). + + +## Getting Started + +The easiest way to use this code is by installing the latest version into a virtual environment via `pip`: + +```sh +$ python3 -m venv venv +$ source venv/bin/activate +$ pip install cathpy +``` + +If everything is installed and working properly then the following should work: + +```sh +$ cath-align-summary -d tests/data/funfams/ +file aln_len seq_count dops gap_per +tests/data/funfams/1.10.8.10-ff-14534.reduced.sto 69 51 61.53 12.53 +tests/data/funfams/1.10.8.10-ff-15516.reduced.sto 66 429 100.00 13.04 +tests/data/funfams/1.10.8.10-ff-5069.reduced.sto 59 14 7.81 3.15 +tests/data/funfams/1.10.8.10-ff-15593.reduced.sto 63 203 95.88 17.70 +``` + +Now go and [have a look at the documentation](https://cathpy.readthedocs.io/en/latest/). + +## Contributing + +There are many ways to contribute, all of which are most welcome. + + * 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) + * 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) + * 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) + +When 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. + +If 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. + +## Development + +If you are developing, then this is the general recommended flow: + +Get access to the latest version of the code and create a new branch (with a descriptive summary of your new feature/bugfix): + +```sh +$ git clone git@github.com:UCL/cathpy.git +$ cd cathpy +$ git checkout -b my-awesome-new-feature +``` + +Install the code (as editable package) into virtual environment + +```sh +$ python3 -m venv venv +$ source venv/bin/activate +$ pip install -e . +``` + +Write your tests, make your changes then make sure your tests (and all the other tests) still pass: + +```sh +$ vim tests/my_new_feature_test.py +$ vim cathpy/my_new_feature.py +$ pytest +``` + +Then push your changes back to GitHub and raise a pull request through the web pages. + +```sh +$ git push +``` + +## FAQ + +**What is cathpy?** + +`cathpy` is a python package that contains bioinformatics tools and libraries +used in [CATH](http://cathdb.info) (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](https://biopython.org/) first. + +The `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. + +## External software + +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. + +#### GroupSim + +Characterization and Prediction of Residues Determining Protein Functional Specificity. +**Capra JA and Singh M (2008).**<br> +*Bioinformatics, 24(13): 1473-1480, 2008.* + +#### Scorecons + +Scoring residue conservation. +**Valdar WSJ (2002)**<br> +*Proteins: Structure, Function, and Genetics. 43(2): 227-241, 2002.* + +## References + +The most recent paper describing the CATH protein structure database: + +CATH: expanding the horizons of structure-based functional annotations for genome sequences. +**Sillitoe I, et al (2018)**<br> +*Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D280–D284, https://doi.org/10.1093/nar/gky1097* + + + + + +%prep +%autosetup -n cathpy-0.4.1 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-cathpy -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Wed May 31 2023 Python_Bot <Python_Bot@openeuler.org> - 0.4.1-1 +- Package Spec generated @@ -0,0 +1 @@ +4dbdb3e76ca803022b34bf9669c1adf0 cathpy-0.4.1.tar.gz |