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diff --git a/python-psims.spec b/python-psims.spec new file mode 100644 index 0000000..4652304 --- /dev/null +++ b/python-psims.spec @@ -0,0 +1,292 @@ +%global _empty_manifest_terminate_build 0 +Name: python-psims +Version: 1.2.4 +Release: 1 +Summary: Writers and controlled vocabulary manager for PSI-MS's mzML and mzIdentML standards +License: Apache Software License +URL: https://github.com/mobiusklein/psims +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/20/cb/dcfe05da20f8af92093b0bf2c2335f806500d789bbb03c8622722e7a252c/psims-1.2.4.tar.gz +BuildArch: noarch + +Requires: python3-lxml +Requires: python3-six +Requires: python3-sqlalchemy +Requires: python3-numpy +Requires: python3-h5py +Requires: python3-hdf5plugin +Requires: python3-pynumpress +Requires: python3-h5py +Requires: python3-hdf5plugin +Requires: python3-pynumpress + +%description +# psims +Prototype work for a unified API for writing Proteomics Standards Initiative standardized formats +for mass spectrometry: + +1. mzML +2. mzIdentML +3. mzMLb + +See the [Documenation](https://mobiusklein.github.io/psims) for more information + +## Installation +With pip: +```sh +pip install psims +``` + +With conda: +```sh +conda install -c bioconda -c conda-forge -c defaults psims +``` + +## mzML Minimal Example + +```python +from psims.mzml.writer import MzMLWriter + +# Load the data to write +scans = get_scan_data() + +with MzMLWriter(open("out.mzML", 'wb'), close=True) as out: + # Add default controlled vocabularies + out.controlled_vocabularies() + # Open the run and spectrum list sections + with out.run(id="my_analysis"): + spectrum_count = len(scans) + sum([len(products) for _, products in scans]) + with out.spectrum_list(count=spectrum_count): + for scan, products in scans: + # Write Precursor scan + out.write_spectrum( + scan.mz_array, scan.intensity_array, + id=scan.id, params=[ + "MS1 Spectrum", + {"ms level": 1}, + {"total ion current": sum(scan.intensity_array)} + ]) + # Write MSn scans + for prod in products: + out.write_spectrum( + prod.mz_array, prod.intensity_array, + id=prod.id, params=[ + "MSn Spectrum", + {"ms level": 2}, + {"total ion current": sum(prod.intensity_array)} + ], + # Include precursor information + precursor_information={ + "mz": prod.precursor_mz, + "intensity": prod.precursor_intensity, + "charge": prod.precursor_charge, + "scan_id": prod.precursor_scan_id, + "activation": ["beam-type collisional dissociation", {"collision energy": 25}], + "isolation_window": [prod.precursor_mz - 1, prod.precursor_mz, prod.precursor_mz + 1] + }) +``` + +## Citing + +If you use `psims` in an academic project, please cite: + + Klein, J. A., & Zaia, J. (2018). psims - A declarative writer for mzML and mzIdentML for Python. Molecular & Cellular Proteomics, mcp.RP118.001070. https://doi.org/10.1074/mcp.RP118.001070 + + +%package -n python3-psims +Summary: Writers and controlled vocabulary manager for PSI-MS's mzML and mzIdentML standards +Provides: python-psims +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-psims +# psims +Prototype work for a unified API for writing Proteomics Standards Initiative standardized formats +for mass spectrometry: + +1. mzML +2. mzIdentML +3. mzMLb + +See the [Documenation](https://mobiusklein.github.io/psims) for more information + +## Installation +With pip: +```sh +pip install psims +``` + +With conda: +```sh +conda install -c bioconda -c conda-forge -c defaults psims +``` + +## mzML Minimal Example + +```python +from psims.mzml.writer import MzMLWriter + +# Load the data to write +scans = get_scan_data() + +with MzMLWriter(open("out.mzML", 'wb'), close=True) as out: + # Add default controlled vocabularies + out.controlled_vocabularies() + # Open the run and spectrum list sections + with out.run(id="my_analysis"): + spectrum_count = len(scans) + sum([len(products) for _, products in scans]) + with out.spectrum_list(count=spectrum_count): + for scan, products in scans: + # Write Precursor scan + out.write_spectrum( + scan.mz_array, scan.intensity_array, + id=scan.id, params=[ + "MS1 Spectrum", + {"ms level": 1}, + {"total ion current": sum(scan.intensity_array)} + ]) + # Write MSn scans + for prod in products: + out.write_spectrum( + prod.mz_array, prod.intensity_array, + id=prod.id, params=[ + "MSn Spectrum", + {"ms level": 2}, + {"total ion current": sum(prod.intensity_array)} + ], + # Include precursor information + precursor_information={ + "mz": prod.precursor_mz, + "intensity": prod.precursor_intensity, + "charge": prod.precursor_charge, + "scan_id": prod.precursor_scan_id, + "activation": ["beam-type collisional dissociation", {"collision energy": 25}], + "isolation_window": [prod.precursor_mz - 1, prod.precursor_mz, prod.precursor_mz + 1] + }) +``` + +## Citing + +If you use `psims` in an academic project, please cite: + + Klein, J. A., & Zaia, J. (2018). psims - A declarative writer for mzML and mzIdentML for Python. Molecular & Cellular Proteomics, mcp.RP118.001070. https://doi.org/10.1074/mcp.RP118.001070 + + +%package help +Summary: Development documents and examples for psims +Provides: python3-psims-doc +%description help +# psims +Prototype work for a unified API for writing Proteomics Standards Initiative standardized formats +for mass spectrometry: + +1. mzML +2. mzIdentML +3. mzMLb + +See the [Documenation](https://mobiusklein.github.io/psims) for more information + +## Installation +With pip: +```sh +pip install psims +``` + +With conda: +```sh +conda install -c bioconda -c conda-forge -c defaults psims +``` + +## mzML Minimal Example + +```python +from psims.mzml.writer import MzMLWriter + +# Load the data to write +scans = get_scan_data() + +with MzMLWriter(open("out.mzML", 'wb'), close=True) as out: + # Add default controlled vocabularies + out.controlled_vocabularies() + # Open the run and spectrum list sections + with out.run(id="my_analysis"): + spectrum_count = len(scans) + sum([len(products) for _, products in scans]) + with out.spectrum_list(count=spectrum_count): + for scan, products in scans: + # Write Precursor scan + out.write_spectrum( + scan.mz_array, scan.intensity_array, + id=scan.id, params=[ + "MS1 Spectrum", + {"ms level": 1}, + {"total ion current": sum(scan.intensity_array)} + ]) + # Write MSn scans + for prod in products: + out.write_spectrum( + prod.mz_array, prod.intensity_array, + id=prod.id, params=[ + "MSn Spectrum", + {"ms level": 2}, + {"total ion current": sum(prod.intensity_array)} + ], + # Include precursor information + precursor_information={ + "mz": prod.precursor_mz, + "intensity": prod.precursor_intensity, + "charge": prod.precursor_charge, + "scan_id": prod.precursor_scan_id, + "activation": ["beam-type collisional dissociation", {"collision energy": 25}], + "isolation_window": [prod.precursor_mz - 1, prod.precursor_mz, prod.precursor_mz + 1] + }) +``` + +## Citing + +If you use `psims` in an academic project, please cite: + + Klein, J. A., & Zaia, J. (2018). psims - A declarative writer for mzML and mzIdentML for Python. Molecular & Cellular Proteomics, mcp.RP118.001070. https://doi.org/10.1074/mcp.RP118.001070 + + +%prep +%autosetup -n psims-1.2.4 + +%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-psims -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Mon May 15 2023 Python_Bot <Python_Bot@openeuler.org> - 1.2.4-1 +- Package Spec generated |