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|
%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
|
