Package for analyzing MS with Python
It can provide the following functionalities now:
- mzXMLParser for fast and efficient mzXML parse
- FPIC method for extracting PICs from raw LC-MS dataset effectively and quickly
In future, more file formats will be supported and more methods will be implemented into PyMass package, so researchers can create complex analysis workflows for LC-MS datasets in Python with ease.
- Visual Studio Community 2015 with Update 3
- Anaconda Python 3.6.0 64bit
- SWIG 3.0.10
- CMake 3.7.1
- Eigen 3.3.3
- Threading Building Blocks 2017 Update 6
- expat
- base64SIMD
- Download pymass
- Unzip it into pymass directory
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Open "VS2015 x64 Native Tools Command Prompt"
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Run following commands in the prompt
cd pymass mkdir build cd build cmake .. -G "NMake Makefiles" -DCMAKE_BUILD_TYPE=Release nmake nmake install
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Go to pymass/python directory
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Download MM14 dataset from this url and unzip it
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Run following Python code fragment to parse mzXML file and extract PICs from it
from _pymass import mzXMLParser, FPICs import sys mzfile="MM14_20um.mzxml" mzfile=mzfile.encode(sys.getfilesystemencoding()) parser=mzXMLParser() lcms = parser.parseFile(mzfile) pics = FPICs(lcms, 300.0, 100.0, 0.5)
For any questions, please contact: