FingerID Files

This is FingerID-1.3.1 release.


License:
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FingerID is licensed under GPLv3.


Features:
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1. Fingerprint generation order bug fixed
2. Code is re-organized, comments are added. 
3. Metlin XML format mass spectra parser is added. 
4. Kernel function are fixed to probability product kernels with peaks+mass_loss (kernel type 4 in the older version). 
5. Setup script is provided. 
6. Test case is updated.


Prerequisite:
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1. FingerID is running on Unix/Linux like system.
2. Openbabel 2.3.0 is installed and the system variable BABELPATH to the folder contains binaries (i.e. the bin folders after build where the babel and other executables reside in).
3. Libsvm-3.17 python interface is installed and the system variable PYTHONPATH contains the folder of ".../libsvm-3.17/python/"


Install:
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Three ways to use the package:
1. "python setup.py install" if you have root permission.
2. "python setup.py install --user" if you do not have root permission.
3. In the script, add this package folder to sys.path with sys.path.append(".../fingerid_1.3") if you do not want to install at all.


Instructions:
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A test case uses FingerID-1.3 can be found in ".../fingerid_1.3/tests/fingerid_tests.py" with all the necessary instructions including parameter setting, pip-line running.


References:
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Shen, H., Zamboni, N., Heinonen, M., Rousu, J.: Metabolite identification through machine learning— tackling casmi challenge using fingerid. Metabolites 3(2), 484–505 (2013)

Heinonen, M., Shen, H., Zamboni, N., Rousu, J.: Metabolite identification and molecular fingerprint prediction through machine learning. Bioinformatics 28(18), 2333–2341 (2012)