clean repo for public

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
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+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/

LICENSE

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+MIT License
+
+Copyright (c) 2020 tkschmidt
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+

README.md

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+
+# MasterSpectrum
+This software was used for my master thesis in 2016. The aim was to find diagnostic ions and eventually remove them to improve identification of MS/MS spectra. It finally shined in 2018 as a tool to quickly find systematic side products of 21 post-translational protein modifications https://doi.org/10.1074/mcp.TIR118.000783.
+
+The original filtering option was also the reason for repository name *mgf_filter*
+
+## What is does?
+**MasterSpectrum** is a representation of one or more spectra and consists of MasterPeaks.
+The aggregation has to be fuzzy in m/z space because same measurenment of the same peptide can result in different decimal places. After inserting a spectrum into a Masterspectrum every peak is normalized to a relative value between [0, 1] based on the most
+intense peak. This is necessary to provide an easier way to compare intensity between different measurenments.
+
+
+Insertion of a peak triggers a search for similar MasterPeaks. A peak is defined as similar
+to a MasterPeak if the peak lies within a predefined m/z window of a found MasterPeak.
+These windows can be defined relative to the m/z value of the actual peak (ppm) or by
+a fix distance (Da). As a standard setting for all analysis a windows size of 20 ppm was
+used.
+
+### A search can result in three different actions:
+1. If no similar peak is found, a peak is converted to MasterPeak and is placed into MasterSpectrum according to its m/z value. Every new MasterPeak saves also the number of already aggregated peaks and its starting m/z value
+2. If a similar peak is found, the search has to be further refined.  
+  - If the next MasterPeak above or below the found m/z value is not similar to the searched peak, the first found MasterPeak and the inserted peak merge 
+  - If the next MasterPeak above or below the found m/z is also similar to the searched peak, all three peaks are merged Merging of one or two MasterPeaks with a new peak results alwawys in a new MasterPeak. The M/z values are adjusted to the weighted average of all found MasterPeaks and the new peak. 
+
+
+To speed up insertion, all function calls that consist of numeric calculation (i) (re)calculation of m/z windows, (ii) weighted averages and (iii) normalisation were replaced with C functions. 
+
+Results of MasterSpectrum can be saved as a CSV file for analysis or reimported if more aggregation with additional MGF files is necessary.
+Because MasterSpectrum allows a fast search in m/z space it was also used for different tasks e.g. creating a filter for peaks.
+To ensure correctness of MasterSpectrum within its specification and because it works on loosly defined files as MGF files a test suit of 40 test cases for the basic implementation of MasterSpectrum was added. All test cases can be run with minimised real data and
+takes about 20 seconds. After all a code coverage of about 82 % was achieved.
+
+# Installation
+The package is not (yet) pushed to Pypi, but it is easily installable via pip (requires a up-to-date pip version `pip install -U pip`)
+```
+pip install -e git+https://github.com/kusterlab/[email protected]#egg=mgf_filter
+```
+
+## Platform Dependency
+MasterSpectrum is available on Windows, UNIX/Linux and Mac OSX and the only necessary dependency is a working Python installation and a C compiler.
+
+# How to run it
+
+```
+MasterSpectrum create /MGF/PATH/lorem.mgf /tmp/ True
+```
+First argument => path to mgf
+Second argument => output folder
+Third argument => aggregation take **not** care of precursor charge
+
+## Output
+
+| mz               | intensity          | counts | left border      | right border     | start_mz  | ms1_charge | rel_intensity_ratio | counts_ratio | 
+|------------------|--------------------|--------|------------------|------------------|-----------|------------|---------------------|--------------| 
+| 175.10254        | 0.0107771314851379 | 1      | 175.0990379492   | 175.1060420508   | 175.10254 | 0          | 0                   | 0            | 
+| 175.106629101904 | 1.60120116043193   | 27     | 175.103126969322 | 175.110131234486 | 175.10474 | 0          | 0                   | 0            | 
+| 175.1121535397   | 0.119175527922278  | 3      | 175.108651296629 | 175.115655782771 | 175.11229 | 0          | 0                   | 0            | 
+| 175.119032460438 | 430.916364238763   | 4338   | 175.115530079789 | 175.122534841087 | 175.11354 | 0          | 0                   | 0            | 
+| 175.133620190728 | 0.25654267792363   | 9      | 175.130117518324 | 175.137122863132 | 175.13344 | 0          | 0                   | 0            | 
+
+### Explanation
+
+| Output variable     	| explanation                                                                         	|
+|---------------------	|-------------------------------------------------------------------------------------	|
+| mz                  	| mz of the aggregated MasterPeak                                                     	|
+| intensity           	| intensity weighted m/z average of all peaks                                         	|
+|                     	| number of aggregated peaks in a MasterPeak                                          	|
+| left border         	| left border of MasterPeak                                                           	|
+| right border        	| right border of MasterPeak                                                          	|
+| start_mz            	| original mz value of the first peak in a MasterPeak (to investigate drift of peaks) 	|
+| ms1_charge          	| deprecated                                                                          	|
+| rel_intensity_ratio 	| feature used for folded MasterSpectra                                               	|
+| counts_ratio        	| feature used for folded MasterSpectra                                               	|
+
+
+## Help
+**MasterSpectrum** provides a lot of different functionalities and the help manual should provide a good starting point.
+
+```
+>>> MasterSpectrum -h 
+
+
+usage: MasterSpectrum [-h]
+                      {create,fold,patch,bruteforce_patch,extract,precursor,mascotExclusion,seperateMgfbyScore,allDelta,reinstate,deleteAminoAcidDelta,apl}
+                      ...
+
+mgf_filter
+
+positional arguments:
+  {create,fold,patch,bruteforce_patch,extract,precursor,mascotExclusion,seperateMgfbyScore,allDelta,reinstate,deleteAminoAcidDelta,apl}
+                        commands
+    create              takes an MGF files and creates a MasterSpectrum based
+                        on a 20 ppm window, it can ignore charges
+    fold                it takes two MGF files and creates a relative spectrum
+                        between both runs based on a 20 ppm window. it cant
+                        ignore charges
+    patch               creates a MasterSpectrum based on 1-N exclusion lists
+    bruteforce_patch    creates a MasterSpectrum similar to the already
+                        published results
+    extract             extract important information from a pepxml
+    precursor           generates a MasterSpectrum with m/z values relative to
+                        precursor value
+    mascotExclusion     delete peaks based on a provided peptide length and/or
+                        an additional mass
+    seperateMgfbyScore  generate two spectra seperated by a provided score
+                        cuttoff
+    allDelta            calculate all possible deltas given a minimal relative
+                        intensity
+    reinstate           takes two mgfs and reports difference in intensity
+                        world as a new MGF file
+    deleteAminoAcidDelta
+                        takes a list of possible amino acid deltas and deletes
+                        such peaks in a MasterSpectrum
+    apl                 convert an folder full of apl files to a single MGF
+                        file
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+```