Metadata-Version: 2.1
Name: pythoms
Version: 1.0.3.1
Summary: A Python library to aid in the processing and interpretation of mass spectrometric data.
Home-page: https://github.com/larsyunker/PythoMS
Author: Lars Yunker
License: MIT
Keywords: mass spectrometry,mass spec,mzML,isotope pattern,HUPO PSI-MS
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Operating System :: OS Independent
Classifier: Natural Language :: English
Description-Content-Type: text/markdown
Requires-Dist: numpy (>=1.14.2)
Requires-Dist: openpyxl (>=2.5.2)
Requires-Dist: matplotlib (>=2.1.2)
Requires-Dist: scipy (>=1.1.0)
Requires-Dist: sympy (>=1.1.1)
Requires-Dist: obonet
Requires-Dist: numpy

# mass-spec-python-tools: mass spec made easier

### What is it?
This is a collection of scripts to aid in the processing and interpretation of mass spectrometric data. 

The project was created by Lars Yunker at the University of Victoria, Victoria, B.C.

### Requirements and Installation:
This package has been written for python 3.5+.

##### Getting started

This framework is available on PyPI. To install, execute

`pip install pythoms`

in the command line.

PyPI installations do not include the scripts in this repository.
If you wish to use these scripts, download the entire repository to a
folder on your computer, run `pip install -r requirements.txt` with that
folder as the current working directory (installs the dependencies),
and execute the scripts as needed.

* Python users interested in applying the scripts directly can edit the
    input parameters in the files.
* Developers can import many of the classes to create scripts tailored to
    their needs.

### Errors and Contributing
If you encounter an error, please submit an Issue in Github with as much
information as possible.

Things that are helpful to include:
* the raw file you were trying to parse (zip it first)
* the exact parameters you were using
* any additional files you were supplying to the script
* the error output

We welcome contributions, so if you're interested in contributing please
email larsy[at]uvic{dot}ca. Particularly, we are in need of mzML file
examples where the data was not generated by Proteowizard (intially from
a Waters instrument).

### Scripts:

##### PyRSIR
This script takes supplied raw and parameters files and generates
reconstructred single ion monitoring traces. For specific instructions
on using the PyRSIM script, see [this tutorial video](https://www.youtube.com/watch?v=zc8i54EiCGY)

##### isotope pattern overlay
Takes a supplied mass spectrum and overlays the predicted isotope pattern
onto it.

##### video frame renderer
A tool for generating a series of images showing mass spectrum and
traces which can be combined into a video.

##### y-axis zoom figure
Renders a series of images which zoom into the y-axis to illustrate the
dynamic range of mass spectrometers.

### Highlighted Modules
##### molecule
Contains classes for describing the physico-chemical properties of molecules.
The `IPMolecule` class contains algorithms for predicting the
isotope pattern of said molecule.

##### spectrum
Contains an efficient helper class for combining spectra of different
shape and managing impractically precise x values.

##### mzML
Contains classes for interacting with mzML files in a pythonic manner.

### License
These tools are licensed under the MIT license.

