Wrap pythomics parser for TACC execution

[mwes]

From Chris Mitchell on SD2E/data-etl

random note -- I made some parsers for msf/mzml/etc. files here: https://github.com/pandeylab/pythomics/blob/master/pythomics/proteomics/parsers.py -- I make no promises on their completness, it's very much an as-i-needed-it in grad school. But there are some things that are inconsistent between PD versions (1.4 vs 2+) it addresses and some inconsistencies with ranking (ie confidence lvl 3 is high whereas search rank 1 is high. If you invert this, you are going to have a bad time)

GitHub
pandeylab/pythomics
pythomics - The Pandey Lab is involved in a number of -omic analyses, notably proteomics, transcriptomics, and genomics. This is a set of tools to unify and streamline our computational approaches.

you can pip install that library or just pilfer snippets

or use a reference if you want

also, a spectra viewer that is cross platform and can load msf/mzml/etc.: http://chris7.github.io/SpectraViewer/
chris7.github.io

Spectraviewer
A cross-platform viewer utilizing the QT SDK and pyqtgraph to visualize mass spectrometry peaklist files. Also supported are opening of results from search engines from X!Tandem, Mascot, and Proteome Discoverer as well as raw spectra files. The impetus for this project was a way to view mass spec data on linux since a majority of viewers were lacking.

there are some differences in msf files, like they do not store the complete spectra for a scan for PSMs

so I would recommend complementing all msf files w/ the raw data if you are doing any work on the raw data, as the data thermo stores is not complete