This python module allows to extract data from the RAW-file-format produces by devices from Thermo Fisher Scientific.

Overview

fisher_py

This Python module allows access to Thermo Orbitrap raw mass spectrometer files. Using this library makes it possible to automate the analysis of mass spectra, without having to export the data first with another tool. This module is a wrapper that builds uppon the RawFileReader project which is a library developed for C#. Structures have been implemented to make processing data more convenient for Python users.

Installation

fisher_py can be installed via the package repository PyPi:

pip install fisher_py

System Requirements

fishery_py shoud work on any modern desktop operating system (Linux, Windows, Mac OS) with Python 3.6 (or higher) installed.

  • Windows: Tested on Windows 10 Pro x64
  • Linux: Tested on Ubuntu 20.04 LTS x64
  • Mac OS: Not tested

The module relies on the RawFileReader DLLs (Dynamic-Linked-Libraries) to be loaded at runtime (using pythonnet). Since Microsoft introduced .NET Standard it is possible to load DLLs compiled with this framework to be loaded on non-Windows systems (such as Mac OS and Linux). However, systems other than Windows may require additional setup steps in order for fisher_py to work. If you have trouble problems installing fisher_py it is probably because of pythonnet not being able to compile. To resolve this the usualy path is to install mono (https://www.mono-project.com/). There are several guides online to do this but one that was tested can be found here.

Examples

The following example demonstrates how to extract and plot data from a raw-file:

import matplotlib.pyplot as plt
from fisher_py import RawFile
from fisher_py.data.business import TraceType
raw_file = RawFile('my_file.raw')

target_mass = 848.36862
mass_tolerance_ppm = 10
rt, i = raw_file.get_chromatogram(target_mass, mass_tolerance_ppm, TraceType.MassRange)
mz, i2, charges, real_rt = raw_file.get_scan_ms1(1)
print(real_rt)

plt.figure()
plt.plot(rt, i)

plt.figure()
plt.plot(mz, i2)

plt.show()

This example may be fine for some use-cases but the RawFile class only provides limited access to all the functionalities and can serve as an example how to use the module wihtin a project. For an example that uses more of the modules capabilites have a look at raw_file_reader_examle.py.

License and copyright

fisher_py (Copyright 2021 ethz-institute-of-microbiology) is licensed under the MIT license.

Third-party licenses and copyright

RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved. See RawFileReaderLicense.md for licensing information. Note: anyone recieving RawFileReader as part of a larger software distribution (in the current context, as part of fisher_py) is considered an "end user" under section 3.3 of the RawFileReader License, and is not granted rights to redistribute RawFileReader.

Get the stats of a (or more) Hypixel player(s)

Hypixel_Stats Get the statistics of a (or more) Hypixel player(s) Who needs this? Everyone who plays a lot of Minecraft and often plays on mc.hypixel.

Finnomator 1 Feb 12, 2022
Make creating Excel XLSX files fun again

Poi: Make creating Excel XLSX files fun again. Poi helps you write Excel sheet in a declarative way, ensuring you have a better Excel writing experien

Ryan Wang 11 Apr 01, 2022
Cisco IOS-XE Operations Program. Shows operational data using restconf and yang

XE-Ops View operational and config data from devices running Cisco IOS-XE software. NoteS The build folder is the latest build. All other files are fo

18 Jul 23, 2022
It really seems like Trump is trying to get his own social media started. Not a huge fan tbh.

FuckTruthSocial It really seems like Trump is trying to get his own social media started. Not a huge fan tbh. (When TruthSocial actually releases, I'l

0 Jul 18, 2022
A basic python project which replicates the functionalities on an 8 Ball.

Magic-8-Ball To the people who wish to make decisions using a Magic 8 Ball but can't get one? I gotchu. This is a basic python project which replicate

3 Jun 24, 2021
An OrpheusDL Tidal module

OrpheusDL - Tidal A Tidal module for the OrpheusDL modular archival music program Report Bug · Request Feature Table of content About OrpheusDL - Tida

Daniel 54 Dec 29, 2022
Wordle is fun, so let's ruin it with computers.

ruin-wordle Wordle is fun, so let's ruin it with computers. Metrics This repository assesses two metrics about each algorithm: Success: how many of th

Charles Tapley Hoyt 11 Feb 11, 2022
Snack Rice - A Rice University servery finder, customized for your needs!

Snack Rice - A Rice University servery finder, customized for your needs!

Aidan Gerber 3 Sep 25, 2022
tagls is a language server based on gtags.

tagls tagls is a language server based on gtags. Why I wrote it? Almost all modern editors have great support to LSP, but language servers based on se

daquexian 31 Dec 01, 2022
Grimoire is a Python library for creating interactive fiction as hyperlinked html.

Grimoire Grimoire is a Python library for creating interactive fiction as hyperlinked html. Installation pip install grimoire-if Usage Check out the

Scott Russell 5 Oct 11, 2022
Fithub is a website application for athletes and fitness enthusiasts of all ages and experience levels.

Fithub is a website application for athletes and fitness enthusiasts of all ages and experience levels. Our website allows users to easily search, filter, and sort our comprehensive database of over

Andrew Wu 1 Dec 13, 2021
Utils to quickly evaluate many 🤗 models on the GLUE tasks

Utils to quickly evaluate many 🤗 models on the GLUE tasks

Przemyslaw K. Joniak 1 Dec 22, 2021
A small Python library which gives you the IEEE-754 representation of a floating point number.

ieee754 ieee754 is small Python library which gives you the IEEE-754 representation of a floating point number. You can specify a precision given in t

Bora Canbula 5 Dec 20, 2022
Refer'd Resume Scanner

Refer'd Resume Scanner I wanted to share a free resource we built to assist applicants with resume building. Our resume scanner identifies potential s

Refer'd 74 Mar 07, 2022
PyCASCLib: CASC interface for Warcraft III

PyCASCLib CASC interface for Warcraft III. This repo provides bindings for JCASC: https://github.com/DrSuperGood/JCASC Installation Jdk is required fo

2 Jun 04, 2022
Object-oriented programming exercise session held in Petnica.

OOP vežba ⚠️ The code in this repo is used for a OOP practice session held in Petnica. All instructions in the README file are written in Serbian. Ops

Pavle Ćirić 1 Jan 30, 2022
Application launcher and environment management

Application launcher and environment management for 21st century games and digital post-production, built with bleeding-rez and Qt.py News Date Releas

10 Nov 03, 2022
Convert-Decimal-to-Binary-Octal-and-Hexadecimal

Convert-Decimal-to-Binary-Octal-and-Hexadecimal We have a number in a decimal number, and we have to convert it into a binary, octal, and hexadecimal

Maanyu M 2 Oct 08, 2021
A python script to make leaderboards using a CSV with the runners name, IDs and Flag Emojis

SrcLbMaker A python script to make speedrun.com global leaderboards. Installation You need python 3.6 or higher. First, go to the folder where you wan

2 Jul 25, 2022
This is a simple python script for checking A/L Examination results of srilankan students

AL-Result-Checker This is a simple python script for checking A/L Examination results of srilankan students INSTALLATION [Termux] [Linux] : apt-get up

Razor Kenway 8 Oct 24, 2022