A python command line tool for the quantification of peptidoform/proteoforms
Project description
Proteoformquant
Proteoformquant is a Python tool for quantitative analysis of proteoforms from mass spectrometry data.
Setup/Installation
Via PyPi repository (Recommended)
1. Install Proteoformquant package
The simplest way to use Proteformquant is to downloading it as a package from the PyPi repository using pip.
pip install proteoformquant
You should then be able to run Proteoformquant by running the following line in a terminal
2. Run Proteoformquant
proteoformquant
Access help by running
proteoformquant -h
More information on how to use proteoformquant is avaible in the 'usage' section of this document.
Via github (Alternative) (not available currently)
You also have the possibility to clone the repository from github and manually install the dependencies. You will need to create a Conda environment.
1. Install Conda (and Mamba)
If not already done, install Conda (https://docs.conda.io/projects/conda/en/stable/user-guide/install/index.html#regular-installation)
If you wish to use Mamba to create the Conda environment (faster) you can install mamba by running the following command in a terminal:
conda install mamba -n base -c conda-forge
2. Clone proteoformquant repository
git clone https://github.com/arthur-grimaud/Proteoformquant.git
3. Create and activate the environment
Next, create the environment using either Conda or Mamba by running the following command in the folder where 'environment.yml' is located
# With Conda
conda env create --file environment.yml
#With Manba
mamba env create --file environment.yml
you should now be able to activate the environment with:
mamba activate pfq-env
4. Run Proteoformquant
Run Proteoformquant by running the 'proteoformquant.py' script in 'src/proteoformquant'
python3 src/proteoformquant/proteoformquant.py
Usage
(n.b the command line listed here are given for the installation of Proteoformquant as a package. you will need to adapt the commands if you use the second installation method)
Proteoform requires 3 input files: -spectra file (.mgf or .mzml) -indentification file (.mzid) -a parameter file (.json)
A parameter file can be generated by running.
proteoformquant -cp
If you do not change the name or location of the parameter file you can run proteoformquant as follow
proteoformquant -i path/to/identification/file.mzid -s path/to/spectra/file.mgf
by default this will create an output file 'output/' in the local directory. If you wish to change that use the -d parameter
proteoformquant -i path/to/identification/file.mzid -s path/to/spectra/file.mgf -d path/to/my_output_folder
similarly you can change the outfile name with the -o parameter
proteoformquant -i path/to/identification/file.mzid -s path/to/spectra/file.mgf -d path/to/my_output_folder -o output_file_1
Contributing
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License
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