RunAssessor

The RunAssessor package provides functionality for assessing a set of input mass spectrometry proteomics mzML files, extracting all information that can be gleaned from the files prior to any attempt to identify the peptides therein.

Installation

Clone the repo and install dependencies:

git clone https://github.com/edeutsch/RunAssessor.git
cd RunAssesor
pip install -r requirements.txt

Quick Start

RunAssessor processes mass spectrometry data in the .mzML format. .mzML.gz files are also supported.

python ~/RunAssessor/bin/assess_mzMLs.py ~/file_path/mass_spec_data.mzML.gz

RunAssessor can also accept multiple .mzML or '.mzML.gz' files at a time

python ~/RunAssessor/bin/assess_mzMLs.py --write_sdrf_files --verbose *.mzML

Running a quick test

In RunAssessor/tests/data/ there is a small .mzML.gz file that can be used to quickly try RunAssessor

cd tests/data
python ../../bin/assess_mzMLs.py chlo_6_tiny.mzML.gz

There is also a set of larger .mzML.gz files of different kinds that are used to test RunAssessor in RunAssessor/tests/large_files/. You can try RunAssessor on those files. Files in large_files will generate a more substantial JSON and summary file compared to chlo_6_tiny.mzML.gz.

cd tests/large_files
python large_test_file_downloader.py
python ../../bin/assess_mzMLs.py *.mzML.gz   # Or single file of your choice

Usage of the main RunAssessor programs

assess_mzMLs.py

The assess_mzMLs.py program is the main RunAssessor program that accepts a set of input mzML files along with various parameters and processes the mzML files accordingly. This is generally the only program that needs to be executed.

Command-line Arguments

assess_metadata.py

The assess_metadata.py program reads an existing study_metadata.json file and recomputes recommended parameters and potentially outputs to different formats. This program is generally not routinely used, but can be helpful if, for example, a large set of input files are analyzed and a study_metadata.json file is written, but the --write_sdrf_file was not provided to assess_mzMLs.py. This tool can take the previous analysis and write out the SDRF file based on the existing JSON file, without reprocessing all mzML files again.

Command-line Arguments

rename_msruns.py

Renames raw files in current directory to replace special characters in filenames with underscores and writes a mapping document of changes. Some special characters in filename can cause problems in downstream processing tools (for example: spaces, parentheses, ampersands, and more). This program fixes the filenames in a repeatable way and records how the filenames have been adjusted in an output file. This is not needed for normal RunAssessor operation, but may be useful for large-scale reprocessing efforts when certain tools have trouble with special characters in filenames.