ThermoRawFileParser

Wrapper around the .net (C#) ThermoFisher ThermoRawFileReader library for running on Linux with mono. It takes a thermo RAW file as input and outputs a metadata file and the spectra in 3 possible formats

• MGF: only MS2 spectra
• mzML: both MS1 and MS2 spectra
• Apache Parquet: under development

RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved

Requirements

Mono (install mono-complete if you encounter "assembly not found" errors).

Usage

mono ThermoRawFileParser.exe -i=/home/user/data_input/raw_file.raw -o=/home/user/data_input/output/ -f=0 -g -m=0 -c=PXD00001

The optional parameters only work in the -option=value format. The tool can output some RAW file metadata -m=0|1 (0 for JSON format, 1 for TXT format) and the spectra file -f or both. For the MGF format, -p flag is used to exclude MS2 profile mode data (the MGF files can get big when the MS2 spectra were acquired in profile mode).

ThermoRawFileParser.exe usage is (use -option=value for the optional arguments):
  -h, --help                 Prints out the options.
  -i, --input=VALUE          The raw file input.
  -o, --output=VALUE         The output directory.
  -f, --format=VALUE         The output format for the spectra (0 for MGF, 1
                               for MzMl, 2 for Parquet)
  -m, --metadata=VALUE       The metadata output format (0 for JSON, 1 for TXT).
  -g, --gzip                 GZip the output file if this flag is specified (
                               without value).
  -p, --profiledata          Exclude MS2 profile data if this flag is specified
                               (without value). Only for MGF format!
  -c, --collection[=VALUE]   The optional collection identifier (PXD identifier
                               for example).
  -r, --run[=VALUE]          The optional mass spectrometry run name used in
                               the spectrum title. The RAW file name will be
                               used if not specified.
  -s, --subfolder[=VALUE]    Optional, to disambiguate instances where the same
                               collection has 2 or more MS runs with the same
                               name.

Download

Click here to go to the release page.

Build

If you want to build the project using nuget, put the ThermoFisher.CommonCore.RawFileReader.4.0.26.nupkg package in your local nuget directory.

Logging

The default log file is ThermoRawFileParser.log. The log settings can be changed in log4net.config.

Docker

Basic docker

Use the Dockerfile_basic docker file to build an image. It fetches to source code from github and builds it.

docker build --no-cache -t thermorawparser -f Dockerfile_basic .

Run example:

docker run -v /home/user/raw:/data_input -i -t thermorawparser mono /src/bin/Debug/ThermoRawFileParser.exe -i=/data_input/raw_file.raw -o=/data_input/output/ -f=0 -g -m=0 -c=PXD00001

Biocontainers docker

Use the Dockerfile docker file to build an image. It fetches to source code from github and builds it.

docker build --no-cache -t thermorawparser .

Run example:

docker run -v /home/user/raw:/data_input -i -t --user biodocker thermorawparser mono /home/biodocker/bin/bin/Debug/ThermoRawFileParser.exe -i=/data_input/raw_file.raw -o=/data_input/output/ -f=0 -g -m=0 -c=PXD00001

or with the bash script (ThermoRawFileParser.sh):

docker run -v /home/user/raw:/data_input -i -t --user biodocker thermorawparser /bin/bash /home/biodocker/bin/ThermoRawFileParser.sh -i=/data_input/raw_file.raw -o=/data_input/output/ -f=0 -g -m=0 -c=PXD00001