Wrapper around the .net (C#) ThermoFisher ThermoRawFileReader library for running on Linux with mono (works on Windows too). 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
Mono (install mono-complete if you encounter "assembly not found" errors).
mono ThermoRawFileParser.exe -i=/home/user/data_input/raw_file.raw -o=/home/user/data_input/output/ -f=0 -g -m=0 -c=PXD00001
For running on Windows, omit mono. 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.
Click here to go to the release page.
If you want to build the project using nuget, put the ThermoFisher.CommonCore.RawFileReader.4.0.26.nupkg package in your local nuget directory.
The default log file is ThermoRawFileParser.log. The log settings can be changed in log4net.config.
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
Create example for reusing the container:
docker create -v /home/user/raw:/data_input --name=rawparser -it thermorawparser
docker start rawparser
docker exec rawparser mono /src/bin/x64/Debug/ThermoRawFileParser.exe -i=/data_input/raw_file.raw -o=/data_input/output/ -f=0 -g -m=0 -c=PXD00001
docker exec rawparser mono /src/bin/x64/Debug/ThermoRawFileParser.exe -i=/data_input/another_raw_file.raw -o=/data_input/output/ -f=0 -g -m=0 -c=PXD00001
docker stop rawparser
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/x64/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