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
- mzML and indexed mzML
- Apache Parquet: under development
As of version 1.2.0, 2 subcommands are available (shoutout to the eubic 2020 developers meeting, see usage for examples):
- query: returns one or more spectra in JSON PROXI by scan number(s)
- xic: returns chromatogram data based on JSON filter input
These features are still under development, remarks or suggestions are more than welcome.
RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved
- Hulstaert N, Shofstahl J, Sachsenberg T, Walzer M, Barsnes H, Martens L, Perez-Riverol Y: ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion [PMID 31755270].
- If you use ThermoRawFileParser as part of a publication, please include this reference.
Mono (install mono-complete if you encounter "assembly not found" errors).
Click here to go to the release page (with release notes starting from v1.1.7).
You can find the ThermoRawFileParserGUI here.
You can read release notes (starting from version 1.1.7) in the wiki page
mono ThermoRawFileParser.exe -i=/home/user/data_input/raw_file.raw -o=/home/user/data_input/output/ -f=0 -g -m=0
with only the mimimal required argument -i or -d this becomes
mono ThermoRawFileParser.exe -i=/home/user/data_input/raw_file.raw
or
mono ThermoRawFileParser.exe -d=/home/user/data_input/
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, 1 for TXT) and the spectra file -f=0|1|2|3|4 (0 for MGF, 1 for mzML, 2 for indexed mzML, 3 for Parquet, 4 for no output) or both. Use the -p flag to disable the thermo native peak picking.
Usage is ThermoRawFileParser.exe [subcommand] [options]
optional subcommands are xic|query (use [subcommand] -h for more info]):
-h, --help Prints out the options.
--version Prints out the version of the executable.
-i, --input=VALUE The raw file input (Required). Specify this or an
input directory -d.
-d, --input_directory=VALUE
The directory containing the raw files (Required).
Specify this or an input raw file -i.
-b, --output=VALUE The output file. Specify this or an output
directory -o. Specifying neither writes to the
input directory.
-o, --output_directory=VALUE
The output directory. Specify this or an output
file -b. Specifying neither writes to the input
directory.
-s, --stdout Write to standard output. Cannot be combined with
file or directory output. Implies silent logging,
i.e. logging level 0
-f, --format=VALUE The spectra output format: 0 for MGF, 1 for mzML,
2 for indexed mzML, 3 for Parquet, 4 for None (
no output); both numeric and text (case
insensitive) value recognized. Defaults to
indexed mzML if no format is specified.
-m, --metadata=VALUE The metadata output format: 0 for JSON, 1 for TXT,
2 for None (no output); both numeric and text (
case insensitive) value recognized. Defaults to
None
-c, --metadata_output_file=VALUE
The metadata output file. By default the metadata
file is written to the output directory.
-g, --gzip GZip the output file.
-p, --noPeakPicking[=VALUE]
Don't use the peak picking provided by the native
Thermo library. By default peak picking is
enabled. Optional argument allows disabling peak
peaking only for selected MS levels and should
be a comma-separated list of integers (1,2,3)
and/or intervals (1-3), open-end intervals (1-)
are allowed
-z, --noZlibCompression Don't use zlib compression for the m/z ratios and
intensities. By default zlib compression is
enabled.
-a, --allDetectors Extract additional detector data: UV/PDA etc
-l, --logging=VALUE Optional logging level: 0 for silent, 1 for
verbose, 2 for default, 3 for warning, 4 for
error; both numeric and text (case insensitive)
value recognized.
-e, --ignoreInstrumentErrors
Ignore missing properties by the instrument.
-x, --excludeExceptionData Exclude reference and exception data
-L, --msLevel=VALUE Select MS levels (MS1, MS2, etc) included in the
output, should be a comma-separated list of
integers (1,2,3) and/or intervals (1-3), open-
end intervals (1-) are allowed
-P, --mgfPrecursor Include precursor scan number in MGF file TITLE
-N, --noiseData Include noise data in mzML output
-w, --warningsAreErrors Return non-zero exit code for warnings; default
only for errors
-u, --s3_url[=VALUE] Optional property to write directly the data into
S3 Storage.
-k, --s3_accesskeyid[=VALUE]
Optional key for the S3 bucket to write the file
output.
-t, --s3_secretaccesskey[=VALUE]
Optional key for the S3 bucket to write the file
output.
-n, --s3_bucketName[=VALUE]
S3 bucket name
Output file extension is determined by the used output format and (optional) gzip compression, for example, if format is MGF without gzip compression, the output file will receive .mgf extension, if format is mzML with gzip compression the output file will have .mzML.gz extension. All user input will be standardized to fulfill abovementioned requirements.
A (java) graphical user interface is also available here that enables the selection of an input RAW directory or one ore more RAW files.
Enables the retrieval spectra by (a) scan number(s) in PROXI format.
mono ThermoRawFileParser.exe query -i=/home/user/data_input/raw_file.raw -o=/home/user/output.json n="1-5, 20, 25-30"
ThermoRawFileParser.exe query --help
usage is:
-h, --help Prints out the options.
-i, --input=VALUE The raw file input (Required).
-n, --scans=VALUE The scan numbers. e.g. "1-5, 20, 25-30"
-b, --output=VALUE The output file. Specifying none writes the output
file to the input file parent directory.
-p, --noPeakPicking Don't use the peak picking provided by the native
Thermo library. By default peak picking is
enabled.
-s, --stdout Pipes the output into standard output. Logging is
being turned off
-w, --warningsAreErrors Return non-zero exit code for warnings; default
only for errors
-l, --logging=VALUE Optional logging level: 0 for silent, 1 for
verbose, 2 for default, 3 for warning, 4 for
error; both numeric and text (case insensitive)
value recognized.
Return one or more chromatograms based on query JSON input.
mono ThermoRawFileParser.exe xic -i=/home/user/data_input/raw_file.raw -j=/home/user/xic_input.json
ThermoRawFileParser.exe xic --help
-h, --help Prints out the options.
-i, --input=VALUE The raw file input (Required). Specify this or an
input directory -d
-d, --input_directory=VALUE
The directory containing the raw files (Required).
Specify this or an input file -i.
-j, --json=VALUE The json input file (Required).
-p, --print_example Show a json input file example.
-b, --output=VALUE The output file. Specify this or an output
directory. Specifying neither writes to the
input directory.
-o, --output_directory=VALUE
The output directory. Specify this or an output
file. Specifying neither writes to the input
directory.
-6, --base64 Encodes the content of the xic vectors as base 64
encoded string.
-s, --stdout Pipes the output into standard output. Logging is
being turned off.
-w, --warningsAreErrors Return non-zero exit code for warnings; default
only for errors
-l, --logging=VALUE Optional logging level: 0 for silent, 1 for
verbose, 2 for default, 3 for warning, 4 for
error; both numeric and text (case insensitive)
value recognized.
Provide one of the following filters:
- M/Z and tolerance (tolerance unit optional, defaults to
ppm) - M/Z start and end
- sequence and tolerance (tolerance unit optional, defaults to
ppm)
optionally one can define starting and ending retention times, provide filter string (defaults to ms, i.e. only MS1 scans), and a comment (free text) field; any valid filter string is supported,
however only basic validation is performed, see issue #158 for details. Comment can contain any text and will be preserved in the output.
An example input JSON file:
[
{
"mz":488.5384,
"tolerance":10,
"tolerance_unit":"ppm"
},
{
"mz":575.2413,
"tolerance":10,
"rt_start":630,
"rt_end":660,
"scan_filter":"ms2"
},
{
"mz_start":749.7860,
"mz_end" : 750.4,
"rt_start":630,
"rt_end":660
},
{
"sequence":"TRANNEL",
"tolerance":10
},
{
"mz":1014.5099732499732,
"rt_start":14.0600881872,
"rt_end":14.4167198290667,
"tolerance":5,
"tolerance_unit":"ppm",
"comment":"Only ion trap scans"
"scan_filter":"ITMS"
}
}
]
ThermoRawFileParser is available in the Galaxy ToolShed and is deployed at the European Galaxy Server.
By default the parser only logs to console. To enable logging to file, uncomment the file appender in the log4net.config file.
<log4net>
<root>
<level value="INFO" />
<appender-ref ref="console" />
<!--<appender-ref ref="file" />-->
</root>
<appender name="console" type="log4net.Appender.ConsoleAppender">
<layout type="log4net.Layout.PatternLayout">
<conversionPattern value="%date %level %logger - %message%newline" />
</layout>
</appender>
<!--<appender name="file" type="log4net.Appender.RollingFileAppender">
<file value="ThermoRawFileParser.log" />
<appendToFile value="true" />
<rollingStyle value="Size" />
<maxSizeRollBackups value="5" />
<maximumFileSize value="10MB" />
<staticLogFileName value="true" />
<layout type="log4net.Layout.PatternLayout">
<conversionPattern value="%date [%thread] %level %logger - %message%newline" />
</layout>
</appender>-->
</log4net>
First check the latest version tag on biocontainers/thermorawfileparser/tags. Then pull and run the container with
docker run -i -t -v /home/user/raw:/data_input quay.io/biocontainers/thermorawfileparser:<tag> ThermoRawFileParser.sh --help