compomics/ThermoRawFileParser

Name: ThermoRawFileParser

Owner: Computational Omics and Systems Biology Group

Description: null

Created: 2018-03-21 13:40:06.0

Updated: 2018-03-22 13:24:32.0

Pushed: 2018-03-22 13:24:31.0

Homepage: null

Size: 746

Language: C#

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README

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 MS2 spectra (centroided) in MGF format.

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

Usage

The optional parameters only work in the -option=value format. The metadata file is only created when the -m is specified.

moRawFileParser.exe usage (use -option=value for the optional arguments)
, --help                 Prints out the options.
, --input=VALUE          The raw file input.
, --output=VALUE         The metadata and mgf output directory.
, --metadata             Write the metadata output file if this flag is
                           specified (without value).
, --collection[=VALUE]   The optional collection identifier (PXD identifier
                           for example).
, --run[=VALUE]          The optional mass spectrometry run name used in
                           the spectrum title. The RAW file name will be
                           used if not specified.
, --subfolder[=VALUE]    Optional, to disambiguate instances where the same
                           collection has 2 or more MS runs with the same
                           name.

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

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

er build --no-cache -t thermorawparser .

Run example:

er 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/ -m -c=PXD00001

or with the bash script (ThermoRawFileParser.sh):

er 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/ -m -c=PXD00001