Data processing, and annotation for metabolomics analysis by low-resolution GC-MS
Project description
MetaMS
MetaMS is a workflow for metabolomics data processing and annotation
Current Version
2.0.0
Data input formats
- ANDI NetCDF for GC-MS (.cdf)
- CoreMS self-containing Hierarchical Data Format (.hdf5)
- ChemStation Agilent (Ongoing)
Data output formats
- Pandas data frame (can be saved using pickle, h5, etc)
- Text Files (.csv, tab separated .txt, etc)
- Microsoft Excel (xlsx)
- JSON for workflow metadata
- Self-containing Hierarchical Data Format (.hdf5) including raw data and ime-series data-point for processed data-sets with all associated metadata stored as json attributes
Data structure types
- GC-MS
Available features
Signal Processing
- Baseline detection, subtraction, smoothing
- Manual and automatic noise threshold calculation
- First and second derivatives peak picking methods
- Peak Area Calculation
- EIC Chromatogram deconvolution(TODO)
Calibration
- Retention Index Linear XXX method
Compound Identification
- Automatic local (SQLite) or external (MongoDB or PostgreSQL) database check, generation, and search
- Automatic molecular match algorithm with all spectral similarity methods
MetaMS Installation
- PyPi:
pip3 install metams
- From source:
pip3 install --editable .
To be able to open chemstation files a installation of pythonnet is needed:
-
Windows:
pip3 install pythonnet
-
Mac and Linux:
brew install mono pip3 install pythonnet
Usage
metaMS dump_json_template MetamsFile.json
metaMS dump_corems_json_template CoremsFile.json
Modify the MetamsFile.json and CoremsFile.json accordingly to your dataset and workflow parameters make sure to include CoremsFile.json path inside the MetamsFile.json: "corems_json_path": "path_to_CoremsFile.json"
metaMS run-gcms-workflow path_to_MetamsFile.json
MINIWDL
pip3 install miniwdl
miniwdl run wdl/metaMS.wdl -i wdl/metams_input.json --verbose --no-cache --copy-input-files
MetaMS Docker
A docker image containing the MetaMS command line as the entry point
If you don't have docker installed, the easiest way is to install docker for desktop
-
Pull from Docker Registry:
docker pull corilo/metams:latest
-
Build the image from source:
docker build -t metams:latest .
-
Run Workflow from Container:
$(data_dir) = dir_containing the gcms data, MetamsFile.json and CoremsFile.json
docker run -v $(data_dir):/metaB/data corilo/metams:latest run-gcms-workflow /metaB/data/MetamsFile.json
-
Getting the parameters templates:
docker run -v $(data_dir):/metaB/data corilo/metams:latest dump_json_template /metaB/data/MetamsFile.json
docker run -v $(data_dir):/metaB/data corilo/metams:latest dump_corems_json_template /metaB/data/CoremsFile.json
Project details
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