Mass spectrometry query language python implementation
Mass Spec Query Language
The Mass Spec Query Language (MassQL) is a domain specific language meant to be a succinct way to express a query in a mass spectrometry centric fashion. It is inspired by SQL, but it attempts to bake in assumptions of mass spectrometry to make querying much more natural for mass spectrometry users. Broadly we attempt to design it according to several principles:
- Expressiveness - Capture complex mass spectrometry patterns that the community would like to look for
- Precision - Exactly prescribe how to find data without ambiguity
- Scalable - Easily facilitating the querying of one spectrum all the way up to entire repositories of data
- Relatively Natural - MassQL should be relatively easy to read and write and even use to communicate ideas about mass spectrometry, you know like a language.
This is the repository to define the language and reference implementation. This contains several parts
- Language Grammar
- Reference Implementation Python API
- Command line Utility to execute
- NextFlow Workflow For Large Scale Analysis
- ProteoSAFe workflow
- Dash interactive exploration
Mingxun Wang is the main creator and developer of MassQL. Contact me for contributing or using it!
Checkout specifics for the language, examples, and design patterns at the documentation.
To install massql
pip install massql
Here is the most basic operation you can do
from massql import msql_engine results_df = msql_engine.process_query(input_query, input_filename)
If you want to push in a data frame you already have, you can specify it
from massql import msql_engine from massql import msql_fileloading # Loading Data ms1_df, ms2_df = msql_fileloading.load_data(input_filename) # Executing Query results_df = msql_engine.process_query(input_query, input_filename, ms1_df=ms1_df, ms2_df=ms2_df)
Command Line Tool
You can use the command line tool
massql to query things or put things into a pipeline.
A few examples of what you can do
massql test.mzML "QUERY scaninfo(MS2DATA)" --output_file results.tsv
Parsing query into intermediate JSON string
Visualization of Query
Visualization image of MS1 spectra
Visualization image of MS2 spectra
To run tests, you'll need to first fetch some fixtures that are not bundled with the git repo:
cd tests && sh ./get_data.sh
You will also want to install the extra requirements for the test suite:
pip install -r requirements_test.txt
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