massql 0.0.8

Mass spectrometry query language python implementation

Mass Spec Query Languge

The Mass Spec Query language is meant to be concise querying of mass spec patterns that can scale from one single scan to a whole repository. Here we include the formal grammar and reference implementation in Python.

Repository Structure

This is the repository to define the language and reference implementation. This contains several parts

1. Language Grammar
2. Reference Implementation Python API
3. Commandline Utility to execute
4. NextFlow Workflow For Large Scale Analysis
5. ProteoSAFe workflow
6. Dash interactive exploration

Developers/Contact

Mingxun Wang is the main creator and developer of MassQL. Contact me for contributing or using it!

Docs

Here

Python API

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

Web API

API Version

/api

Parsing query into intermediate JSON string

/parse?query=<query string>

Example Link

Visualization of Query

Visualization image of MS1 spectra

/visualize/ms1

Example Link

Visualization image of MS2 spectra

/visualize/ms2

License

MIT License