pyBaf2Sql

About

This package is a Python wrapper for Bruker's Baf2Sql data access library to be used with other Python packages. Functions have been taken and modified from Baf2Sql and TIMSCONVERT.

Installation

This package can be installed to a Python virtual environment using pip.

pip install git+https://github.com/gtluu/pyBaf2Sql

Example Usage

import numpy as np
import pandas as pd
from pyBaf2Sql.init_baf2sql import init_baf2sql_api
from pyBaf2Sql.classes import BafData
from pyBaf2Sql.baf import read_double


# Initialize the Baf2Sql library using the packaged .dll or .so files for Windows or Linux, respectively.
dll = init_baf2sql_api()

data = BafData(bruker_d_folder_name='some_timstof_data.d', baf2sql=dll)

# Get all spectra from a BAF file as a list of pd.DataFrames with columns for m/z and intensity in centroid mode.
spectra_dfs = []
for frame in range(1, data.analysis['Spectra'].shape[0]+1):
    frame_dict = data.analysis['Spectra'][data.analysis['Spectra']['Id'] == frame].to_dict(orient='records')[0]
    mz_array = np.array(read_double(baf2sql=dll, handle=data.handle, identity=int(frame_dict['LineMzId'])),
                        dtype=np.float64)
    intensity_array = np.array(read_double(baf2sql=dll, handle=data.handle, identity=frame_dict['LineIntensityId']),
                               dtype=np.float64)
    spectra_dfs.append(pd.DataFrame({'mz': mz_array, 'intensity': intensity_array}))

# Print number of spectra parsed from TSF file.
print(len(spectra_dfs))
# Print spectrum from first frame.
print(spectra_dfs[0])