bruker-reader 0.1.3

Reader for Bruker FTICR BAF files

bruker-reader

This is a simple python package for reading FTICR spectra from Bruker BAF files.

It's heavily based off of the R rtms package (https://cran.r-project.org/package=rtms), who did the heavy lifting of reverse engineering the file format.

Usage

Usage is simple. Create a reader by pointing it to the .d directory:

	>>> from bruker_reader import BAFReader
	>>> rdr = BAFReader("/path/to/data/sample.d")
	>>> spec = rdr.read_spectrum()
	... # returns pandas DataFrame with 'mz' and 'intensity' columns

You can read partial spectra as well, which can dramatically speed up access:

	>>> rdr.read_spectrum(from_mass=451.0, to_mass=509)

BAF files also store a list of the N largest peaks (where N is configurable when setting up a run). Note, this is not necessarily the same as the total peaks collected after calibrating; but it may still be useful.

	>>> rdr.read_peaks()
	# Returns a pandas DataFrame of `mz` and `intensity` values.

To ease the process of reading multiple Bruker .d files stored in a data dir, the BAFCache class can be used. It creates an easy lookup for spectra files, as well as caches the metadata for the spectrum upon first use:

	>>> from bruker_reader import BAFCache
	# Assuming `/path/to/data` contains `samp1.d`, `samp2.d` ...
	>>> bcache = BAFCache('/path/to/data')

	# Access samples by key
	>>> samp1 = bcache['samp1'].read_spectrum()

	# You can also access by numeric index:
	>>> bcache[12]
	
	# BAFCache has typical iterable behavior:
	>>> if 'samp11' in bcache: ...
	>>> for rdr in bcache: ...
	
	# Getting directory info
	>>> bcache.samples  # Returns a list of sample ids
	>>> bcache.files    # Returns a dict of sample -> filepath