process_mzs_mzML.py

'''
Takes an mzML object which contains a list of intensities, a
list of mzs, and a value for the threshold intensity for filtering.

pymzml citation
Bald, T., Barth, J., Niehues, A., Specht, M., Hippler, M., and Fufezan, C. (2012) pymzML - Python module for high throughput bioinformatics on mass spectrometry data, Bioinformatics, doi: 10.1093/bioinformatics/bts066
'''


import pymzml


def process_mzs(file_name, threshold=.1):  # What fraction of the max intensity will be used for a threshold

    # Sets up mzML reader
    ms_run = pymzml.run.Reader(
            file_name,
            obo_version='1.2.0',
            extraAccessions=[
                ('MS:1000129', ['value']),
                ('MS:1000130', ['value']),
            ]
    )

    # For elements that clear the filter
    keepers_neg_mz = []
    keepers_pos_mz = []

    '''
    Loops through positive list and negative list and adds mz values to the keeper list when the intensity is
    above a threshold and catches any errors that are thrown (test data still had some issues with encoded data
    not decoding properly but the try and except handles that).
    '''
    # Variable to make sure loop continues even if an error is thrown
    # for each spectrum in a "run" (iteration)
    for spectrum in ms_run:
        try:
            # Calculate the max value and then generate a threshold based on that.
            maxS = max(spectrum.i)
            thresh = maxS * threshold

            # Looks at each peak intensity, and if it is past the threshold, adds it to the neg or pos list
            for peak in spectrum.peaks:
                if peak[1] > thresh:

                    # Check for polarity once intensity is determined to be high enough
                    negative_polarity = spectrum.get('MS:1000129', False)
                    if negative_polarity == '':
                        keepers_neg_mz.append(peak[0])

                    positive_polarity = spectrum.get('MS:1000130', False)
                    if positive_polarity == '':
                        keepers_pos_mz.append(peak[0])

        except:
            pass

    # Removes duplicates
    filtered_neg_mz = list(set(keepers_neg_mz))
    filtered_pos_mz = list(set(keepers_pos_mz))

    # Combines list where negatives are in the 0 position and positives in the 1
    combo_set = [filtered_neg_mz, filtered_pos_mz]
    return combo_set