def missing_peak_finder(sample, filename, points=13, null_ions=[73, 147],\ crop_ions=[50,540], threshold=1000, rt_window=1, filetype='mzml'): """ @summary: Integrates raw data around missing peak locations to fill in NAs in the data matrix @param sample: The sample object containing missing peaks @type sample: pyms.MissingPeak.Class.Sample @param andi_file: Name of the raw data file @type andi_file: stringType @param points: Peak finding - Peak if maxima over 'points' \ number of scans (Default 3) @type points: intType @param null_ions: Ions to be deleted in the matrix @type null_ions: listType @param crop_ions: Range of Ions to be considered @type crop_ions: listType @param threshold: Minimum intensity of IonChromatogram allowable to fill\ missing peak @type threshold: intType @param rt_window: Window in seconds around average RT to look for \ missing peak @type rt_window: floatType @param filetype: either mzml or netcdf @type filetype: stringType @author: Sean O'Callaghan """ ### some error checks on null and crop ions ### a for root,files,dirs in os.path.walk(): loop print "Sample:", sample.get_name(), "File:", filename if filetype.lower() == 'cdf': data = ANDI_reader(filename) elif filetype.lower() == 'mzml': data = mzML_reader(filename) else: print "file type not valid" # build integer intensity matrix im = build_intensity_matrix_i(data) for null_ion in null_ions: im.null_mass(null_ion) im.crop_mass(crop_ions[0], crop_ions[1]) # get the size of the intensity matrix n_scan, n_mz = im.get_size() # smooth data for ii in range(n_mz): ic = im.get_ic_at_index(ii) ic1 = savitzky_golay(ic, points) ic_smooth = savitzky_golay(ic1, points) ic_base = tophat(ic_smooth, struct="1.5m") im.set_ic_at_index(ii, ic_base) for mp in sample.get_missing_peaks(): mp_rt = mp.get_rt() common_ion = mp.get_ci() qual_ion_1 = float(mp.get_qual_ion1()) qual_ion_2 = float(mp.get_qual_ion2()) ci_ion_chrom = im.get_ic_at_mass(common_ion) print "ci = ", common_ion qi1_ion_chrom = im.get_ic_at_mass(qual_ion_1) print "qi1 = ", qual_ion_1 qi2_ion_chrom = im.get_ic_at_mass(qual_ion_2) print "qi2 = ", qual_ion_2 ###### # Integrate the CI around that particular RT ####### #Convert time to points # How long between scans? points_1 = ci_ion_chrom.get_index_at_time(float(mp_rt)) points_2 = ci_ion_chrom.get_index_at_time(float(mp_rt) - rt_window) print "rt_window = ", points_1 - points_2 rt_window_points = points_1 - points_2 maxima_list = get_maxima_list_reduced(ci_ion_chrom, mp_rt, \ rt_window_points) large_peaks = [] for rt, intens in maxima_list: if intens > threshold: q1_index = qi1_ion_chrom.get_index_at_time(rt) q2_index = qi2_ion_chrom.get_index_at_time(rt) q1_intensity = qi1_ion_chrom.get_intensity_at_index(q1_index) q2_intensity = qi2_ion_chrom.get_intensity_at_index(q2_index) if q1_intensity > threshold / 2 and q2_intensity > threshold / 2: large_peaks.append([rt, intens]) print('found %d peaks above threshold' % len(large_peaks)) areas = [] for peak in large_peaks: apex = ci_ion_chrom.get_index_at_time(peak[0]) ia = ci_ion_chrom.get_intensity_array().tolist() area, left, right, l_share, r_share = ion_area(ia, apex, 0) areas.append(area) ######################## areas.sort() if len(areas) > 0: biggest_area = areas[-1] mp.set_ci_area(biggest_area) mp.set_exact_rt("{:.3f}".format(float(mp_rt) / 60.0)) print "found area:", biggest_area, "at rt:", mp_rt else: print "Missing peak at rt = ", mp_rt mp.set_ci_area('na')
def missing_peak_finder(sample, filename, points=13, null_ions=[73, 147],\ crop_ions=[50,540], threshold=1000, rt_window=1, filetype='cdf'): """ @summary: Integrates raw data around missing peak locations to fill in NAs in the data matrix @param sample: The sample object containing missing peaks @type sample: pyms.MissingPeak.Class.Sample @param andi_file: Name of the raw data file @type andi_file: stringType @param points: Peak finding - Peak if maxima over 'points' \ number of scans (Default 3) @type points: intType @param null_ions: Ions to be deleted in the matrix @type null_ions: listType @param crop_ions: Range of Ions to be considered @type crop_ions: listType @param threshold: Minimum intensity of IonChromatogram allowable to fill\ missing peak @type threshold: intType @param rt_window: Window in seconds around average RT to look for \ missing peak @type rt_window: floatType @author: Sean O'Callaghan """ ### some error checks on null and crop ions ### a for root,files,dirs in os.path.walk(): loop print "Sample:", sample.get_name(), "File:", filename if filetype == 'cdf': data = ANDI_reader(filename) elif filetype == 'mzml': data = mzML_reader(filename) else: print "file type not valid" # build integer intensity matrix im = build_intensity_matrix_i(data) for null_ion in null_ions: im.null_mass(null_ion) im.crop_mass(crop_ions[0], crop_ions[1]) # get the size of the intensity matrix n_scan, n_mz = im.get_size() # smooth data for ii in range(n_mz): ic = im.get_ic_at_index(ii) ic1 = savitzky_golay(ic, points) ic_smooth = savitzky_golay(ic1, points) ic_base = tophat(ic_smooth, struct="1.5m") im.set_ic_at_index(ii, ic_base) for mp in sample.get_missing_peaks(): mp_rt = mp.get_rt() common_ion = mp.get_ci() qual_ion_1 = float(mp.get_qual_ion1()) qual_ion_2 = float(mp.get_qual_ion2()) ci_ion_chrom = im.get_ic_at_mass(common_ion) print "ci = ",common_ion qi1_ion_chrom = im.get_ic_at_mass(qual_ion_1) print "qi1 = ", qual_ion_1 qi2_ion_chrom = im.get_ic_at_mass(qual_ion_2) print "qi2 = ", qual_ion_2 ###### # Integrate the CI around that particular RT ####### #Convert time to points # How long between scans? points_1 = ci_ion_chrom.get_index_at_time(float(mp_rt)) points_2 = ci_ion_chrom.get_index_at_time(float(mp_rt)-rt_window) print "rt_window = ", points_1 - points_2 rt_window_points = points_1 - points_2 maxima_list = get_maxima_list_reduced(ci_ion_chrom, mp_rt, \ rt_window_points) large_peaks = [] for rt, intens in maxima_list: if intens > threshold: q1_index = qi1_ion_chrom.get_index_at_time(rt) q2_index = qi2_ion_chrom.get_index_at_time(rt) q1_intensity = qi1_ion_chrom.get_intensity_at_index(q1_index) q2_intensity = qi2_ion_chrom.get_intensity_at_index(q2_index) if q1_intensity > threshold/2 and q2_intensity > threshold/2: large_peaks.append([rt, intens]) print('found %d peaks above threshold'%len(large_peaks)) areas = [] for peak in large_peaks: apex = ci_ion_chrom.get_index_at_time(peak[0]) ia = ci_ion_chrom.get_intensity_array().tolist() area, left, fight, l_share, r_share = ion_area(ia, apex, 0) areas.append(area) ######################## areas.sort() if len(areas)>0: biggest_area = areas[-1] mp.set_ci_area(biggest_area) print "found area:", biggest_area, "at rt:", mp_rt else: print "Missing peak at rt = ", mp_rt mp.set_ci_area('na')
"""proc.py """ import sys sys.path.append("/x/PyMS") from pyms.GCMS.IO.MZML.Function import mzML_reader # read the raw data mzml_file = "/x/PyMS/data/TP1U-11-16_86-2207.mzML" data = mzML_reader(mzml_file) # raw data operations print "minimum mass found in all data: ", data.get_min_mass() print "maximum mass found in all data: ", data.get_max_mass() # time time = data.get_time_list() print "number of retention times: ", len(time) print "retention time of 1st scan: ", time[0], "sec" print "index of 400sec in time_list: ", data.get_index_at_time(400.0) # TIC tic = data.get_tic() print "number of scans in TIC: ", len(tic) print "start time of TIC: ", tic.get_time_at_index(0), "sec" # raw scans scans = data.get_scan_list() print "number of masses in 1st scan: ", len(scans[0])