T1 = PairwiseAlignment(F1, Dw, Gw) A1 = align_with_tree(T1, min_peaks=2) A1.write_csv("output/Art.csv", "output/Aarea.csv") print "Aligning expt B" expr_list = [] expr_dir = "../61b/output/" for expr_code in exprB_codes: file_name = os.path.join(expr_dir, expr_code + ".expr") expr = load_expr(file_name) expr_list.append(expr) F2 = exprl2alignment(expr_list) T2 = PairwiseAlignment(F2, Dw, Gw) A2 = align_with_tree(T2, min_peaks=2) # between replicates alignment parameters Db = 10.0 # rt modulation Gb = 0.30 # gap penalty A2.write_csv("output/Brt.csv", "output/Barea.csv") print "Aligning input {1,2}" T9 = PairwiseAlignment([A1, A2], Db, Gb) A9 = align_with_tree(T9) A9.write_csv("output/rt.csv", "output/area.csv") aligned_peaks = A9.aligned_peaks() store_peaks(aligned_peaks, "output/peaks.bin")
peak_list = BillerBiemann(im, points=9, scans=2) print "Number of peaks found: ", len(peak_list) # Filter peaks # Filter the peak list, # first by removing all intensities in a peak less than a given relative # threshold, # then by removing all peaks that have less than a given number of ions above # a given value # Parameters # percentage ratio of ion intensity to max ion intensity r = 2 # minimum number of ions, n n = 3 # greater than or equal to threshold, t t = 10000 # trim by relative intensity pl = rel_threshold(peak_list, r) # trim by threshold new_peak_list = num_ions_threshold(pl, n, t) print "Number of filtered peaks: ", len(new_peak_list) # store peak list store_peaks(new_peak_list, 'output/peaks.bin')
T1 = PairwiseAlignment(F1, Dw, Gw) A1 = align_with_tree(T1, min_peaks=2) A1.write_csv('output/Art.csv', 'output/Aarea.csv') print 'Aligning expt B' expr_list = [] expr_dir = "../61b/output/" for expr_code in exprB_codes: file_name = os.path.join(expr_dir, expr_code + ".expr") expr = load_expr(file_name) expr_list.append(expr) F2 = exprl2alignment(expr_list) T2 = PairwiseAlignment(F2, Dw, Gw) A2 = align_with_tree(T2, min_peaks=2) # between replicates alignment parameters Db = 10.0 # rt modulation Gb = 0.30 # gap penalty A2.write_csv('output/Brt.csv', 'output/Barea.csv') print 'Aligning input {1,2}' T9 = PairwiseAlignment([A1, A2], Db, Gb) A9 = align_with_tree(T9) A9.write_csv('output/rt.csv', 'output/area.csv') aligned_peaks = A9.aligned_peaks() store_peaks(aligned_peaks, 'output/peaks.bin')
# Filter peaks # Filter the peak list, # first by removing all intensities in a peak less than a given relative # threshold, # then by removing all peaks that have less than a given number of ions above # a given value # Parameters # percentage ratio of ion intensity to max ion intensity r = 2 # minimum number of ions, n n = 3 # greater than or equal to threshold, t t = 10000 # trim by relative intensity pl = rel_threshold(peak_list, r) # trim by threshold new_peak_list = num_ions_threshold(pl, n, t) print "Number of filtered peaks: ", len(new_peak_list) # store peak list store_peaks(new_peak_list, 'output/peaks.bin')