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')