Exemplo n.º 1
0
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")
Exemplo n.º 2
0
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')
Exemplo n.º 3
0
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')
Exemplo n.º 4
0

 # 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')