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Porting to Python3 #1

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e2df56e
updated to comply with Py3: print to print()
Jun 6, 2019
38eb9d7
call to map() fixed to comply with Python3
Jun 6, 2019
274b493
minor fix
Jun 6, 2019
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2 changes: 1 addition & 1 deletion file_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ def file_read (file):
lines_of_file = block_lines.split('\n') #divide into lines at carriage rtns
del lines_of_file [0] # header
del lines_of_file [-1] # last line is blank so remove it
print lines_of_file [0]
print (lines_of_file [0])
return lines_of_file

def file_write (file,data):
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27 changes: 15 additions & 12 deletions noise.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
## Traces that exceed the limit are popped from the list and the failing points are explicitly listed to the terminal
## Output is tab delimited columns of verified traces 'verified.txt'


import sys
from math import *
import platform
from trace_tools import mean, variance, rmsd, traces_scale, trace_scale, traces_average, baselines_quality, baseline_subtract
Expand Down Expand Up @@ -46,9 +46,9 @@ def clean_bad_baselines(input_traces, baseline_range=[0,99]):
b_end = baseline_range[1]
mean_sigma2_bs, rmsd_sigma2_bs, bs_variances = baselines_quality (input_traces, b_start, b_end)

print 'Mean baseline variance = ', mean_sigma2_bs
print 'RMSD of baseline variance =', rmsd_sigma2_bs
print bs_variances
print ('Mean baseline variance = ', mean_sigma2_bs)
print ('RMSD of baseline variance =', rmsd_sigma2_bs)
print (bs_variances)

## discard any trace with excessive baseline noise - Sigma2Bs gt Mean + 4 RMSD
ex_noise_traces_to_pop = []
Expand Down Expand Up @@ -83,7 +83,7 @@ def construct_diffs(input_traces, UNITARY_CURRENT=.5, baseline_range=[0,99]):
diff.append((input_traces[x+1][y]-input_traces[x][y])/2)
difference_traces.append(diff)

print 'Constructed ', len(difference_traces), ' difference traces'
print ('Constructed ', len(difference_traces), ' difference traces')

## calculate mean current, invert and subtract baseline
mean_I_inverted_bs_sub = mean_inverse_baseline_sub(input_traces, b_start, b_end)
Expand All @@ -99,7 +99,7 @@ def construct_diffs(input_traces, UNITARY_CURRENT=.5, baseline_range=[0,99]):
limit = 7 * sqrt(UNITARY_CURRENT * I + mean_sigma2_bs)
limits.append(limit)

print 'Verifying variance of difference traces'
print ('Verifying variance of difference traces')

excess_points, excess_limits, excess_differences = [],[],[]

Expand Down Expand Up @@ -130,8 +130,8 @@ def construct_diffs(input_traces, UNITARY_CURRENT=.5, baseline_range=[0,99]):
if len(excess_points[i]) > 0:
message = "Trace {} contained {} points greater than the limit and was removed from set\n".format(i, len(excess_points[i]))
messages += message
print message
print zip(excess_limits[i],excess_differences[i])
print (message)
print (zip(excess_limits[i],excess_differences[i]))
difference_traces_to_pop.append(i)
if input_traces_to_pop.count(i) == 0: #Check if this trace was already discarded last time
input_traces_to_pop.append(i)
Expand Down Expand Up @@ -171,8 +171,11 @@ def final_prep(input_traces, difference_traces, baseline_range):
for d_trace in difference_traces:
isochrone.append(d_trace[isochronous_point])

mean_dZt_squared = mean (map (square, isochrone))

if sys.version_info[0] > 2:
mean_dZt_squared = mean (list(map (square, isochrone)))
else:
mean_dZt_squared = mean (map (square, isochrone))

#factor of '2' because of dZt = 1/2 * {y(i+1)-y(i)}; Heinemann and Conti
final_ensemble_variance.append(2 * mean_dZt_squared)

Expand All @@ -195,10 +198,10 @@ def write_output (difference_traces, header_line, filename='verified.txt'):
output_lines.insert(0, header_line)
output_file = filename

print 'Writing {} difference traces to {} with mean and variance in first two columns...'.format(len(difference_traces), output_file)
print ('Writing {} difference traces to {} with mean and variance in first two columns...'.format(len(difference_traces), output_file))

file_write (output_file,output_lines)
print 'Done'
print ('Done')



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2 changes: 1 addition & 1 deletion verifyTk.py
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Expand Up @@ -163,7 +163,7 @@ def on_help():
def callback_fname(self):
### there is no need to do anything until the analysis starts
#this is just for debugging
print self.v.get()
print (self.v.get())

def callback5(self):
'Called by PLOT variance current button.'
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