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#!/usr/bin/env python
# Author: Duy Tin Truong (duytin.truong@unitn.it)
# at CIBIO, University of Trento, Italy
__author__ = 'Duy Tin Truong (duytin.truong@unitn.it)'
__version__ = '0.1'
__date__ = '1st Sep 2014'
import numpy
import sys
def dist2file(dist, labels, ofn):
with open(ofn, 'w') as ofile:
ofile.write('ID')
for label in labels:
ofile.write('\t%s'%label)
ofile.write('\n')
for i in range(len(labels)):
ofile.write('%s\t'%labels[i])
for j in range(len(labels)):
if j == len(labels) - 1:
ofile.write('%f\n'%dist[i][j])
else:
ofile.write('%f\t'%dist[i][j])
def statistics(vals):
vals = numpy.array(vals)
result = {}
if len(vals.shape) == 1:
num_elems = len(vals)
nrows = num_elems
ncols = 1
else:
nrows, ncols = vals.shape
num_elems = nrows * ncols
if num_elems > 0:
result['nrows'] = nrows
result['ncols'] = ncols
result['size'] = num_elems
result['average'] = numpy.average(vals)
result['min'] = numpy.min(vals)
result['max'] = numpy.max(vals)
result['median'] = numpy.percentile(vals, 50)
result['percentile_25'] = numpy.percentile(vals, 25)
result['percentile_75'] = numpy.percentile(vals, 75)
else:
result['nrows'] = nrows
result['ncols'] = ncols
result['size'] = num_elems
result['average'] = 0
result['min'] = 0
result['max'] = 0
result['median'] = 0
result['percentile_25'] = 0
result['percentile_75'] = 0
str_result = ''
for key in ['nrows',
'ncols',
'size',
'average',
'min',
'max',
'median',
'percentile_25',
'percentile_75']:
str_result += '%s: %s\n'%(key, result[key])
return result, str_result
def dict2str(dict_var):
result = ''
for key in dict_var:
result += '%s: %s\n'%(key, dict_var[key])
return result
def openr( fn, mode = "r" ):
if fn is None:
return sys.stdin
return bz2.BZ2File(fn) if fn.endswith(".bz2") else open(fn,mode)
def openw( fn ):
if fn is None:
return sys.stdout
return bz2.BZ2File(fn,"w") if fn.endswith(".bz2") else open(fn,"w")
def is_number(s):
try:
int(s)
return True
except ValueError:
return False
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