s_mart: SMART/Java/Python/misc/Utils.py comparison

comparison SMART/Java/Python/misc/Utils.py @ 38:2c0c0a89fad7

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author	m-zytnicki
date	Thu, 02 May 2013 09:56:47 -0400
parents	769e306b7933
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+#
+# Copyright INRA-URGI 2009-2010
+#
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software. You can use,
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info".
+#
+# As a counterpart to the access to the source code and rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty and the software's author, the holder of the
+# economic rights, and the successive licensors have only limited
+# liability.
+#
+# In this respect, the user's attention is drawn to the risks associated
+# with loading, using, modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean that it is complicated to manipulate, and that also
+# therefore means that it is reserved for developers and experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or
+# data to be ensured and, more generally, to use and operate it in the
+# same conditions as regards security.
+#
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+#
+"""Some useful functions"""
+import sys, os
+import random
+import subprocess
+def writeFile(fileName, content):
+"""
+Write the content of a file
+"""
+handle = open(fileName, "w")
+handle.write(content)
+handle.close()
+def sumOfLists(list1, list2):
+"""
+Element by element sum
+"""
+if len(list1) != len(list2):
+sys.exit("Cannot sum list whose sizes are different!")
+return [list1[i] + list2[i] for i in range(len(list1))]
+def protectBackslashes(string):
+"""
+Protect the backslashes in a path by adding another backslash
+"""
+return string.replace("\\", "\\\\")
+def getHammingDistance(string1, string2):
+"""
+Compute Hamming distance between two strings
+"""
+if len(string1) != len(string2):
+raise Exception("Error, size of %s and %s differ" % (string1, string2))
+return sum(ch1 != ch2 for ch1, ch2 in zip(string1, string2))
+def getLevenshteinDistance(string1, string2):
+"""
+Compute Levenshtein distance between two strings
+"""
+if len(string1) < len(string2):
+return getLevenshteinDistance(string2, string1)
+if not string1:
+return len(string2)
+previousRow = xrange(len(string2) + 1)
+for i, c1 in enumerate(string1):
+currentRow = [i + 1]
+for j, c2 in enumerate(string2):
+insertions    = previousRow[j + 1] + 1
+deletions     = currentRow[j] + 1
+substitutions = previousRow[j] + (c1 != c2)
+currentRow.append(min(insertions, deletions, substitutions))
+previousRow = currentRow
+return previousRow[-1]
+def getMinAvgMedMax(values):
+"""
+Get some stats about a dict
+@param values: a distribution (the value being the number of occurrences of the key)
+@type values: dict int to int
+@return: a tuple
+"""
+minValues = min(values.keys())
+maxValues = max(values.keys())
+sumValues = sum([value * values[value] for value in values])
+nbValues = sum(values.values())
+allValues = []
+for key in values:
+for i in range(values[key]):
+allValues.append(key)
+sortedValues = sorted(allValues)
+sorted(values.values())
+if (nbValues % 2 == 0):
+medValues = (sortedValues[nbValues / 2 - 1] + sortedValues[nbValues / 2]) / 2.0
+else:
+medValues = sortedValues[(nbValues + 1) / 2 - 1]
+return (minValues, float(sumValues) / nbValues, medValues, maxValues)
+def xor(value1, value2):
+"""
+Logical xor
+@param value1: a value
+@type value1: anything
+@param value2: a value
+@type value2: anything
+"""
+return bool(value1) != bool(value2)
+def diff(fileName1, fileName2):
+"""
+Compare two files
+@param fileName1: a file name
+@type fileName1: string
+@param fileName2: another file name
+@type fileName2: string
+@return: None if the files are the same, a string otherwise
+"""
+handle1 = open(fileName1)
+lines1 = handle1.readlines()
+handle2 = open(fileName2)
+lines2 = handle2.readlines()
+if len(lines1) != len(lines2):
+print "Sizes of files differ (%d != %d)" % (len(lines1), len(lines2))
+return False
+for i in xrange(len(lines1)):
+if lines1[i] != lines2[i]:
+print "Line %d differ ('%s' != '%s')" % (i, lines1[i].strip(), lines2[i].strip())
+return False
+return True
+def binomialCoefficient(a, b):
+"""
+Compute cumulated product from a to b
+@param a: a value
+@type    a: int
+@param b: a value
+@type    b: int
+"""
+if a > b / 2:
+a = b-a
+p = 1.0
+for i in range(b-a+1, b+1):
+p *= i
+q = 1.0
+for i in range(1, a+1):
+q *= i
+return p / q
+memory = {}
+# def fisherExactPValue(a, b, c, d):
+#     """
+#     P-value of Fisher exact test for 2x2 contingency table
+#     """
+#     if (a, b, c, d) in memory:
+#         return memory[(a, b, c, d)]
+#     n = a + b + c + d
+#     i1 = binomialCoefficient(a, a+b)
+#     i2 = binomialCoefficient(c, a+c)
+#     i3 = binomialCoefficient(c+d, n)
+#     pValue = i1 * i2 / i3
+#     memory[(a, b, c, d)] = pValue
+#     return pValue
+def fisherExactPValue(a, b, c, d):
+if (a, b, c, d) in memory:
+return memory[(a, b, c, d)]
+scriptFileName = "tmpScript-%d.R" % (random.randint(0, 10000))
+rScript = open(scriptFileName, "w")
+rScript.write("data = matrix(c(%d, %d, %d, %d), nr=2)\n" % (a, b, c, d))
+rScript.write("fisher.test(data)\n")
+#rScript.write("chisq.test(data)\n")
+rScript.close()
+rCommand = "R"
+if "SMARTRPATH" in os.environ:
+rCommand = os.environ["SMARTRPATH"]
+command = "\"%s\" CMD BATCH %s" % (rCommand, scriptFileName)
+status = subprocess.call(command, shell=True)
+if status != 0:
+sys.exit("Problem with the execution of script file %s, status is: %s" % (scriptFileName, status))
+outputRFileName = "%sout" % (scriptFileName)
+outputRFile = open(outputRFileName)
+pValue = None
+pValueTag = "p-value "
+for line in outputRFile:
+line = line.strip()
+if line == "": continue
+for splittedLine in line.split(","):
+splittedLine = splittedLine.strip()
+if splittedLine.startswith(pValueTag):
+pValue = float(splittedLine.split()[-1])
+break
+if pValue == None:
+sys.exit("Problem with the cannot find p-value! File %s, values are: %d, %d, %d, %d" % (scriptFileName, a, b, c, d))
+os.remove(scriptFileName)
+os.remove(outputRFileName)
+memory[(a, b, c, d)] = pValue
+return pValue
+def fisherExactPValueBulk(list):
+scriptFileName = "tmpScript-%d.R" % (random.randint(0, 10000))
+rScript = open(scriptFileName, "w")
+for element in list:
+rScript.write("fisher.test(matrix(c(%d, %d, %d, %d), nr=2))$p.value\n" % (int(element[0]), int(element[1]), int(element[2]), int(element[3])))
+rScript.close()
+rCommand = "R"
+if "SMARTRPATH" in os.environ:
+rCommand = os.environ["SMARTRPATH"]
+command = "\"%s\" CMD BATCH %s" % (rCommand, scriptFileName)
+status = subprocess.call(command, shell=True)
+if status != 0:
+sys.exit("Problem with the execution of script file %s, status is: %s" % (scriptFileName, status))
+outputRFileName = "%sout" % (scriptFileName)
+outputRFile = open(outputRFileName)
+pValue = None
+pValueTag = "[1] "
+results = {}
+cpt = 0
+for line in outputRFile:
+line = line.strip()
+if line == "": continue
+if line.startswith(pValueTag):
+pValue = float(line.split()[-1])
+results[list[cpt][0:2]] = pValue
+cpt += 1
+if pValue == None:
+sys.exit("Problem with the cannot find p-value!")
+if cpt != len(list):
+sys.exit("Error in the number of p-values computed by R in file '%s'!" % (scriptFileName))
+os.remove(scriptFileName)
+os.remove(outputRFileName)
+return results

Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/misc/Utils.py @ 38:2c0c0a89fad7