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authorZachary Sloan2013-01-11 23:59:41 +0000
committerZachary Sloan2013-01-11 23:59:41 +0000
commit2b2970d167c5b555e0e0ad0b34b72f817c1fac91 (patch)
tree36fa8c708138fff03593e0f50cc933bcb62b5592 /wqflask/basicStatistics/corestats.py
parent1db9237a05fd27c80dc963db9916072594156198 (diff)
parentd39b691994a395c45fa242de6d64d12a5470af10 (diff)
downloadgenenetwork2-2b2970d167c5b555e0e0ad0b34b72f817c1fac91.tar.gz
Merge branch 'flask' of http://github.com/zsloan/genenetwork
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+#!/usr/bin/env python
+
+# corestats.py (COREy STATS)
+# Copyright (c) 2006-2007, Corey Goldberg (corey@goldb.org)
+#
+# statistical calculation class
+# for processing numeric sequences
+#
+# license: GNU LGPL
+#
+# This library is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public
+# License as published by the Free Software Foundation; either
+# version 2.1 of the License, or (at your option) any later version.
+
+
+
+import sys
+
+
+class Stats:
+
+ def __init__(self, sequence):
+ # sequence of numbers we will process
+ # convert all items to floats for numerical processing
+ self.sequence = [float(item) for item in sequence]
+
+
+ def sum(self):
+ if len(self.sequence) < 1:
+ return None
+ else:
+ return sum(self.sequence)
+
+
+ def count(self):
+ return len(self.sequence)
+
+
+ def min(self):
+ if len(self.sequence) < 1:
+ return None
+ else:
+ return min(self.sequence)
+
+
+ def max(self):
+ if len(self.sequence) < 1:
+ return None
+ else:
+ return max(self.sequence)
+
+
+ def avg(self):
+ if len(self.sequence) < 1:
+ return None
+ else:
+ return sum(self.sequence) / len(self.sequence)
+
+
+ def median(self):
+ if len(self.sequence) < 1:
+ return None
+ else:
+ self.sequence.sort()
+ return self.sequence[len(self.sequence) // 2]
+
+
+ def stdev(self):
+ if len(self.sequence) < 1:
+ return None
+ else:
+ avg = self.avg()
+ sdsq = sum([(i - avg) ** 2 for i in self.sequence])
+ stdev = (sdsq / (len(self.sequence) - 1)) ** .5
+ return stdev
+
+
+ def percentile(self, percentile):
+ if len(self.sequence) < 1:
+ value = None
+ elif (percentile >= 100):
+ sys.stderr.write('ERROR: percentile must be < 100. you supplied: %s\n'% percentile)
+ value = None
+ else:
+ element_idx = int(len(self.sequence) * (percentile / 100.0))
+ self.sequence.sort()
+ value = self.sequence[element_idx]
+ return value
+
+
+
+
+# Sample script using this class:
+# -------------------------------------------
+# #!/usr/bin/env python
+# import corestats
+#
+# sequence = [1, 2.5, 7, 13.4, 8.0]
+# stats = corestats.Stats(sequence)
+# print stats.avg()
+# print stats.percentile(90)
+# -------------------------------------------