Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into production

1 files changed, 83 insertions, 0 deletions

diff --git a/wqflask/utility/corestats.py b/wqflask/utility/corestats.py
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+++ b/wqflask/utility/corestats.py
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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
+
+#ZS: Should switch to using some third party library for this; maybe scipy has an equivalent
+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 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)
+# -------------------------------------------
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