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Program to calculate the Node degree to be called as a Hub Protein

/ Published in: Python
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  1. #!/usr/bin/python
  2.  
  3. # Program to calculate the Node degree to be called as a Hub Protein
  4. # Author: Kumaran Kandasamy
  5. # Contact: kkandsamy@cemm.oeaw.ac.at
  6.  
  7. class IsHubProtein:
  8.     def __init__(self,
  9.                  PINPath,
  10.                  percentile = 0.95
  11.                  ):
  12.         # Read the PIN File
  13.         inFile = file(PINPath,'r')
  14.         mainData = inFile.readlines()
  15.         inFile.close()
  16.  
  17.         nodeDegree = {};
  18.         for line in mainData[1:]:
  19.             line = line.strip().split('\t')
  20.             n1 = str(line[0]).strip()
  21.             if not nodeDegree.has_key(n1):nodeDegree[n1] = 0
  22.             nodeDegree[n1] += 1
  23.  
  24.             n2 = str(line[1]).strip()
  25.             if not nodeDegree.has_key(n2):nodeDegree[n2] = 0
  26.             nodeDegree[n2] += 1
  27.  
  28.         # Number of Nodes in PIN
  29.         x = len(nodeDegree)
  30.         # To get to the Specified percentile; If not specified it will be 95%
  31.         y = int(percentile * x)
  32.  
  33.         degreeBin = {}; degreeUniq = [];
  34.         for node,degree in nodeDegree.items():
  35.             if not degreeBin.has_key(degree):degreeBin[degree] = 0
  36.             degreeBin[degree] += 1
  37.             if degree not in degreeUniq:degreeUniq.append(degree)
  38.         degreeUniq.sort()
  39.  
  40.         n = 0; degreeForHub = None;
  41.         for degree in degreeUniq:
  42.             n = n + degreeBin[degree]
  43.             #print degree, degreeBin[degree], n
  44.             if n > y:
  45.                 degreeForHub = degree
  46.                 break
  47.  
  48.         self.degreeForHub = degreeForHub
  49.         self.nodedehree = nodeDegree
  50.  
  51.         return None
  52.  
  53. def main():
  54.     PINFilePath = '/home/kkandasamy/work/databases/interact-innatedb-human-2011-01-17.txt'
  55.     data = IsHubProtein(PINFilePath, 0.95)
  56.     print data.degreeForHub
  57.     return None
  58.  
  59. if __name__ == '__main__':
  60.     main()

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