How to compare clusters?

Question

Hopefully this can be done with python! I used two clustering programs on the same data and now have a cluster file from both. I reformatted the files so that they look like

Answer 1

So just for help, as I see lots of different answers in the comment, I'll give you a very, very simple implementation of a script that you can start from.

Note that this does not answer your full question but points you in one of the directions in the comments.

Normally if you have no experience I'd argue to go a head and read up on Python (which i'll do anyways, and i'll throw in a few links in the bottom of the answer)

On to the fun stuffs! :)

class Cluster(object):
  '''
  This is a class that will contain your information about the Clusters.
  '''
  def __init__(self, number):
    '''
    This is what some languages call a constructor, but it's not.
    This method initializes the properties with values from the method call.
    '''
    self.cluster_number = number
    self.family_name = None
    self.bacteria_name = None
    self.bacteria = []

#This part below isn't a part of the class, this is the actual script.
with open('bacteria.txt', 'r') as file:
  cluster = None
  clusters = []
  for index, line in enumerate(file):
    if line.startswith('Cluster'):
      cluster = Cluster(index)
      clusters.append(cluster)
    else:
      if not cluster.family_name:
        cluster.family_name = line
      elif not cluster.bacteria_name:
        cluster.bacteria_name = line
      else:
        cluster.bacteria.append(line)

I wrote this as dumb and overly simple as I could without any fancy stuff and for Python 2.7.2 You could copy this file into a .py file and run it directly from command line python bacteria.py for example.

Hope this helps a bit and don't hesitate to come by our Python chat room if you have any questions! :)

• http://learnpythonthehardway.org/
• http://www.diveintopython.net/
• http://docs.python.org/2/tutorial/inputoutput.html
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