Hi Forum,

I am a total newbie, so please be gentle!!

I am trying to extract data in many text files that looks like this:

0.0 -0.9
0.3 -0.4
0.6 -1.0
0.9 0.3

These colums always appear on the same line number. What I want to do is to get a list of all column1row1:column2row1 of all files, then a list of all column1row2:column2row2 and so on to finally be able to further process these lists

So far I have got the following code:

#!/usr/bin/python

import os
import re

class Data(object):

      def __init__(self,l,p):
          self.l = l
          self.p = p
          self.type = 'data'
def read_output(file=None):
    """Reading in contents of output.txt"""
    if file is None:
       raise "No file has been passed to me!"
    file =open(toread, "r")
    data = file.readlines()
    count = 0
    hit={}
    for line in data:
        count = count + 1
        if (line.startswith("0.0") and count == 15):
           elems = line.split()
           l = float(elems[0])
           p = float(elems[1])
           hit[elems[1]]
           print hit
           print "Found relevant entry for lead %s with a persistence of %s" % (l,p)
        if (line.startswith("0.3") and count == 16):
           elems = line.split()
           l = float(elems[0])
           p = float(elems[1])
           print "Found relevant entry for l %s with a p of %s" % (l,p)    
        if (line.startswith("0.6") and count == 17):
           elems = line.split()
           l = float(elems[0])
           p = float(elems[1])
           print "Found relevant entry for l %s with a p of %s" % (l,p)    
        if (line.startswith("0.9") and count == 18):
           elems = line.split()
           l = float(elems[0])
           p = float(elems[1])
           print "Found relevant entry for l %s with a p of %s" % (l,p)     
        else:

           continue
    file.close()

match_file = "output.txt"

cwd = os.getcwd()
children = os.listdir(cwd)
children.sort()
#print "these are the children",children
for child in children:
    path = os.path.join(cwd,child)
    if os.path.isdir(path):
       files = os.listdir(path)
       matches = []
       l = 0.0
       p = 0.0
       for file in files:
           if file.startswith(match_file):
              matches.append(os.path.join(path,file))
         
       if len(matches) == 0:
          continue
       data = Data(l,p)
       matches.sort()
       for match in matches:
           compressed = False
           if match.find(".bz2") != 1:
              compressed = True
              os.system("bunzip2 %s" % match)
              toread = match.replace(".bz2","")
           else:
              toread = match
           input = read_output(file=toread)

The error I get is:

Traceback (most recent call last):
File "./calculatemeans.py", line 84, in <module>
input = read_output(file=toread)
File "./calculatemeans.py", line 32, in read_output
hit[elems[1]]
KeyError: '-0.428899'

Can someone help me please?

Sorry for being so silly!

Marianne

Please use code tags when posting code in this forum. It makes your code readable and preserves indentation.
[code=python] # Code goes in here

[/code]

that aside, the keyerror you're getting is when you try to call an element in a dictionary that doesn't exist. Here's an illustration:

>>> d = {}
>>> d['blue'] = 'Tooth'
>>> d['blue']
'Tooth'
>>> d['red']
Traceback (most recent call last):
  File "<input>", line 1, in <module>
KeyError: 'red'
>>>

You see that when I tried to access the member 'red', python raised the AttributeError. So you'll need to modify whatever code you're using that is doing direct access to a dictionary.

A better solution is to use get(), which will return None if the item is not found:

>>> d.get( 'blue' )
'Tooth'
>>> d.get( 'red' )
>>>

HTH

0.0 -0.9
0.3 -0.4
0.6 -1.0
0.9 0.3

These colums always appear on the same line number. What I want to do is to get a list of all column1row1:column2row1 of all files, then a list of all column1row2:column2row2 and so on

One way is to append to a list. So in the following code, "l" and "p" should be lists, and you should use append instead of =.

if (line.startswith("0.0") and count == 15):
   elems = line.split()
   l = float(elems[0])
   p = float(elems[1])

## as for this line giving an error message, you haven't added anything
## to hit so it doesn't exist
hit[elems[1]]
print hit
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