Question

I am new in python and I would like some help for a small problem. I have a file whose each line has an ID plus an associated number. More than one numbers can be associated to the same ID. How is it possible to get only the ID plus the largest number associated with it in python?

Example:

Input: ID_file.txt

ENSG00000133246 2013
ENSG00000133246 540
ENSG00000133246 2010
ENSG00000253626 465
ENSG00000211829 464
ENSG00000158458 2577
ENSG00000158458 2553

What I want is the following:

ENSG00000133246 2013
ENSG00000253626 465
ENSG00000211829 464
ENSG00000158458 2577

Thanks in advance for any help!

Answer 1

I would think there are many ways to do this I would though use a dictionary

from collections import defaultdict

id_value_dict = defaultdict()
for line in open(idfile.txt).readlines():
    id, value = line.strip().split()
    if id not in id_value_dict:
        id_value_dict[id] = int(value)
    else:
        if id_value_dict[id] < int(value):
            id_value_dict[id] = int(value)

Next step is to get the dictionary written out

out_ref = open(outputfile.txt,'w')
for key, value in id_value_dict:
    outref.write(key + '\t' + str(value)

outref.close()

There are slicker ways to do this, I think the dictionary could be written in a one-liner using a lamda or a list-comprehension but I like to start simple

Just in case you need the results sorted there are lots of ways to do it but I think it is critical to understand working with lists and dictionaries in python as I have found that the learning to think about the right data container is usually the key to solving many of my problems but I am still a new. Any way if you need the sorted results a straightforward was is to

 id_value_dict.keys().sort() 

SO this is one of the slick things about python id_value__dict.keys() is a list of the keys of the dictionary sorted

 out_ref = open(outputfile.txt,'w')
 for key in id_value_dict.keys():
     outref.write(key + '\t' + str(id_value_dict[key])

 outref.close()

its really tricky because you might want (I know I always want) to code

  my_sorted_list = id_value_dict.keys().sort()

However you will find that my_sorted_list does not exist (NoneType)