Comparing elements from different lists using python

Question

I have generated two multi-component lists with the following script:

list1 = list()
for line in infile1.readlines():
    list1.append(line.split('\t'))

list2 = list()
for line in infile2.readlines():
    list2.append(line.split(‘\t’))

The lists look like this:

list1 = ('1960', 'chr17', '+', 'RNF213'), ('1963', 'chr16', '+', 'SF3B3'), ('1964', 'chr4', '-', 'GPRIN3')...

list2 = ('1482', 'miR-K12-1'), ('1018', 'miR-K12-4-5p'), ('1960', 'miR-K12-12')...

The first element from the first entry in list1 (in this case "1960") will match the first element of one or more entries in list2. What I would like to do is locate each match and then add the last element of the list2 entry to the list1 entry. An example of the desired output would be:

('1960', 'chr17', '+', 'RNF213', 'miR-K12-12')

I have tried this, but it returns nothing:

result = []
for list1[0] in list1:
    if list1[0] == list2[0]:
        result.append((list1[0:], list2[1]))

What happens if there are more than one matching entries in list2? — Martijn Pieters
– Martijn Pieters, Commented Sep 4, 2014 at 15:50
I'm assuming if there are multiple matches they should all be appended. — Martijn Pieters
– Martijn Pieters, Commented Sep 4, 2014 at 15:54

Martijn Pieters · Accepted Answer · 2014-09-04 15:59:59Z

Put the values from list 2 into a dictionary; each unique value in the first column pointing to a list of values from the second column. Because you have tab-separated values, you should really use the csv module here:

import csv

lines2 = {}

with open(filename2, 'rb') as infile2:
    reader = csv.reader(infile2, delimiter='\t')
    for row in reader:
        lines2.setdefault(row[0], []).append(row[1])

dict.setdefault() sets a default value (a list object here) if the key is not yet present in the dictionary. This allows us to append to an empty list for the first value, then subsequently to the already-existing list for the rest.

Now you can trivially look up matching lines when processing the other file:

with open(filename1, 'rb') as infile1:
    reader = csv.reader(infile1, delimiter='\t')
    for row in reader:
        row += lines2.get(row[0], [])
        print row

Demo:

>>> import csv
>>> list1 = ['\t'.join(r) for r in [('1960', 'chr17', '+', 'RNF213'), ('1963', 'chr16', '+', 'SF3B3'), ('1964', 'chr4', '-', 'GPRIN3')]]
>>> list2 = ['\t'.join(r) for r in [('1482', 'miR-K12-1'), ('1018', 'miR-K12-4-5p'), ('1960', 'miR-K12-12')]]
>>> lines2 = {}
>>> reader = csv.reader(list2, delimiter='\t')
>>> for row in reader:
...     lines2.setdefault(row[0], []).append(row[1])
... 
>>> lines2
{'1482': ['miR-K12-1'], '1960': ['miR-K12-12'], '1018': ['miR-K12-4-5p']}
>>> reader = csv.reader(list1, delimiter='\t')
>>> for row in reader:
...     row += lines2.get(row[0], [])
...     print row
... 
['1960', 'chr17', '+', 'RNF213', 'miR-K12-12']
['1963', 'chr16', '+', 'SF3B3']
['1964', 'chr4', '-', 'GPRIN3']

chishaku · Accepted Answer · 2014-09-04 16:36:04Z

2

EDIT: Don't use this method. I'm leaving it up though because someone else might be able to learn from @Martijn's comments.

list1 = [('1960', 'chr17', '+', 'RNF213'), ('1963', 'chr16', '+', 'SF3B3'), ('1964', 'chr4', '-', 'GPRIN3')]
list2 = [('1482', 'miR-K12-1'), ('1018', 'miR-K12-4-5p'), ('1960', 'miR-K12-12')]

results = []
for x in list1:
    for y in list2:
        if x[0] == y[0]:
            results.append( x + (y[-1], ))
print results
>>>
[('1960', 'chr17', '+', 'RNF213', 'miR-K12-12')]

edited Sep 4, 2014 at 16:36

answered Sep 4, 2014 at 15:59

chishaku

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5 Comments

Martijn Pieters Over a year ago

This does way too much work. This takes M * N loops (where M and N are the sizes of the two lists). Using a dictionary gives you a M + N solution instead; e.g. loop once over each list, sequentially.

Martijn Pieters Over a year ago

If list1 is 10,000 elements long, and list 2 contains 5,000 elements, your version requires 50 million iterations. Mine just 15,000.

chishaku Over a year ago

Thanks for elucidating. I've got some old code to go update!

Antti Haapala Over a year ago

Hmm want to give +1 for the "don't use this method"

Lauren Gay Over a year ago

Thank you! I tried your method and it worked perfectly.

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