[ Python: Sorting a two files based on the order of one ]

I've been trying to do this task all day, and I really want to learn how to do it using Python. I want to take two tab-delimited files, one with an ID only and the other with the same ID and some description. I can easily merge these files on the shared ID field with unix join, but for that I need to sort both and I want to keep the ordering of the first file.

Ive tried some code below, and my method has been to try and add things to a tuple, as from my understanding, they will keep their order as you add to it. I havent been able to get anything to work though. Can anyone help?

Sample files:

file1 ->
111889
1437390
123
27998
2525778
12
1345

file2 ->
2525778'\t'item778
1345'\t'item110
123'\t'item1000
12'\t'item8889
111889'\t'item1111
1437390'\t'item222
27998'\t'item12

output ->
111889'\t'item1111
1437390'\t'item222
123'\t'item1000
27998'\t'item12
2525778'\t'item778
12'\t'item8889
1345'\t'item110

This what I have so far:

import sys

add_list = ()

with open(sys.argv[1], 'rb') as file1, open(sys.argv[2], 'rb') as file2:
        for line2 in file2:
                f1, f2, f3 = line2.split('\t')
                #print f1, f2, f3
                for row in file1:
                        #print row
                        if row != f1:
                                break
                        else:
                                add_list.append(f1,f2,'\n')
                                break  

Answer 1

The key is to use Python dictionaries, they are perfect for this task…

Here is a complete answer:

import sys

# Each id is mapped to its item name
# (split() splits at whitespaces (including tabulation and newline), with no empty output strings):
items = dict(line.split() for line in open(sys.argv[2]))  # Inspired by mgilson's answer

with open(sys.argv[1]) as ids:
    for line in ids:
        id = line.rstrip()  # newline removed
        print '{}\t{}'.format(id, items[id])

Here is the result:

% python out.py file1.txt file2.txt
111889  item1111
1437390 item222
123     item1000
27998   item12
2525778 item778
12      item8889
1345    item110

PS: Note that I did not open the files in rb mode, as there is no need to keep the original newline bytes, here, since we get rid of trailing newlines.

Answer 2

I would create a dictionary which maps the ID to the field value from the second file:

with open('file2') as fin:
   d = dict(x.split(None, 1) for x in fin)

Then I would use the first file to construct the output in order from the dictionary:

with open('file1') as fin, open('output', 'w') as fout:
    for line in fin:
        key = line.strip()
        fout.write('{key}\t{value}\n'.format(key=key, value=d[key])

Answer 3

out = {}
with open(sys.argv[1], 'rb') as file1, open(sys.argv[2], 'rb') as file2:
    d2 = {}
    for line in file2:
        (key, val) = line.split('\t')
        d2[key] = val
    lines = file1.readlines()
    out = { x:d2[x] for x in lines }

I am not sure about your sorting basis.