[ 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.