I'm trying to parse a tab-separated file in Python where a number placed k tabs apart from the beginning of a row, should be placed into the k-th array.
Is there a built-in function to do this, or a better way, other than reading line by line and do all the obvious processing a naive solution would perform?
You can use the csv module to parse tab seperated value files easily.
import csv
with open("tab-separated-values") as tsv:
for line in csv.reader(tsv, dialect="excel-tab"): #You can also use delimiter="\t" rather than giving a dialect.
...
Where line is a list of the values on the current row for each iteration.
Edit: As suggested below, if you want to read by column, and not by row, then the best thing to do is use the zip() builtin:
with open("tab-separated-values") as tsv:
for column in zip(*[line for line in csv.reader(tsv, dialect="excel-tab")]):
...
file is the least problematic, esp. because it doesn't even exist in 3. Y'all can have "for file in files:` when you pry it from my cold, dead hands! ;^)file in 2.x. Good point, however. Edited.I don't think any of the current answers really do what you said you want. (Correction: I now see that @Gareth Latty / @Lattyware has incorporated my answer into his own as an "Edit" near the end.)
Anyway, here's my take:
Say these are the tab-separated values in your input file:
1 2 3 4 5
6 7 8 9 10
11 12 13 14 15
16 17 18 19 20
then this:
with open("tab-separated-values.txt") as inp:
print( list(zip(*(line.strip().split('\t') for line in inp))) )
would produce the following:
[('1', '6', '11', '16'),
('2', '7', '12', '17'),
('3', '8', '13', '18'),
('4', '9', '14', '19'),
('5', '10', '15', '20')]
As you can see, it put the k-th element of each row into the k-th array.
Like this:
>>> s='1\t2\t3\t4\t5'
>>> [x for x in s.split('\t')]
['1', '2', '3', '4', '5']
For a file:
# create test file:
>>> with open('tabs.txt','w') as o:
... s='\n'.join(['\t'.join(map(str,range(i,i+10))) for i in [0,10,20,30]])
... print >>o, s
#read that file:
>>> with open('tabs.txt','r') as f:
... LoL=[x.strip().split('\t') for x in f]
...
>>> LoL
[['0', '1', '2', '3', '4', '5', '6', '7', '8', '9'],
['10', '11', '12', '13', '14', '15', '16', '17', '18', '19'],
['20', '21', '22', '23', '24', '25', '26', '27', '28', '29'],
['30', '31', '32', '33', '34', '35', '36', '37', '38', '39']]
>>> LoL[2][3]
23
If you want the input transposed:
>>> with open('tabs.txt','r') as f:
... LoT=zip(*(line.strip().split('\t') for line in f))
...
>>> LoT[2][3]
'32'
Or (better still) use the csv module in the default distribution...
[x.split('\t') for f.split('\n')] makes no sense. There's no x and files objects don't have a split() method.You can easily do it like this way by python pandas pd.read_csv ('file_name.tsv', sep='\t')
[Note: need to install pandas with this command pip install pandas]
