Python: count how many lines have a specific word

Question

[Illinu]

I don't know what's wrong with this code. I want to count from a blast report, how many hits correspond to a specific species (the keyword). So my idea is to loop through each line and when the keyword is found, add 1 to count and go to the next line, this because sometimes the name of the species is present more than once in the subject name.

#!/usr/bin/python
import sys
      ##usage: python filterbyword.py file keyword
file = open(sys.argv[1],'r')
keyword = sys.argv[2]
count = 0
for line in file:
    while True:
        if keyword not in line:
            continue
        else:
            break
    count = count + 1
print count

[Pierre Lindenbaum]

what's wrong with `grep` ?

[Ram]

I was gonna ask that (along with why not awk for more advanced grepping), but maybe OP wishes to add this functionality as a module to existing code?

[Illinu]

OMG you are right! How didn't I think about grep. Shame on me!!

Answer 1

[Alex Reynolds]

The problem is, specifically, that your while loop is inside the for loop.

So if the keyword is not in the line, then your script keeps iterating through the while loop, and it appears to "hang".

All you have to do is take out the while loop and test directly:

for line in file:
    if keyword in line:
        count = count + 1

[Illinu]

Ok, thanks, I did this but the problem is I don't know if it is adding up each time the word is in the line or if it would add up only once and jump to the next line.

[Alex Reynolds]

The test should only be done once per line, but you can verify this by trying it out with test input that contains multiple instances of a keyword on a line, and seeing if the final count matches what you expect.

[george.ry]

Exactly as Alex says. Your whole mini-script can even just be compacted into:

with open(sys.argv[1]) as f:
    count = sum(sys.argv[2] in line for line in f)

Answer 2

[GouthamAtla]

What is happening with this script ? If it not looping again for next search, try to useseek()method. Something like file.seek(0)

[dariober]

(Haven't tested it) but for line in file should iterate through the file.

[Alex Reynolds]

Why would you seek to the start of a file on each iteration?

Answer 3

[dariober]

You are incrementing count regardless of whether keyword is in line or not. Maybe you want:

#!/usr/bin/python
import sys
      ##usage: python filterbyword.py file keyword
file = open(sys.argv[1],'r')
keyword = sys.argv[2]
count = 0
for line in file:
    while True:
        if keyword not in line:
            continue
        else:
            count += 1
            break
print count

Or even simpler:

for line in file:
    if keyword in line:
        count+=1
print count

[Illinu]

The simpler one is what I was using but then I got confused about whether there would be an addition for each time the word appears in the line. I don't want that, I want to have one count for each line with the word, not a count for each time the word is in the file.

[dariober]

Just try it. if keyword in line simply tests that statement, it doesn't count how many times the keyword is found in line.