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I am trying to parse a file with a limited knowledge in python with some loops but seems I'm doing something wrong. I want to get the genes(sp...) if values in lst are between the numbers in the middle. Here's the file (ast.txt):

SPAC212.11  1   5662    -1

SPAC212.10  5726    6331    -1

SPAC212.09c 7619    9274    1

SPNCRNA.70  11027   11556   -1

SPAC212.08c 11784   12994   1

SPAC212.07c 13665   14555   1

SPAC212.12  15855   16226   1

SPAC212.06c 18042   18306   1

and here's my code:

lst=[2,6000,18042,11784]

f=open('asd.txt','r')

g=f.readlines()[0:]

for line in g:
    for s in lst:
        if (s)>=int(line.split()[1:2]) and (s)<=int(line.split()[2:3]):
            line.split()[0:1]
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1  
Please make use of the code markers function in the editor and separate your code from the file data. –  RyPeck 43 mins ago
 
I didn't know that function but im trying know.Thanks. –  mehmet 39 mins ago
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1 Answer

up vote 1 down vote accepted

A few suggestions:

output = [] # lines to keep; empty for now

with open("asd.txt", 'r') as f: # use with to handle file open/close

    for line in f: # iterate through lines

        line = line.strip().split() # split the line once

        if any(int(line[1]) <= n <= int(line[2]) for n in lst): # check

            output.append(line[:]) # add copy to output

# use lines in output

Note that this will keep the line in split() form as a list of str values, e.g.:

output == [['SPAC212.07c', '13665', '14555', '1'], ...]
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Well i tried your code but output list was empty,i don't know why.But i changed your code just a little and it works good. for n in lst: if int(line[1]) <= n <= int(line[2]): output.append(line[0:1]) Thanks a lot! –  mehmet 9 mins ago
 
Apologies, edited to copy the whole line. Note that line[0:1] == line[0]. –  jonrsharpe 3 mins ago
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