how to compare string in one line with string in next line?

Question

I have a file with about 16,000 lines in it. All of them have the same format. Here is a simple example if it:

ATOM    139  C1  DPPC   18      17.250  58.420  10.850  1.00  0.00

<...>

ATOM    189  C1  DPPC   19      23.050  20.800  11.000  1.00  0.00

I need to check if lines that contains string DPPC and has identifier 18 forms 50 line block before the identifier switches to 19, etc.

So for now, I have the following code:

cnt = 0
with open('test_file.pdb') as f1:
    with open('out','a') as f2:
        lines = f1.readlines()
        for i, line in enumerate(lines):
             if "DPPC" in line:
                   A = line.strip()[22:26]
                   if A[i] == A [i+1]:
                       cnt = cnt + 1
                   elif A[i] != A[i+1]:
                       cnt = 0

And here I stuck. I found some examples how to compare subsequent lines but similar approach did not work here. I still cannot figure out how to compare the value of A in line[i] with the value of A in the line[i+1].

Answer 1

Since your data appears to be fixed width fields in fixed width records, you can use the struct module to quickly break each line up into individual fields.

Parsing all the fields of each line may be overkill when you only need to process one of them, but I'm doing it the way shown to illustrate how it's done in case you need to do other processing — and using the struct module makes it relatively fast in any case.

Let's say the input file consisted of only the following lines of data:

ATOM    139  C1  DPPC   18      17.250  58.420  10.850  1.00  0.00
ATOM    139  C1  DPPC   18      17.250  58.420  10.850  1.00  0.00
ATOM    139  C1  DPPC   18      17.250  58.420  10.850  1.00  0.00
ATOM    139  C1  DPPC   18      17.250  58.420  10.850  1.00  0.00
ATOM    139  C1  DPPC   18      17.250  58.420  10.850  1.00  0.00
ATOM    139  C1  DPPC   18      17.250  58.420  10.850  1.00  0.00
ATOM    139  C1  DPPC   18      17.250  58.420  10.850  1.00  0.00
ATOM    139  C1  DPPC   18      17.250  58.420  10.850  1.00  0.00
ATOM    139  C1  DPPC   18      17.250  58.420  10.850  1.00  0.00
ATOM    189  C1  DPPC   19      23.050  20.800  11.000  1.00  0.00
ATOM    189  C1  DPPC   19      23.050  20.800  11.000  1.00  0.00
ATOM    189  C1  DPPC   19      23.050  20.800  11.000  1.00  0.00
ATOM    189  C1  DPPC   19      23.050  20.800  11.000  1.00  0.00
ATOM    189  C1  DPPC   19      23.050  20.800  11.000  1.00  0.00
ATOM    189  C1  DPPC   19      23.050  20.800  11.000  1.00  0.00
ATOM    189  C1  DPPC   19      23.050  20.800  11.000  1.00  0.00
ATOM    189  C1  DPPC   20      23.050  20.800  11.000  1.00  0.00
ATOM    189  C1  DPPC   20      23.050  20.800  11.000  1.00  0.00
ATOM    189  C1  DPPC   20      23.050  20.800  11.000  1.00  0.00

All you need to do is remember what the value of field was on the previous line to allow a comparison of it to the current one. To start the process, the first line has to be read and parsed separately, so there's a prev value to compare with on subsequent lines. Also note that the 5th field is the one indexed by [4] because the first starts at [0].

import struct

# negative widths represent ignored padding fields
fieldwidths = 4, -4, 3, -2, 2, -2, 4, -3, 2, -6, 6, -2, 6, -2, 6, -2, 4, -2, 4
fmtstring = ' '.join('{}{}'.format(abs(fw), 'x' if fw < 0 else 's')
                                    for fw in fieldwidths)
fieldstruct = struct.Struct(fmtstring)
parse = fieldstruct.unpack_from  # a function to split line up into fields

with open('test_file.pdb') as f1:
    prev = parse(next(f1))[4]  # remember value of fifth field
    cnt = 1
    for line in f1:
        curr = parse(line)[4]  # get value of fifth field
        if curr == prev:  # same as last one?
            cnt += 1
        else:
            print('{} occurred {} times'.format(prev, cnt))
            prev = curr
            cnt = 1
    print('{} occurred {} times'.format(prev, cnt))  # for last line

Output:

18 occurred 9 times
19 occurred 7 times
20 occurred 3 times

Answer 2

You can also easily solve this with a parallel list:

data = []
with open('data.txt', 'r') as datafile:
    for line in datafile:
        line=line.strip()
        if line:
            data.append(line);


keywordList = []
for line in data:
    line = line.split()
    if (line[4] not in keywordList):
        keywordList.append(line[4])


counterList = []
for item in keywordList:
    counter = 0
    for line in data:
        line = line.split()
        if (line[4] == item):
            counter+=1
    counterList.append(counter)


for i in range(len(keywordList)):
    print("%s: %d"%(keywordList[i],counterList[i]));

But if you are familiar with dict, I'll go with Lutz's answer.

Answer 3

Try this (explanations in the comments).

data = """ATOM    139  C1  DPPC   18      17.250  58.420  10.850  1.00  0.00
ATOM    139  C1  DPPC   18      17.250  58.420  10.850  1.00  0.00
ATOM    139  C1  DPPC   18      17.250  58.420  10.850  1.00  0.00
ATOM    139  C1  DPPC   18      17.250  58.420  10.850  1.00  0.00
ATOM    139  C1  DPPC   18      17.250  58.420  10.850  1.00  0.00
ATOM    139  C1  DPPC   18      17.250  58.420  10.850  1.00  0.00
ATOM    139  C1  DPPC   18      17.250  58.420  10.850  1.00  0.00
ATOM    139  C1  DPPC   18      17.250  58.420  10.850  1.00  0.00
ATOM    139  C1  DPPC   18      17.250  58.420  10.850  1.00  0.00
ATOM    189  C1  DPPC   19      23.050  20.800  11.000  1.00  0.00
ATOM    189  C1  DPPC   19      23.050  20.800  11.000  1.00  0.00
ATOM    189  C1  DPPC   19      23.050  20.800  11.000  1.00  0.00
ATOM    189  C1  DPPC   19      23.050  20.800  11.000  1.00  0.00
ATOM    189  C1  DPPC   19      23.050  20.800  11.000  1.00  0.00
ATOM    189  C1  DPPC   19      23.050  20.800  11.000  1.00  0.00
ATOM    189  C1  DPPC   19      23.050  20.800  11.000  1.00  0.00
ATOM    189  C1  DPPC   19      23.050  20.800  11.000  1.00  0.00
ATOM    189  C1  DPPC   19      23.050  20.800  11.000  1.00  0.00
ATOM    189  C1  DPPC   19      23.050  20.800  11.000  1.00  0.00"""

# The last code seen in the 5th column.
code = None

# The count of lines of the current code.
count = 0

for line in data.split("\n"):
    # Get the 5th column.
    c = line.split()[4]

    # The code in the 5th column changed.
    if c != code:
        # If we aren't at the start of the file, print the count
        # for the code that just ended.
        if code:
            print("{}: {}".format(code, count))

        # Rember the new code.
        code = c

    # Count the line
    count = count + 1

# Print the count for the last code.
print("{}: {}".format(code, count))

Output:

18: 9
19: 19