Extract lines containing specific words

Question

Input:

ID   aa
AA   Homo sapiens
DR   ac
BB   ad
FT   ae
//
ID   ba
AA   mouse
DR   bc
BB   bd
FT   be
//
ID   ca
AA   Homo sapiens
DR   cc
BB   cd
FT   ce
//

Expected output:

DR   ac
FT   ae
//
DR   cc
FT   ce
//

Code:

word = 'Homo sapiens'
with open(input_file, 'r') as txtin, open(output_file, 'w') as txtout:
    
    for block in txtin.read().split('//n'):   # reading a file in blocks
        if word in block:   # extracted block containing the word, 'Homo sapiens'
            extracted_block = block + '//n'

            for line in extracted_block.strip().split('n'):   # divide each block into lines
                if line.startswith('DR   '):
                    dr = line 

                elif line.startswith('FT   '):
                    ft = line

I read the input_file based on ‘//’ (block). And, if the word ‘Homo sapiens’ is included in the blocks, I extracted the blocks. Also, in the block, the line starting with ‘DR ‘ is defined as dr, and the line starting with ‘FT ‘ is defined as ft. How should I write ‘output’ using dr and ft to get ‘Expected output’?

Asked By: LoganLee

||

Source

Answer 1

If you are open to a regex based solution, then one option would be to read the entire file into a string and then use re.findall:

with open(input_file, 'r') as file:
    inp = file.read()

matches = re.findall(r'(?<=//n)ID.*?nAAs+Homo sapiensn(DRs+w+n)BBs+w+n(FTs+w+n//n?)', '//n' + inp)
for match in matches:
    for line in match:
        print(line, end='')

This prints:

DR   ac
FT   ae
//
DR   cc
FT   ce
//

Here is a demo showing that the pattern can correctly identify the blocks and DR/FT lines within each matching block.

Answered By: Tim Biegeleisen

Answer 2

You can write a simple parser with a flag. In summary, when you reach a line with AA and the word, set the flag True to keep the following fields of interest, until you reach a block end in which case you reset the flag.

word = 'Homo sapiens'

with open(input_file, 'r') as txtin, open(output_file, 'w') as txtout:
    keep = False
    for line in txtin:
        if keep and line.startswith(('DR', 'FT', '//')):
            txtout.write(line)
        if line.startswith('//'):
            keep = False # reset the flag on record end
        elif line.startswith('AA') and word in line:
            keep = True

Output:

DR   ac
FT   ae
//
DR   cc
FT   ce
//

NB. This requires AA to be before the fields to save. If not, you have to parse block by block (keeping the data in memory) with a similar logic

Answered By: mozway

Extract lines containing specific words

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