Ubuntu – Use bash to extract number from between square brackets

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My file looks like this:

[581]((((((((501:0.00024264,451:0.00024264):0.000316197,310:0.000558837):0.00857295,((589:0.000409158,538:0.000409158):0.000658084,207:0.00106724
):0.00806454):0.0429702,(((198:0.00390205,91:0.00390205):0.016191,79:0.0200931):0.0147515,(187:0.00133008,50:0.00133008):0.0335145):0.0172574):0.
127506,((140:0.00253019,117:0.00253019):0.0533693,(((533:0.00728707,(463:8.80494e-05,450:8.80494e-05):0.00719902):0.0217722,389:0.0290593):0.0253
931,(((141:0.018004,107:0.018004):0.0143861,(111:0.00396127,(106:0.00161229,12:0.00161229):0.00234898):0.0284289):0.0145736,(129:0.0195982,((123:
0.0105973,66:0.0105973):0.0084867,10:0.019084):0.000514243):0.0273656):0.00748854):0.00144709):0.123708):0.000944439,((181:0.00108761,71:0.00108761):0.0819772);  
[50]((((((((501:0.00024264,451:0.00024264):0.000316197,310:0.000558837):0.00857295,((589:0.000409158,538:0.000409158):0.000658084,207:0.00106724):0.00806454):0.0429702,(((198:0.00390205,91:0.00390205):0.016191,79:0.0200931):0.0147515,(187:0.00133008,50:0.00133008):0.0335145):0.0172574):0.127506,((140:0.00253019,117:0.00253019):0.0533693,(((533:0.00728707,(463:8.80494e-05,450:8.80494e-05):0.00719902):0.0217722,389:0.0290593):0.0253931,(((141:0.018004,107:0.018004):0.0143861,(111:0.00396127,(106:0.00161229,12:0.00161229):0.00234898):0.0284289):0.0145736,(129:0.0195982,((123:0.0105973,66:0.0105973):0.0084867,10:0.019084):0.000514243):0.0273656):0.00748854):0.00144709):0.123708):0.000944439,((181:0.00108761,71:0.00108761):0.0819772);

Every new line starts with the pattern [number]. Every line ends with the pattern );.

I need to extract the numbers in the square brackets from the beginning of every line, and write them into a new file. I don't know how many lines the file has beforehand.

Best Answer

You can achieve this with just a single grep command. This is because GNU grep lets you use a Perl regular expression (-P), which supports zero-width lookaround assertions (\K and (?= ), in this case):

grep -oP '^\[\K\d+(?=\])' infile

As written, that will send the output to your terminal. To redirect it to a file, use:

grep -oP '^\[\K\d+(?=\])' infile > outfile

This method has the advantage of brevity and simplicity. It matches text that

  • is preceded by (\K)

    • a [ character(\[) -- \ is needed as [ otherwise has a special meaning in regular expressions
    • that appears at the beginning of a line (^);

  • consists of one or more (+) digits (\d);

  • is followed by ((?= ))

    • a ] character (\]) -- like with [, \ forces ] to be matched literally.
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