Use bash to extract number from between square brackets

Question

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.

Answer 1

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.

Answer 2

Using sed:

• < inputfile sed -n 's/^\[\([0-9]*\)\].*$/\1/p' > out

---

Command breakdown:

• < inputfile: redirects the content of inputfile to stdin
• -n: suppresses output
• > out: redirects the content of stdout to out

Regex breakdown:

• s: performs a substitution
• /: starts the regex
• ^: matches the start of the line
• \[: matches a [ character
• \(: starts the capturing group
• [0-9]*: matches any number of digits
• \): stops the capturing group
• \]: matches a ] character
• .*: matches any number of any character
• $: matches the end of the line
• /: stops the regex / starts the replacement
• \1: replaces with the first capturing group
• /: stops the replacement
• p: prints only the matching lines

---

Using grep+tr (if you need a method that runs both on Ubuntu and on another OS whose grep doesn't support PCRE--otherwise, refer to Eliah Kagan's grep-only version):

• < inputfile grep -o '^\[[0-9]*\]' | tr -d '[]' > out

Command breakdown:

• < inputfile in grep: redirects the content of inputfile to stdin
• -o in grep: prints only the match
• -d in tr: deletes the characters
• > out in tr: redirects the content of stdout to out

Regex breakdown:

• ^: matches the start of the line
• \[: matches a [ character
• [0-9]*: matches any number of digits
• \]: matches a ] character

Answer 3

the perl way:

perl -ne 'print "$1\n" if /^\[([0-9]*)\].*/' testdata > out

or with awk:

awk 'match($0, /^\[[0-9]*\]/) {print substr($0, RSTART + 1, RLENGTH - 2)}' testdata > out

---

Used Regex in both cases:

^\[[0-9]*\]

Explanation

• /^\[[0-9]*\]/

  • ^ assert position at start of the string

  • \[ matches the character [ literally

  • [0-9]* match a single character present in the list below

    • Quantifier: * Between zero and unlimited times, as many times as possible, giving back as needed [greedy]

    • 0-9 a single character in the range between 0 and 9

  • \] matches the character ] literally

  
  _{(source: debuggex.com)}

  _{Debuggex Demo}

Answer 4

Use this in Bash:

 grep -oh '\[[0-9].*\]' mytestfile | sed 's/.*\[\([^]]*\)\].*/\1/g' > myresultfile

Answer 5

python solution using re module and considering two situations :

#!/usr/bin/env python2
import re
with open('/path/to/file.txt') as f:
    for line in f:
        digits_case_1 = re.search(r'(?<=^\[)\d+(?=\])', line)
        digits_case_2 = re.search(r'(?<=^\[)\d+(?=\].*\);$)', line)
        if digits_case_1:
            print 'Not considering ");" at end: ' + digits_case_1.group()
        if digits_case_2:
            print 'Considering ");" at end: ' + digits_case_2.group()

Output :

Not considering ");" at end: 581
Not considering ");" at end: 50
Considering ");" at end: 50

Here i have considered two situations as your question does not seem clear to me.

• digits_case_1 will print the digits match between [] at the start of the line, it will not consider whether the line is ending with ); or not.

• digits_case_2 will print digits between [] at the start of the line only if the line is ending with );.

Answer 6

cat $FILE | awk -F\] '{ print $1 }' | grep '\[' | tr -d '['

Where the progression is:^§

$ FILE=/tmp/tmp.tmp

$ cat $FILE
[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);

$ cat $FILE | awk -F\] '{ print $1 }'
[581
):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

$ cat $FILE | awk -F\] '{ print $1 }' | grep '\['
[581
[50

$ cat $FILE | awk -F\] '{ print $1 }' | grep '\[' | tr -d '['
581
50

$

^§ For those without access to the man command.