2

My file looks like

    //
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    [2271]((((21:0.125204,20:0.125204):0.00994299,(28:0.0790047,(7:0.0146105,5:0.0146105):0.0643943):0.0561423):0.0578754,(((23:0.0386924,((((26:0.0160606,22:0.0160606):0.00378,(19:0.0160596,16:0.0160596):0.00378096):0.00242531,12:0.0222659):0.0146336,((29:0.0160393,(17:0.00712055,14:0.00712055):0.00891871):0.0195068,11:0.0355461):0.00135346):0.00179282):0.0468499,4:0.0855423):0.0451632,((25:0.059669,(30:0.0155625,13:0.0155625):0.0441064):0.0223692,(3:0.0288957,1:0.0288957):0.0531425):0.0486673):0.062317):0.60861,((((47:0.0363305,(((62:0.00660739,58:0.00660739):0.011345,(70:0.00496959,54:0.00496959):0.0129828):0.0065665,((68:0.00291155,53:0.00291155):0.0178013,(66:0.0163583,((65:0.0045002,(69:0.00305355,59:0.00305355):0.00144664):0.000757378,(61:0.00311373,52:0.00311373):0.00214385):0.0111007):0.00435459):0.003806):0.0118116):0.111837,(76:0.0395418,(40:0.00641035,34:0.00641035):0.0331314):0.108625):0.0327298,((((46:0.00103749,42:0.00103749):0.0373456,(48:0.0259862,41:0.0259862):0.0123969):0.00173179,39:0.0401149):0.106275,((((44:0.00708562,36:0.00708562):0.0773928,(37:0.025,27:0.025):0.0594785):0.00501024,18:0.0894887):0.0248315,(15:0.0649576,6:0.0649576):0.0493626):0.0320701):0.0345064):0.0680223,((((80:0.0173948,73:0.0173948):0.0162433,(67:0.0129751,((63:0.00435012,57:0.00435012):0.00727273,(60:0.00848091,(64:0.00386096,((56:0.00203231,55:0.00203231):0.00103,51:0.0030623):0.000798654):0.00461996):0.00314194):0.00135223):0.0206631):0.0296773,(33:0.0415374,((75:0.0372575,(45:0.0371022,38:0.0371022):0.000155282):0.0029007,((43:0.0101608,32:0.0101608):0.0242563,31:0.0344171):0.00574108):0.00137926):0.021778):0.147776,((((74:0.0336172,((79:0.0258073,(77:0.0203659,(78:0.00390563,72:0.00390563):0.0164602):0.00544144):0.00767555,49:0.0334829):0.000134364):0.0132633,(35:0.0137148,24:0.0137148):0.0331656):0.0721567,(10:0.0147938,8:0.0147938):0.104243):0.0343567,((71:0.0427659,50:0.0427659):0.0221428,(9:0.0467372,2:0.0467372):0.0181715):0.0884852):0.0576977):0.0378275):0.552713);
    [687]((((21:0.125204,20:0.125204):0.00994299,(28:0.0790047,(7:0.0146105,5:0.0146105):0.0643943):0.0561423):0.0578754,((4:0.128716,(23:0.0386924,((((26:0.0160606,22:0.0160606):0.00378,(19:0.0160596,16:0.0160596):0.00378096):0.00242531,12:0.0222659):0.0146336,((29:0.0160393,(17:0.00712055,14:0.00712055):0.00891871):0.0195068,11:0.0355461):0.00135346):0.00179282):0.0900232):0.0019898,((25:0.059669,(30:0.0155625,13:0.0155625):0.0441064):0.0223692,(3:0.0288957,1:0.0288957):0.0531425):0.0486673):0.062317):0.60861,((((47:0.0363305,(((62:0.00660739,58:0.00660739):0.011345,(70:0.00496959,54:0.00496959):0.0129828):0.0065665,((68:0.00291155,53:0.00291155):0.0178013,(66:0.0163583,((65:0.0045002,(69:0.00305355,59:0.00305355):0.00144664):0.000757378,(61:0.00311373,52:0.00311373):0.00214385):0.0111007):0.00435459):0.003806):0.0118116):0.111837,(76:0.0395418,(40:0.00641035,34:0.00641035):0.0331314):0.108625):0.0327298,((((46:0.00103749,42:0.00103749):0.0373456,(48:0.0259862,41:0.0259862):0.0123969):0.00173179,39:0.0401149):0.106275,((((44:0.00708562,36:0.00708562):0.0773928,(37:0.025,27:0.025):0.0594785):0.00501024,18:0.0894887):0.0248315,(15:0.0649576,6:0.0649576):0.0493626):0.0320701):0.0345064):0.0680223,((((80:0.0173948,73:0.0173948):0.0162433,(67:0.0129751,((63:0.00435012,57:0.00435012):0.00727273,(60:0.00848091,(64:0.00386096,((56:0.00203231,55:0.00203231):0.00103,51:0.0030623):0.000798654):0.00461996):0.00314194):0.00135223):0.0206631):0.0296773,(33:0.0415374,((75:0.0372575,(45:0.0371022,38:0.0371022):0.000155282):0.0029007,((43:0.0101608,32:0.0101608):0.0242563,31:0.0344171):0.00574108):0.00137926):0.021778):0.147776,((((74:0.0336172,((79:0.0258073,(77:0.0203659,(78:0.00390563,72:0.00390563):0.0164602):0.00544144):0.00767555,49:0.0334829):0.000134364):0.0132633,(35:0.0137148,24:0.0137148):0.0331656):0.0721567,(10:0.0147938,8:0.0147938):0.104243):0.0343567,((71:0.0427659,50:0.0427659):0.0221428,(9:0.0467372,2:0.0467372):0.0181715):0.0884852):0.0576977):0.0378275):0.552713);
    [186]((((21:0.125204,20:0.125204):0.00994299,(28:0.0790047,(7:0.0146105,5:0.0146105):0.0643943):0.0561423):0.0578754,((4:0.128716,(23:0.0386924,((((26:0.0160606,22:0.0160606):0.00378,(19:0.0160596,16:0.0160596):0.00378096):0.00242531,12:0.0222659):0.0146336,((29:0.0160393,(17:0.00712055,14:0.00712055):0.00891871):0.0195068,11:0.0355461):0.00135346):0.00179282):0.0900232):0.0019898,((25:0.059669,(30:0.0155625,13:0.0155625):0.0441064):0.0223692,(3:0.0288957,1:0.0288957):0.0531425):0.0486673):0.062317):0.60861,((((47:0.0363305,(((62:0.00660739,58:0.00660739):0.011345,(70:0.00496959,54:0.00496959):0.0129828):0.0065665,((68:0.00291155,53:0.00291155):0.0178013,(66:0.0163583,((65:0.0045002,(69:0.00305355,59:0.00305355):0.00144664):0.000757378,(61:0.00311373,52:0.00311373):0.00214385):0.0111007):0.00435459):0.003806):0.0118116):0.111837,(76:0.0395418,(40:0.00641035,34:0.00641035):0.0331314):0.108625):0.0327298,((((44:0.00708562,36:0.00708562):0.0773928,(37:0.025,27:0.025):0.0594785):0.00501024,18:0.0894887):0.0248315,(15:0.0649576,6:0.0649576):0.0493626):0.0665766):0.0680223,((((80:0.0173948,73:0.0173948):0.0162433,(67:0.0129751,((63:0.00435012,57:0.00435012):0.00727273,(60:0.00848091,(64:0.00386096,((56:0.00203231,55:0.00203231):0.00103,51:0.0030623):0.000798654):0.00461996):0.00314194):0.00135223):0.0206631):0.0296773,(33:0.0415374,((75:0.0372575,(45:0.0371022,38:0.0371022):0.000155282):0.0029007,((43:0.0101608,32:0.0101608):0.0242563,31:0.0344171):0.00574108):0.00137926):0.021778):0.147776,((((74:0.0336172,((79:0.0258073,(77:0.0203659,(78:0.00390563,72:0.00390563):0.0164602):0.00544144):0.00767555,49:0.0334829):0.000134364):0.0132633,(35:0.0137148,24:0.0137148):0.0331656):0.0721567,(10:0.0147938,8:0.0147938):0.104243):0.0343567,((((46:0.00103749,42:0.00103749):0.0373456,(48:0.0259862,41:0.0259862):0.0123969):0.00173179,39:0.0401149):0.0339623,((71:0.0427659,50:0.0427659):0.0221428,(9:0.0467372,2:0.0467372):0.0181715):0.00916857):0.0793167):0.0576977):0.0378275):0.552713);

So after the first line every line starts with a number in brackets. I would need to grep the number in brackets and output it into a new file (without [) ..how would that be done>

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3 Answers 3

Reset to default
4 
grep -Po '(?<=\[)\d+(?=\])' file > new_file

-P for Perl regexs so it is possible to use:

  • \d for a digit
  • positive lookbehind and positive lookahead ((?<=\[) and (?=\]))

-o for only matching

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2

Another possibility if your grep doesn't support the -P option but awk is available could be this:

awk -F '[][]' '{ if ($2 != "") print $2 }' file > new_file

-F tells awk to accept both ] and [ as a field delimiter, $2 then contains the number you want and is printed.

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3 Comments

It gives me following warning: escape sequence '\[' treated as plain '[' and it does not print anything. I've always used them in reverse order, and the parser reads it right to avoid an empty character class, like: awk -F '[][]' '...'
I'm not getting the warning with awk version 1.3.3 under bash 4.3.30. But your version is more readable, I'll edit my answer.
My bash is the same that yours, but my awk is the GNU version: GNU Awk 4.1.1. It could make the difference.
1

In three steps using simple commands:

grep -v "//" inputfile |  cut -d"[" -f2  | cut -d"]" -f1

In sed can you remove everything outside the []:

grep -v "//" inputfile |  sed 's/.*\[\(.*\)].*/\1/'
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