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6

Find files with a specific 2-line pattern using awk

rated 0 times [ 6] [ 0] / answers: 1 / hits: 2720 / 2 Years ago, wed, april 13, 2022, 9:36:46

I have a few hundreds of files that has this pattern

@<TRIPOS>ATOM

  2 H18 65.2220 Du 1 RES1 0.0000

@<TRIPOS>BOND

 1  3  5  ar

@<TRIPOS>SUBSTRUCTURE

among them, some of the files are missing the line after the @<TRIPOS>BOND and they look like

@<TRIPOS>ATOM

  2 H18 65.2220 Du 1 RES1 0.0000

@<TRIPOS>BOND

@<TRIPOS>SUBSTRUCTURE

I'm trying to find all the files in my working directory that are missing the numeric line after the @<TRIPOS>BOND and move them to another directory. I know this is a simple task, but I am quite new to Linux.

Note: the files vary in length and line numbers, this is why I am "grepping" the line after the @<TRIPOS>BOND string.

Here's one of my codes, which I was planning to write in a for loop. It doesn't do the job, but I am showing it to show one of my trials.

cat file | grep -A1 '@<TRIPOS>BOND' | awk 'FNR == 2 {print}'

Thank you

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pardsea

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2 Years ago

answered 2 Years ago scusaper · Accepted Answer

If your version of grep supports PCRE mode (-P) you could try a multiline match that finds instances of @<TRIPOS>BOND that are followed (after only a newline) by @<TRIPOS>SUBSTRUCTURE e.g.

grep -lzP 'Q@<TRIPOS>BONDE

Q@<TRIPOS>SUBSTRUCTUREE' *

The Q and E may be unnecessary in this case but are intended to force literal matching (in case @, >, < have special meaning in the Perl regex syntax). The -l tells grep to list the matching files instead of printing the match. You can then use the list of files as an input to the mv command e.g.

grep -lzP 'Q@<TRIPOS>BONDE

Q@<TRIPOS>SUBSTRUCTUREE' * | xargs mv -t /path/to/newdir/

Additional info

You could express the second part of the match as a lookahead but I don't think it has any advantage in this case

grep -lzP 'Q@<TRIPOS>BONDE

(?=Q@<TRIPOS>SUBSTRUCTUREE)' *

Equivalent expressions in pcregrep (which is not part of the standard Ubuntu system, but obtainable from the repository) would be something like

pcregrep -lM 'Q@<TRIPOS>BONDE

Q@<TRIPOS>SUBSTRUCTUREE' *

and

pcregrep -lM 'Q@<TRIPOS>BONDE

(?=Q@<TRIPOS>SUBSTRUCTUREE)' *