GNU bug report logs - #24858
URGENT: Question about grep

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Eric Blake <eblake <at> redhat.com>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#24858: closed (URGENT: Question about grep)
Date: Wed, 02 Nov 2016 15:50:02 +0000

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Your message dated Wed, 2 Nov 2016 10:49:30 -0500
with message-id <8adbf123-5013-9c39-473e-e13eb307d7c5 <at> redhat.com>
and subject line Re: bug#24858: URGENT: Question about grep
has caused the debbugs.gnu.org bug report #24858,
regarding URGENT: Question about grep
to be marked as done.

(If you believe you have received this mail in error, please contact
help-debbugs <at> gnu.org.)


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From: Greta <romano.greta <at> gmail.com>
To: bug-grep <at> gnu.org
Subject: URGENT: Question about grep
Date: Wed, 2 Nov 2016 15:53:45 +0100

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Dear grep developer,

I am Greta Romano and I need your help as soon as possibile.

I want to use grep command to search a string of 6 characters in every 
line of a file (biological file with DNA nucleotide).

The problem is that I need to search these 6 characters in the first 30 
characters of each line. I report you an example:

String to search: GTGTCA

File:

>HWI-ST740:1:C2GCJACXX:1:1101:1279:1825 1:N:0:
_/NGACGCTCTGACCTTGGGGCTGGTCGGGG/__A_TGCTGAGGAGACGGTGACCAGGGTTCCCTGGCCCCACANNNCCAAGCTTCCNNNNNNNNNNNNNNNNNNN
>HWI-ST740:1:C2GCJACXX:1:1101:1349:1847 1:N:0:
_/NTTAGATGAGGGAAACATCTGCATCAAGTT/__G_TTTATCTGTGACAACAAGTGTTGTTCCACTGCCAAAGAGTTTCTTATAATAAAACAATCGGGGTGGCACNNNNN

I want that the research is done only in the underline characters.  So 
what I have to add in grep command to put the limit of 30 characters?

Thank you very much

Best regards

Dr. Greta Romano

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From: Eric Blake <eblake <at> redhat.com>
To: Greta <romano.greta <at> gmail.com>, 24858-done <at> debbugs.gnu.org
Subject: Re: bug#24858: URGENT: Question about grep
Date: Wed, 2 Nov 2016 10:49:30 -0500

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tag 24858 notabug
thanks

On 11/02/2016 09:53 AM, Greta wrote:

> String to search: GTGTCA
> 
> File:
> 
>>HWI-ST740:1:C2GCJACXX:1:1101:1279:1825 1:N:0:
> _/NGACGCTCTGACCTTGGGGCTGGTCGGGG/__A_TGCTGAGGAGACGGTGACCAGGGTTCCCTGGCCCCACANNNCCAAGCTTCCNNNNNNNNNNNNNNNNNNN
> 
>>HWI-ST740:1:C2GCJACXX:1:1101:1349:1847 1:N:0:
> _/NTTAGATGAGGGAAACATCTGCATCAAGTT/__G_TTTATCTGTGACAACAAGTGTTGTTCCACTGCCAAAGAGTTTCTTATAATAAAACAATCGGGGTGGCACNNNNN
> 
> 
> I want that the research is done only in the underline characters.

Underlining doesn't show up in plain text mail (and we prefer plain text
over html bloat on the mailing list).  But I think your point still made
it across

>  So
> what I have to add in grep command to put the limit of 30 characters?

You can't do it with grep.  But you can do it with sed or awk.  Use the
right tool for the job at hand :)

Let's strip your example down to a smaller test case: I want to search
for a one-byte string '1', but only in the first 3 bytes of a file.
With grep, it is not possible; the pattern matches anywhere in the line:

$ printf '012000001\n345000001\n' | grep 1
012000001
345000001

But with sed, we can copy the entire line to hold space, truncate the
line in pattern space, then do the search; if successful, print the line
stored in hold space:

$ printf '012000001\n345000001\n' | \
  sed -n 'h; s/^\(.\{3\}\).*/\1/; /1/ { x;p }'
012000001

And I'll leave the awk program as an exercise for the reader.

Therefore, I'm tagging this as not a bug.

-- 
Eric Blake   eblake redhat com    +1-919-301-3266
Libvirt virtualization library http://libvirt.org

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