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

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From: Bruce Dubbs <bruce.dubbs <at> gmail.com>
To: Greta <romano.greta <at> gmail.com>, 24858 <at> debbugs.gnu.org
Subject: bug#24858: URGENT: Question about grep
Date: Wed, 2 Nov 2016 10:52:39 -0500

Greta wrote:
> 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?

cut -c 30 filename | grep ACGTAC

  -- Bruce

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