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Top Forums Shell Programming and Scripting Search strings and highlight them using Perl or bash/awk/sed Post 302842893 by Jotne on Sunday 11th of August 2013 04:42:03 AM
Old 08-11-2013
I need some help here to help out Smilie
Whit this script I get only one single line, correct is 5, why?
Code:
awk 'NR==FNR {a[$0]=$0;next} {for (i in a) {if ($0~a[i]) print}}' b.txt a.txt
Seq3 TTAAACTTTTTTCAACCCTAATG-----CGGTTTGAACCATTAACC-----------TAAC 48

correct answer is
Code:
Seq1 -------------------------------TTAAAAAGTTTGAGTTCTAAA---------------- 21
Seq2 -----CTTGGCTCTTTCGTAAGTTTTTCATTAAGGAACTTGAATACACGGTTT----AC- 50
Seq3 TTAAACTTTTTTCAACCCTAATG-----CGGTTTGAACCATTAACC-----------TAAC 48
Seq4 --------GAAAGGAGCGGAGTG-GTCACGTGACAAGTTCTCAGACGCACGTGC--TTGT 49
Seq4 --------GAAAGGAGCGGAGTG-GTCACGTGACAAGTTCTCAGACGCACGTGC--TTGT 49

Running a test like this show correctly all possibility
Code:
awk 'NR==FNR {a[$0]=$0;next} {for (i in a) {print $0,a[i]}}' b.txt a.txt
Seq1 -------------------------------TTAAAAAGTTTGAGTTCTAAA---------------- 21 ACG
Seq1 -------------------------------TTAAAAAGTTTGAGTTCTAAA---------------- 21 TAATG
Seq1 -------------------------------TTAAAAAGTTTGAGTTCTAAA---------------- 21 AAAAAG
Seq1 -------------------------------TTAAAAAGTTTGAGTTCTAAA---------------- 21 GACAAGT
Seq1 -------------------------------TTAAAAAGTTTGAGTTCTAAA---------------- 21 CAAGC
Seq1 -------------------------------TTAAAAAGTTTGAGTTCTAAA---------------- 21 GCTTG
Seq2 -----CTTGGCTCTTTCGTAAGTTTTTCATTAAGGAACTTGAATACACGGTTT----AC- 50 ACG
Seq2 -----CTTGGCTCTTTCGTAAGTTTTTCATTAAGGAACTTGAATACACGGTTT----AC- 50 TAATG
Seq2 -----CTTGGCTCTTTCGTAAGTTTTTCATTAAGGAACTTGAATACACGGTTT----AC- 50 AAAAAG
Seq2 -----CTTGGCTCTTTCGTAAGTTTTTCATTAAGGAACTTGAATACACGGTTT----AC- 50 GACAAGT
Seq2 -----CTTGGCTCTTTCGTAAGTTTTTCATTAAGGAACTTGAATACACGGTTT----AC- 50 CAAGC
Seq2 -----CTTGGCTCTTTCGTAAGTTTTTCATTAAGGAACTTGAATACACGGTTT----AC- 50 GCTTG
Seq3 TTAAACTTTTTTCAACCCTAATG-----CGGTTTGAACCATTAACC-----------TAAC 48 ACG
Seq3 TTAAACTTTTTTCAACCCTAATG-----CGGTTTGAACCATTAACC-----------TAAC 48 TAATG
Seq3 TTAAACTTTTTTCAACCCTAATG-----CGGTTTGAACCATTAACC-----------TAAC 48 AAAAAG
Seq3 TTAAACTTTTTTCAACCCTAATG-----CGGTTTGAACCATTAACC-----------TAAC 48 GACAAGT
Seq3 TTAAACTTTTTTCAACCCTAATG-----CGGTTTGAACCATTAACC-----------TAAC 48 CAAGC
Seq3 TTAAACTTTTTTCAACCCTAATG-----CGGTTTGAACCATTAACC-----------TAAC 48 GCTTG
Seq4 --------GAAAGGAGCGGAGTG-GTCACGTGACAAGTTCTCAGACGCACGTGC--TTGT 49 ACG
Seq4 --------GAAAGGAGCGGAGTG-GTCACGTGACAAGTTCTCAGACGCACGTGC--TTGT 49 TAATG
Seq4 --------GAAAGGAGCGGAGTG-GTCACGTGACAAGTTCTCAGACGCACGTGC--TTGT 49 AAAAAG
Seq4 --------GAAAGGAGCGGAGTG-GTCACGTGACAAGTTCTCAGACGCACGTGC--TTGT 49 GACAAGT
Seq4 --------GAAAGGAGCGGAGTG-GTCACGTGACAAGTTCTCAGACGCACGTGC--TTGT 49 CAAGC
Seq4 --------GAAAGGAGCGGAGTG-GTCACGTGACAAGTTCTCAGACGCACGTGC--TTGT 49 GCTTG


Last edited by Jotne; 08-11-2013 at 05:49 AM..
 

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DWWW-FIND(8)							      Debian							      DWWW-FIND(8)

NAME
dwww-find - find documentation related to a search argument SYNOPSIS
dwww-find [--program|--menu|--documentation|--docfile|--doc-base-list] [--skip=number] argument [...] DESCRIPTION
dwww-find is part of the dwww package, which provides access to on-line documentation on a Debian system via WWW. dwww-find searches for a documentation related to a given program, for entries from Debian Documentation Menu, or at least for documents registered with doc-base. It returns a HTML-formatted document with search results. OPTIONS
--program Search for documentation (man pages, info files, etc.) related to program specified by argument. --menu Search for entries in Debian Documentation Menu pages generated by dwww-build-menu(8). --documentation Search in documentation files registered with doc-base. It uses search++(1) for searching. --docfile Search for documentation for package, which contains the file specified by the argument. The file must be located in or below a directory that has been allowed by the system administrator; see dwww(7) for more info. --doc-base-list Show list of registerered doc-base files for given argument, which should be specified as format/document-id, where document-id is an identificator of registered doc-base document, and format is a name of format (e.g. text or pdf) registered by the document, for which the list list is to be generated. --skip=number Works only with --documentation. Skip number of search results. When no options are specified, --program is assumed. FILES
/etc/dwww/dwww.conf Configuration file for dwww. SEE ALSO
dwww(7), dwww-quickfind(8), dwww-build-menu(8), dwww-index++(8), search++(1), Debian doc-base Manual in /usr/share/doc/doc-base/doc-base.html/index.html. AUTHORS
Lars Wirzenius. Robert Luberda. See dwww(7) for copyrights and stuff. dwww 1.11.4 January 15th, 2011 DWWW-FIND(8)
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