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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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ALI2GFF(1)						      General Commands Manual							ALI2GFF(1)

NAME
ali2gff - Module to translate a MUMmer output files into gff formatted output. SYNOPSIS
ali2gff [-r] [-t <.|0|1|2>] [-x <name>] [-y <name>] [-H] [-f] [-h] <MUMmer_output_file> OPTIONS
-h, --help Show summary of options. -r Interchange the order of sequences (sequence 1 on y-axis, sequence 2 on x-axis). -t <.|0|1|2> Put label 'frame' in gff output. -x <name> Specify the species name for species1 (default: "Seq1"). -y <name> Specify the species name for species2 (default: "Seq2"). -i Ignore full sequence identities. -f Write output to file. SEE ALSO
blat2gff(1), gff2aplot(1), parseblast(1), sim2gff(1). AUTHOR
ali2gff was written by Steffi Gebauer-Jung. This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>, for the Debian project (but may be used by others). Mon, 21 Mar 2005 21:44:15 -0300 ALI2GFF(1)
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