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Full Discussion: Outputting characters after a given string and reporting the characters in the row below --sed
Top Forums Shell Programming and Scripting Outputting characters after a given string and reporting the characters in the row below --sed Post 303028713 by Xterra on Sunday 13th of January 2019 05:31:14 PM
Old 01-13-2019
Outputting characters after a given string and reporting the characters in the row below --sed
I have this fastq file:
Code:
@M04961:22:000000000-B5VGJ:1:1101:9280:7106 1:N:0:86
GGGGGGGGGGGGCATGAAAACATACAAACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCAACAGCTTTATCAATACCATGAAAAATATCAACCACACCA
+test-1
GGGGGGGGGGGGGGGGGCCGGGGGFF,EDFFGEDFG,@DGGCGGEGGG7DCGGGF68CGFFFGGGG@CGDGFFDFEFEFF:30CGAFFDFEFF8CAF;;8
@M04961:22:000000000-B5VGJ:1:1121:9280:7106 1:N:0:86
GGCATGAAAACATACAAACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCAACAGCTTTATCAATACCATGAAAAATATCAACCACACCAGAAGCAGCAT
+test 2
GGGGGGGGGGGGGGGGGCCGGGGGF,EDFFGEDFG,@DGGCGGEGGG7DCGGGF68CGFFFGGGG@CGDGFFDFEFEFF:30CGAFFDFEFF8CAF;@8F
@M04961:22:000000000-B5VGJ:1:1151:9280:7106 1:N:0:86
GGCATGAAAACATACAAACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCAACAGCTTTATCAATACCATGAAAAATATCAACCACACCAGAAGCAGCAT
+more tests
GGGGGGGGGGGGGGGGGCCGGGGGF,EDFFGEDFG,@DGGCGGEGGG7DCGGGF68CGFFFGGGG@CGDGFFDFEFEFF:30CGAFFDFEFF8CAF;+8F
@M04961:22:000000000-B5VGJ:1:1101:26069:7790 1:N:0:86
CAGAACGTGAAAAAGCGTCCTGCGTGTAGCGAACTGCGATGGGCATACTGTAACCATAAGGCCACGTATTTTGCAAGCTGGCATGAAAACATACATTTTT
+few more
CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG+GGGG

And I am using this script to output the three characters after this sting GCATGAAAACATACA:
Code:
sed -n '/^@/{n;s/.*GCATGAAAACATACA\(...\).*/Codon:\t\1\tQuality Score: /p}'

This is my current output:
Code:
Codon:  AAC     Quality Score:
Codon:  AAC     Quality Score:
Codon:  AAC     Quality Score:
Codon:  TTT     Quality Score:

However, I would like to output the three characters in the same position two rows below from each sequence, something like this:
Code:
Codon:  AAC     Quality Score: ,ED
Codon:  AAC     Quality Score: GCC
Codon:  AAC     Quality Score: GCC
Codon:  TTT     Quality Score: +GG

Is there a way to accomplish this with sed?
operative system W10; shell cygwin
 

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LEARN ABOUT DEBIAN

fullquottel

FULLQUOTTEL(1)							   User Commands						    FULLQUOTTEL(1)

NAME

       fullquottel - tool for detecting full quotes in mails or postings

SYNOPSIS

       fullquottel [OPTION...] < infile > outfile

DESCRIPTION

       fullquottel - tool for detecting full quotes in mails or postings

       -t, --scorethreshold=NUMBER
	      Threshold for final score that discriminates between Goodquottel and Fullquottel (default: 1.5)

       --quotechars=CHARS
	      Chars used for quoting (default: >|#)

       -d, --debug
	      Debug option (prints single test results; default: off)

       --ownsigtest=1|0
	      Turn on/off ownSigTest (default: on)

       --ownsigtestscore=NUMBER
	      Score for ownSigTest (default: 1.0)

       -f, --ownsigtestfile=SIGFILE
	      Signature file to test against (default: ~/.signature)

       --mstest=1|0
	      Turn on/off msTest (Microsoft attribution lines; default: on)

       --mstestscore=NUMBER
	      Score for msTest (default: 1.0)

       --mstestthreshold=NUMBER
	      Threshold for msTest (at or below which line a Microsoft attribution line ist found; default: 2)

       --quotedtoalltest=1|0
	      Turn on/off quotedToAllTest (ratio quoted lines to all; default: on)

       --quotedtoalltestscore=NUMBER
	      Score for quotedToAllTest (default: 1.0)

       --quotedtoalltestfactor=NUMBER
	      Result = score + ratio * FACTOR (default: 0)

       --quotedtoalltestthreshold=NUMBER
	      Ratio threshold for activating quotedToAllTest (default: 0.5)

       --bottomquotedtoalltest=1|0
	      Turn on/off bottomQuotedToAllTest (ratio quoted lines at bottom to all; default: on)

       --bottomquotedtoalltestscore=NUMBER
	      Score for bottomQuotedToAllTest (default: 1.0)

       --bottomquotedtoalltestfactor=NUMBER
	      Result = score + ratio * FACTOR (default: 0)

       --bottomquotedtoalltestthreshold=NUMBER
	      Ratio threshold for activating bottomQuotedToAllTest (default: 0.5)

       --bottomquotedtoquotedtest=1|0
	      Turn on/off bottomQuotedToQuotedTest (ratio quoted lines at bottom to all quoted lines; default: on)

       --bottomquotedtoquotedtestscore=NUMBER
	      Score for bottomQuotedToQuotedTest (default: 1.0)

       --bottomquotedtoquotedtestfactor=NUMBER
	      Result = score + ratio * FACTOR (default: 0)

       --bottomquotedtoquotedtestthreshold=NUMBER
	      Ratio threshold for activating bottomQuotedToQuotedTest (default: 0.5)

       --singlebottomquotetest=1|0
	      Turn on/off singleBottomQuoteTest (only one quote block, and at the bottom; default: on)

       --singlebottomquotetestscore=NUMBER
	      Score for singleBottomQuoteTest (default: 1.0)

       HINT: All long options (without leading --) can be used in ~/.fullquottelrc

       -?, --help
	      Give this help list

       --usage
	      Give a short usage message

       -V, --version
	      Print program version

       Mandatory or optional arguments to long options are also mandatory or optional for any corresponding short options.

REPORTING BUGS

       Report bugs to <toast@toastfreeware.priv.at>.

SEE ALSO

       The full documentation for fullquottel is maintained in HTML created by doxygen and can be found in

	      /usr/share/doc/fullquottel/html/

fullquottel 0.1.2						    April 2007							    FULLQUOTTEL(1)
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