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Top Forums Shell Programming and Scripting Outputting characters after a given string and reporting the characters in the row below --sed Post 303028725 by Don Cragun on Monday 14th of January 2019 03:28:31 AM
Old 01-14-2019
Making a few wild guesses... If the output you're trying to produce is:
Code:
Codon:	AAC	Quality Score:	,ED
Codon:	TCCAAG	Quality Score:	G7DCGG
Codon:	AAC	Quality Score:	GCC
Codon:	TCCAAG	Quality Score:	DGGCGG
Codon:	AAC	Quality Score:	GCC
Codon:	TCCAAG	Quality Score:	DGGCGG
Codon:	TTT	Quality Score:	+GG

you could try something like:
Code:
awk -v lengths="3 6" -v strings="GCATGAAAACATACA TTTCCAGAAATTGT" '
BEGIN {	nString = split(strings, String)
	split(lengths, OutLen)
	for(i = 1; i <= nString; i++)
		StringLen[i] = length(String[i])
}
/^@/ {	getline CodonLine
	getline
	getline QualityLine
	for(i = 1; i <= nString; i++)
		if(spot = index(CodonLine, String[i]))
			printf("Codon:\t%s\tQuality Score:\t%s\n",
			    substr(CodonLine, spot + StringLen[i], OutLen[i]),
			    substr(QualityLine, spot + StringLen[i], OutLen[i]))
}' file

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rpc_gss_set_defaults(3N)												  rpc_gss_set_defaults(3N)

NAME
rpc_gss_set_defaults - change service, QOP for a session SYNOPSIS
DESCRIPTION
allows an application to change the service (privacy, integrity, authentication, or none) and Quality of Protection (QOP) for a transfer session. New values apply to the rest of the session only unless they are changed again. PARAMETERS
Information on data types for parameters may be found on the rpcsec_gss(3N) manpage. auth An RPC authentication handle returned by service An of type representing one of the following types of security service: authentication, privacy, integrity, or none. qop A string representing Quality of Protection. Valid strings may be found in the file or by using MULTITHREAD USAGE
Thread Safe: Yes Cancel Safe: Yes Fork Safe: No Async-cancel Safe: No Async-signal Safe: No These functions can be called safely in a multithreaded environment. They may be cancellation points in that they call functions that are cancel points. In a multithreaded environment, these functions are not safe to be called by a child process after and before These functions should not be called by a multithreaded application that supports asynchronous cancellation or asynchronous signals. RETURN VALUES
returns if it is successful; otherwise, use to get the error associated with the failure. FILES
File containing valid QOP values SEE ALSO
rpc(3N), rpc_gss_get_mech_info(3N), rpcsec_gss(3N), qop(4). ONC+ Developer's Guide Network Working Group RFC 2078 rpc_gss_set_defaults(3N)
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