Outputting characters after a given string and reporting the characters in the row below --sed Post: 303028723

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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 303028723 by Don Cragun on Monday 14th of January 2019 02:20:01 AM

01-14-2019

Registered User

Quote:

Originally Posted by Xterra

Don
Thanks!
PS. If I would like to search for more than one string (GCATGAAAACATACA and TTTCCAGAAATTGT) and report different number characters (3 and 6. I should be able to do it passing the strings and number of charters as variables, right?

Code:

awk -vlen="3 6" -vstr="GCATGAAAACATACA TTTCCAGAAATTGT" '
BEGIN {	for (MX=n=split (str, TMP); n>0; n--) SRCH[TMP[n]] = n
	String = n
	StringLen = length(String)
}
/^@/ {	matchline = NR + 1
	qualityline = NR + 3
	next
}
NR == matchline {
	if(spot = index($0, String))
		printf("Codon:\t%s\tQuality Score:\t",
		    substr($0, spot + StringLen, len))
	else	qualityline = 0
	next
}
NR == qualityline {
	printf("%s\n", substr($0, spot + StringLen, len))
}' test.txt

I'm pretty sure that the code you have shown us above won't do what you want to do, but from your new description I'm not sure what it is that you're trying to do.

The String variable in my code needs to be a string; not a number representing an index into the TMP[] and/or SRC[] arrays. If you're looking for multiple strings on the 2nd line of each group of input lines you're processing, you need to perform more than one index() operation to search for those strings.

If you could give us a clearer description and show us the output you hope to produce from your new requirements, maybe we could help.

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LEARN ABOUT LINUX

shtool-path

SHTOOL-PATH.TMP(1)					      GNU Portable Shell Tool						SHTOOL-PATH.TMP(1)

NAME

       shtool-path - GNU shtool command dealing with shell path variables

SYNOPSIS

       shtool path [-s|--suppress] [-r|--reverse] [-d|--dirname] [-b|--basename] [-m|--magic] [-p|--path path] str [str ...]

DESCRIPTION

       This command deals with shell $PATH variables. It can find a program through one or more filenames given by one or more str arguments.  It
       prints the absolute filesystem path to the program displayed on "stdout" plus an exit code of 0 if it was really found.

OPTIONS

       The following command line options are available.

       -s, --suppress
	   Supress output. Useful to only test whether a program exists with the help of the return code.

       -r, --reverse
	   Transform a forward path to a subdirectory into a reverse path.

       -d, --dirname
	   Output the directory name of str.

       -b, --basename
	   Output the base name of str.

       -m, --magic
	   Enable advanced magic search for ""perl"" and ""cpp"".

       -p, --path path
	   Search in path. Default is to search in $PATH.

EXAMPLE

	#   shell script
	awk=`shtool path -p "${PATH}:." gawk nawk awk`
	perl=`shtool path -m perl`
	cpp=`shtool path -m cpp`
	revpath=`shtool path -r path/to/subdir`

HISTORY

       The GNU shtool path command was originally written by Ralf S.  Engelschall <rse@engelschall.com> in 1998 for Apache. It was later taken
       over into GNU shtool.

SEE ALSO

       shtool(1), which(1).

18-Jul-2008							   shtool 2.0.8 						SHTOOL-PATH.TMP(1)

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