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Top Forums UNIX for Dummies Questions & Answers Reporting characters after string Post 302970802 by Scrutinizer on Monday 11th of April 2016 11:39:02 PM
Old 04-12-2016
10 occurrences per line ? Or per file?
What is you expected output?

Could you repeat the results with mawk, do you know how to install it?


--
Your GNU sed script will only find one occurrence per line and one occurrence per set of files of regular and reversed/complemented versions (the latter because only part of the file is reversed). Any additional patterns will not be shown and neither will it be shown which files or records these belong to, is that as intended? In the sample in post #1 one it printed the filename and could take multiple files...

Since it only reverse part of the file(s) and searches the whole file(s) there is a risk that it will find a reversed match in a non-reversed part of the file, which would mean a false positive .
To counteract that, you would need something like this, using GNU sed:
Code:
sed -n '0,/AATTCCGG/s/^[ATCG]*AATTCCGG\(.\)\(.\)\(.\)\(.\)[ATCG]*$/\1\2\3\4/p; 0,/CCGGAATT/{y/ATCG/TAGC/; s/^[ATCG]*\(.\)\(.\)\(.\)\(.\)GGCCTTAA[ATCG]*$/\4\3\2\1/p;}' file*

So the sed script it looking for very different things than the awk script us, and is only suited to investigate of there is one occurrence of either pattern in a single (set of) files, and for multiple files you would need a shell loop, which would significantly slow down processing, whereas the awk version can scan multiple files at once.

Last edited by Scrutinizer; 04-12-2016 at 01:31 AM..
 

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GREP(1) 						      General Commands Manual							   GREP(1)

NAME
grep - search a file for lines containing a given pattern SYNOPSIS
grep [-elnsv] pattern [file] ... OPTIONS
-e -e pattern is the same as pattern -c Print a count of lines matched -i Ignore case -l Print file names, no lines -n Print line numbers -s Status only, no printed output -v Select lines that do not match EXAMPLES
grep mouse file # Find lines in file containing mouse grep [0-9] file # Print lines containing a digit DESCRIPTION
Grep searches one or more files (by default, stdin) and selects out all the lines that match the pattern. All the regular expressions accepted by ed and mined are allowed. In addition, + can be used instead of * to mean 1 or more occurrences, ? can be used to mean 0 or 1 occurrences, and | can be used between two regular expressions to mean either one of them. Parentheses can be used for grouping. If a match is found, exit status 0 is returned. If no match is found, exit status 1 is returned. If an error is detected, exit status 2 is returned. SEE ALSO
cgrep(1), fgrep(1), sed(1), awk(9). GREP(1)
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