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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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FBB::mlm(3bobcat)					      OFoldStream manipulator						 FBB::mlm(3bobcat)

NAME
FBB::mlm - Manipulator modifying left margins of OFoldStream objects SYNOPSIS
#include <bobcat/ofoldstream> or #include <bobcat/ofoldstreambuf> Linking option: -lbobcat DESCRIPTION
The mlm class implements a manipulator that can be inserted into OFoldStream objects to modify the stream's left margin by a requested amount. The request cannot result in a negative left margin value. If a negative left margin would be the arithmetic result of the request then left margin 0 will silently be used. Depending on the tab-setting of the OFoldStream the inserted value represents the number of blank space characters or the number of tab-characters that will be added to the left margin. The request will be processed at the next newline character or std::flush or std::endl manipulator that is inserted into the stream. If a line is still empty once an mlm object and a flush manipulator are inserted into the stream then the new left margin will be effective at the next word inserted into that line (cf., the example section below) A bad_cast exception is thrown when the manipulator is inserted into an ostream that is not using a OFoldStreambuf buffer. NAMESPACE
FBB All constructors, members, operators and manipulators, mentioned in this man-page, are defined in the namespace FBB. INHERITS FROM
- CONSTRUCTOR
o mlm(int addValue): The standard copy constructor is available. MEMBER FUNCTIONS
There are no public or protected member functions in this class. EXAMPLE
#include <iostream> #include <bobcat/ofoldstream> using namespace std; using namespace FBB; int main() { OFoldStream out(cout, 0, 80); out << "hello world (left margin is 0)" << mlm(4) << " " "this uses a 4 character wide left margin " << mlm(-10) << flush << "left margin -6 changed to 0, active on this line "; return 0; } FILES
bobcat/mlm - defines the class interface SEE ALSO
bobcat(7), manipulators(3bobcat), lm(3bobcat), ofoldstream(3bobcat) BUGS
None Reported. DISTRIBUTION FILES
o bobcat_3.01.00-x.dsc: detached signature; o bobcat_3.01.00-x.tar.gz: source archive; o bobcat_3.01.00-x_i386.changes: change log; o libbobcat1_3.01.00-x_*.deb: debian package holding the libraries; o libbobcat1-dev_3.01.00-x_*.deb: debian package holding the libraries, headers and manual pages; o http://sourceforge.net/projects/bobcat: public archive location; BOBCAT
Bobcat is an acronym of `Brokken's Own Base Classes And Templates'. COPYRIGHT
This is free software, distributed under the terms of the GNU General Public License (GPL). AUTHOR
Frank B. Brokken (f.b.brokken@rug.nl). libbobcat1-dev_3.01.00-x.tar.gz 2005-2012 FBB::mlm(3bobcat)
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