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Top Forums UNIX for Dummies Questions & Answers Reporting characters after string Post 302970651 by Xterra on Sunday 10th of April 2016 01:46:01 AM
Old 04-10-2016
Reporting characters after string

I have a file that looks like this:
Code:
>ID 1
AATAATTCCGGATCGTGC
>ID 2
TTTGACAGTAGAC
>ID 3
AGACGATGACGAT

I am using the following script to report if AATTCCGGATCG is present in any sequence:
Code:
awk 'FNR==1{n=substr(FILENAME,1,index(FILENAME,".")-1)} { print n "\t" (/AATTCCGGATCG|CGATCCGGAATT/ ? "ATCG" : "NOT Present" ) }

However, what I really need is the four characters right after the given string (AATTCCGG), in my example=ATCG. Importantly, the string can be found reversed GGCCTTAA and complemented A=T; T=A; C=G and G=C, originating the following string =CCGGAATT in the sequence. If the string is found reversed and complemented, the four characters after the string must be reported as reversed and complemented. Thus, the desired output from a file containing the following sequences:
Code:
>ID 1
AATAATTTTGGATCGTGC
>ID 2
TTTGACGTTCCGGAATTCAGTAGAC
>ID 3
AGACGATGACGAT

would be AACG, since sequence 2 contains the corresponding string, only reversed and complemented.
My script can deal with the fact that the sequence is reversed/complemented. However, if any of the positions after the string is mutated, it will not detect it. That's is why I would rather get the characters instead
Any help will be greatly appreciated
Thanks
PS. The string, in this case AATTCCGG or CCGGAATT will never be mutated in a real scenario.
 

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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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