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Top Forums UNIX for Dummies Questions & Answers Extract string between paranthesis Post 302774939 by evelibertine on Sunday 3rd of March 2013 10:55:14 PM
Old 03-03-2013
Extract string between paranthesis

Hi,

I have a file of fasta headers that looks like the following:

Code:
>gi|28476830|ref|NR_001281.1| Homo sapiens protocadherin beta 18 pseudogene (PCDHB18), non-coding RNA
>gi|187937204|ref|NR_023342.1| Homo sapiens keratin associated protein 20-4 (KRTAP20-4), non-coding RNA
>gi|221139737|ref|NR_024072.2| Homo sapiens MRS2 magnesium homeostasis factor homolog (S. cerevisiae) pseudogene 2 (MRS2P2), non-coding RNA
>gi|219881533|ref|NR_003932.2| Homo sapiens ribosomal protein L13a pseudogene 20 (RPL13AP20), non-coding RNA
>gi|93204855|ref|NR_003024.1| Homo sapiens eukaryotic translation initiation factor 3, subunit I pseudogene 1 (EIF3IP1), non-coding RNA
>gi|222831626|ref|NR_026740.1| Homo sapiens placenta-specific 9 pseudogene (LOC389033), non-coding RNA

I want to write a code to extract the string inside parantheses in each line. The difficulty is some of the lines how more than two strings inside parantheses (i.e. line 3) In such cases, I only want to extract the string inside the second paranthesis. My output should look like:

Code:
PCDHB18
KRTAP20-4
MRS2P2
RPL13AP20
EIF3IP1
LOC389033

How do I go about doing this? Thanks!
 

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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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