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Full Discussion: Need help comparing Base Pairs within PERL
Top Forums Shell Programming and Scripting Need help comparing Base Pairs within PERL Post 302655119 by ddreggors on Tuesday 12th of June 2012 09:48:30 PM
Old 06-12-2012
Try this:

Code:
--- test5-old.pl	2012-06-12 21:38:13.986606410 -0400
+++ test5-new.pl	2012-06-12 21:43:51.468953185 -0400
@@ -2,36 +2,24 @@
 #
 use strict;
 use warnings;
-my (@data, $row, @dataline);
+my (@data, $row, @dataline, $dnafile);
+$dnafile = "coutbase.log";
 open(FILE1,"<","UDP3866.pseudo-vs.large.txt") or die $!; @data = <FILE1>; close(FILE1);
 foreach $row (@data) {
 		next unless $row =~ /^\d/;
 		@dataline = split(/\s+/,$row);
 		next unless $dataline[9] ne "NA";
 		next unless $dataline[9] =~ /$dataline[6]/i;
-		print $dataline[0] . "\t" . $dataline[1] . "\t" . $dataline[6] . "\t" .  $dataline[7] . "\t" . $dataline [9] .  "\n";
+		open(COUNTBASE, ">>", \$dnafile) or die $!;
+		print COUNTBASE $dataline[0] . "\t" . $dataline[1] . "\t" . $dataline[6] . "\t" .  $dataline[7] . "\t" . $dataline [9] .  "\n";
+		close COUNTBASE;
 }
-my $outputfile = "COUNTBASE";
-unless (open(COUNTBASE, ">$outputfile")) {print "cant open file\n\n";
-exit;}
-print COUNTBASE "$dataline[7]";
-close (COUNTBASE);
-my $dnafile = <COUNTBASE>;
-#Remove the newline from the dna file name
-chomp $dnafile;
 #Open this file or exit
-unless (open(COUNTBASE, $dnafile)){
-		 print  "can't open file \"$dnafile\"\n\n";
-		exit;
-}
+open(COUNTBASE, "<", \$dnafile) or die $!;
 #store dna information
 my @dna = <COUNTBASE>;
 #close now read file
 close COUNTBASE;
-#turn array into single string
-my $dna = join('', @dna);
-#get rid of blank spaces
-$dna =~ s/\s//g;
 #initialize mutation counts
 my $countExonic = 0;
 my $countIntergenic = 0;

I have attached the file, but this also will give you a quick look at the changes. Everything with a "+" is a change I added, everything with a "-" are lines I removed.
test5-new.pl (2.4 KB) 
 

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LEARN ABOUT REDHAT

mlm

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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