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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

filecache

FileCache(3pm)						 Perl Programmers Reference Guide					    FileCache(3pm)

NAME

       FileCache - keep more files open than the system permits

SYNOPSIS

	   use FileCache;
	   # or
	   use FileCache maxopen => 16;

	   cacheout $path;
	   print $path @data;

	   cacheout $mode, $path;
	   print $path @data;

DESCRIPTION

       The "cacheout" function will make sure that there's a filehandle open for reading or writing available as the pathname you give it. It
       automatically closes and re-opens files if you exceed  your system's maximum number of file descriptors, or the suggested maximum.

       cacheout EXPR
	   The 1-argument form of cacheout will open a file for writing ('>') on it's first use, and appending ('>>') thereafter.

       cacheout MODE, EXPR
	   The 2-argument form of cacheout will use the supplied mode for the initial and subsequent openings. Most valid modes for 3-argument
	   "open" are supported namely; '>', '+>', '<', '<+', '>>',  '|-'  and	'-|'

CAVEATS

       If you use cacheout with '|-' or '-|' you should catch SIGPIPE and explicitly close the filehandle., when it is closed from the other end
       some cleanup needs to be done.

       While it is permissible to "close" a FileCache managed file, do not do so if you are calling "FileCache::cacheout" from a package other
       than which it was imported, or with another module which overrides "close".  If you must, use "FileCache::cacheout_close".

BUGS

       sys/param.h lies with its "NOFILE" define on some systems, so you may have to set maxopen ($FileCache::cacheout_maxopen) yourself.

perl v5.8.0							    2002-06-01							    FileCache(3pm)
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