Someone

#!/usr/bin/perl -w

#Derek Anderson 
#Perl for Bioinformatics Project 1
use Getopt::Std;
use GD::Simple;
use strict;

sub setOpts {
	#Sub that gets a filename from the command line
	my $optString='f:';
	my %opt;
	my %configHash;
	if($#ARGV >=0) {
        	getopts($optString,\%opt) or printError("Error on use $0 -f FILENAME");
       		$configHash{'myFile'}=$opt{'f'} if(defined($opt{'f'}));
    	}
    	else {
        	printError("Error on use $0 -f FILENAME");
    	}
    	return %configHash;
}

sub printError {
	#Sub that prints a message then exits program
	my $errorMsg=$_[0];
	print STDERR $errorMsg."\n";
	exit();
}
sub checkFile {
	#Sub that checks to see if the file is on the system
	my $fileName=$_[0];
	printError("Please check file $fileName") if (! -f $fileName);
}
sub loadFile {
	#Sub that opens a file handel called SEQ
	my $ref=$_[0];
	my %configHash=%$ref;
	open(SEQ,'<',$configHash{'myFile'}) or printError("$! on file $configHash{'file'}");
}

sub parseFile {
	#Sub that parses the fasta file
	my $ref=$_[0];
	my %configHash=%$ref;
	while(<SEQ>) {
		chomp $_;
		$configHash{'String'}.=$_ if(!($_ =~ m/^>/));
	}
	return %configHash;
}

sub findMatch {
	#Sub that finds matches in a string and saves them in an array
	my $ref=$_[0];
	my %configHash=%$ref;
	my @match;
	my @hold;
	my @reg=("(TAGGT[AT]ACCTA)","(TGGGT[AT]ACCCA)","(TTGGT[AT]ACCAA)");
	foreach(@reg) {
		while($configHash{'String'} =~ m/$_/g) {
			my $num=(pos($configHash{'String'})-11);	
			push(@hold,$num);
		}
	}
	$configHash{'hold'} = \@hold;
	return %configHash;
}

sub closeFile {
	#Sub that closes the file handle
	close SEQ;
}

sub loopTh {
	#Sub that makes a png image from a fasta file
	my $ref=$_[0];
	my %configHash=%$ref;
	my $num=0;
	my $len=length($configHash{'String'});
	my @hold = @{$configHash{'hold'}};
	my $start =shift(@hold);
	my $word=0;
	my $over=20;
	my $height=10;
	my $img= GD::Simple->new(620,600);
	$img->moveTo(10,10);
	$img->penSize(15,10);
	while($num <= $len) {#Loop through till there is nothing left in our string
		if($num == ($start) || $over <=11) {#If we are at the start of a math or the line wraps to a new one
			$img->fgcolor('yellow');
			if($over >= 11 && ($word+11 > 100) ) {#If the match wraps lines
				$over=0;
			}
			
			if($over <= 11) {#Print the wraped lines
				$img->string(substr($configHash{'String'},$num,1));
				$over++;
			}
			else {#If all 11 can fit on a line print it
				$img->string(substr($configHash{'String'},$num,11));
				$num=$num+10;
			}
			unless($#hold == -1) {#Get next value we found if there is any left in the array
				$start =shift(@hold);
			}
		}
		else {#if we did not find a match print it red
			$img->fgcolor('red');
			$img->string(substr($configHash{'String'},$num,1));
		}
		
		if($num%100==0) {#wrap to a new line
			$img->fgcolor('black');
			$img->moveTo(10,$height);
			$img->line(599);
			$img->moveTo(10,$height+5);
			$height = $height + 15;
			$word=0;
		}
		$word++;
		$num++;
	}
	print $img->png;
}

sub init {
	#sub that calls all other subs
	my %configHash=setOpts();
	checkFile($configHash{'myFile'});
	loadFile(\%configHash);
	%configHash=parseFile(\%configHash);
	%configHash=findMatch(\%configHash);
	loopTh(\%configHash);
	closeFile();
}

init();