motif finder

assignment6.pl

#not /usr/local/bin/perl

# Reports a match and position of a Motif
#
# Input:
#       One motif pattern file
#       One sequence file

$patternFile;
$searchFile;

displayPrompt();
printf "\nMotif pattern file: " . $patternFile . "\n" . "Sequence file: " . $patternFile . "\n";

$patternText = readFile($patternFile);
$searchText = readFile($searchFile);

print "\nMotif pattern text:\n" . $patternText . "\nSequence text:\n" . $searchText . "\n"; 

$start = 0;
$end = length($searchText) - length($patternText);

for($start; $start < $end; $start++)
{
    $matchSequence = substr($searchText, $start, length($patternText));
    if($patternText eq $matchSequence)
    {
        print "\nMOTIF FOUND AT POSITION " . $start;
    }
}

#print $searchText =~ /$patternText/;

sub displayPrompt
{
    while(not defined($patternFile))
    {
        $testFile = getInput("Please enter a motif pattern file.\n\t");
        if(-f $testFile)
        {
            $patternFile = $testFile;
        }
        else
        {
            printf "\n\"$testFile\" does not exist in the current directory.\n"
        }
    }
    
    while(not defined($searchFile))
    {
        $testFile = getInput("Please enter a sequence file.\n\t");
        if(-f $testFile)
        {
            $searchFile = $testFile;
        }
        else
        {
            printf "\n\"$testFile\" does not exist in the current directory.\n"
        }
    }    
}

sub getInput
{
    my $prompt = shift;
    
    $prompt = "" if not defined $prompt;
    
    $files = "";
    if(defined($patternFile))
    {
        $files = "\Motif pattern file: " . $patternFile . "\n";
    }
    else
    {
        $files = "\Motif pattern file: NONE\n";
    }
    
    if(defined($searchFile))
    {
        $files = $files . "Sequence file: " . $patternFile . "\n";
    }
    else
    {
        $files = $files . "Sequence file: NONE\n";
    }       
    
    $prompt = $files . $prompt;
    
    print($prompt);
    $input = <>;
    chomp($input);
    return $input;
}

sub readFile
{
    my $file = shift;
    
    print "\nRead from file " . $file;
    
    if(not -f $file)
    {
        printf "\n$file is not a valid file in the current directory.\n";
        exit;
    }
    
    $text = "";
    if (open(my $fh, '<:encoding(UTF-8)', $file))
    {
        while(my $line = <$fh>)
        {
            if(not eof)
            {
                chomp $line;
                $text = $text . uc($line); # Uppercase
            }
        }
    }
    else
    {
        print "\nError reading file: " . $file;
    }

    return $text;
}