Contents of tab delimited files, $PYCFILE:

Muskie.pyc
day	invertebrates	fish
1	1	0
183	0	1
365	0	1

##</code><code>##

Northern Pike.pyc
day	invertebrates	fish
1	3000	4000
365	3000	4000

##</code><code>##

#!/usr/bin/perl
#Working With *.pyc files

sub PYCFILENAMEASSIGNMENT{
$PYCFILE = "$FishSpecies".".pyc";
}

sub OPENPYC{

@dayvalues = ();
open PYCFILE, "/Applications/Bioenergetics/User\ Input\ Data\ Files/$PYCFILE" or die "Cannot open $PYCFILE: $!";
@dailypyc=<PYCFILE>;
shift(@dailypyc);
###I believe the problem is in here.
foreach $line (@dailypyc){
	
	print "\n";
	chomp($line);
	@pyclinevalues=split("\t",$line);
	$day = $pyclinevalues[0];
	chomp($day);
	print "Day $day\t";
	push (@dayvalues,$day);
	shift(@pyclinevalues);
	$totalnumberofpycpreyitems = scalar (@pyclinevalues);
	$scalarcounter = 0;
		
		while($pyclinevalues[0]){
		$pyc = $pyclinevalues[0];
		chomp($pyc);
		print "Endens $pyc\t";
		push (@{pycvalues."$scalarcounter"},$pyc);
		$scalarcounter = $scalarcounter + 1;
		shift(@pyclinevalues);
		}
	
	}
close (PYCFILE);
###
$scalarcounter = 0;
$PYCLININTERPLOOP = 1;
until($PYCLININTERPLOOP > $totalnumberofpycpreyitems){

	@projectedpycvalues = ();
	if(${pycvalues."$scalarcounter"}[1]){
		$projecteddeltay = ${pycvalues."$scalarcounter"}[1] - ${pycvalues."$scalarcounter"}[0];
		chomp ($projecteddeltay);
		$projecteddeltax = $dayvalues[1] - $dayvalues[0];
		chomp ($projecteddeltax);
		$newvalue = ${pycvalues."$scalarcounter"}[0];
		chomp ($newvalue);
		$projectedslope = $projecteddeltay/$projecteddeltax;
		chomp ($projectedslope);
		push (@projectedpycvalues,$newvalue);
		$checker = $dayvalues[0];
		chomp ($checker);
		$checker = $checker + 1;

		if($checker < $dayvalues[1]){
			until($checker == $dayvalues[1]){
			$newvalue = $newvalue + $projectedslope;
			push (@projectedpycvalues,$newvalue);
			$checker = $checker + 1;
			}
		}

		if($checker == $dayvalues[1]){
			$newvalue = ${pycvalues."$scalarcounter"}[1];
			push (@projectedpycvalues, $newvalue);
			$checker = $checker + 1;
			}
		}

	$PYCLOOPCOUNTER = 2;
	$totalnumberofpycdatapoints = scalar (@pycpvalues);
		until($PYCLOOPCOUNTER > $totalnumberofpycdatapoints){
			if(${pycvalues."$scalarcounter"}[2]){
				$projecteddeltay = ${pycvalues."$scalarcounter"}[2] - ${pycvalues."$scalarcounter"}[1];
				chomp ($projecteddeltay);
				$projecteddeltax = $dayvalues[2] - $dayvalues[1];
				chomp ($projecteddeltax);
				$newvalue = ${pycvalues."$scalarcounter"}[1];
				chomp ($newvalue);
				$projectedslope = $projecteddeltay/$projecteddeltax;
				chomp ($projectedslope);

				if($checker < $dayvalues[2]){
					until($checker == $dayvalues[2]){
						$newvalue = $newvalue + $projectedslope;
						push (@projectedpycvalues,$newvalue);
						$checker = $checker + 1;
						}
					}

				if($checker == $dayvalues[2]){
					$newvalue = ${pycvalues."$scalarcounter"}[2];
					push (@projectedpycvalues, $newvalue);
					$checker = $checker + 1;
					}
			}

		shift(@dayvalues);
		shift(@pycvalues);
		$PYCLOOPCOUNTER = $PYCLOOPCOUNTER +1;
		}

	print "@projectedpycvalues\n\n";
	$totalnumberofdays = scalar (@projectedpycvalues);
	
	$day = 1;
	foreach $value (@projectedpycvalues){
		chomp($value);
		$dailypyctable{$day} = $value; 
		$day = $day + 1;
		}
	$scalarcounter = $scalarcounter + 1;
	%{dailypyctable."$scalarcounter"} = %dailypyctable;
	$PYCLININTERPLOOP = $PYCLININTERPLOOP + 1;
	}
}

print"Species?\n";
chomp($FishSpecies = <STDIN>);
&PYCFILENAMEASSIGNMENT;
&OPENPYC;

##</code><code>##

Contents of Tab Delimited Files, $TEMFILE

Some Fish.tem

day	temperature
1	19
30	25
61	25
92	25
122	19.3
153	10
180	5
214	4
304	5
334	10.5
365	18.3

##</code><code>##

as opposed to this *.tem file which contains a zero, and 

day	temperature
1	15
30	20
61	20
92	20
122	15
153	7
180	2
214	0
304	2
334	8
365	15

##</code><code>##

#!/usr/bin/perl
sub TEMFILENAMEASSIGNMENT{
$TEMFILE = "$FishSpecies".".tem";
}

sub OPENTEM{

@dayvalues = ();
open TEMP, "/Applications/Bioenergetics/User\ Input\ Data\ Files/$TEMFILE" or die "Cannot open $TEMFILE: $!";
@dailytemp=<TEMP>;
shift(@dailytemp);
foreach $line (@dailytemp){
	chomp($line);
	($day,$temp)=split("\t",$line);
	chomp($day);
	chomp($temp);
	print "$day, $temp\n";
	push (@dayvalues,$day);
	push (@tempvalues,$temp);
	}
close (TEMP);

if($tempvalues[1]){
	$projecteddeltay = $tempvalues[1] - $tempvalues[0];
	chomp ($projecteddeltay);
	$projecteddeltax = $dayvalues[1] - $dayvalues[0];
	chomp ($projecteddeltax);
	$newvalue = $tempvalues[0];
	chomp ($newvalue);

	$projectedslope = $projecteddeltay/$projecteddeltax;
	chomp ($projectedslope);
	push (@projectedtempvalues,$newvalue);
	$checker = $dayvalues[0];
	chomp ($checker);
	$checker = $checker + 1;


		if($checker < $dayvalues[1]){
			until($checker == $dayvalues[1]){
				$newvalue = $newvalue + $projectedslope;
				push (@projectedtempvalues,$newvalue);
				$checker = $checker + 1;
				}
			}

		if($checker == $dayvalues[1]){
			$newvalue = $tempvalues[1];
			push (@projectedtempvalues, $newvalue);
			$checker = $checker + 1;
			}
	}

$TEMLOOPCOUNTER = 2;

$totalnumberoftemdatapoints = scalar (@tempvalues);
until($TEMLOOPCOUNTER > $totalnumberoftemdatapoints){
	if($tempvalues[2]){
		$projecteddeltay = $tempvalues[2] - $tempvalues[1];
		chomp ($projecteddeltay);
		$projecteddeltax = $dayvalues[2] - $dayvalues[1];
		chomp ($projecteddeltax);
		$newvalue = $tempvalues[1];
		chomp ($newvalue);
		
		$projectedslope = $projecteddeltay/$projecteddeltax;
		chomp ($projectedslope);

		if($checker < $dayvalues[2]){
			until($checker == $dayvalues[2]){
			$newvalue = $newvalue + $projectedslope;
			push (@projectedtempvalues,$newvalue);
			$checker = $checker + 1;
			}
		}

		if($checker == $dayvalues[2]){
			$newvalue = $tempvalues[2];
			push (@projectedtempvalues, $newvalue);
			$checker = $checker + 1;
			}
		}

	shift(@dayvalues);
	shift(@tempvalues);
	$TEMLOOPCOUNTER = $TEMLOOPCOUNTER +1;
	}

print "@projectedtempvalues";
$totalnumberofdays = scalar (@projectedtempvalues);

$day = 1;
foreach $value (@projectedtempvalues){
	chomp($value);
	$dailytemptable{$day} = $value; 
	$day = $day + 1;
	}

}

print"Species?\n";
chomp($FishSpecies = <STDIN>);
&TEMFILENAMEASSIGNMENT;
&OPENTEM;