using 2 sets of incremental file handles

Yael Soffer (ysofer@md.huji.ac.il)
Sun, 31 Jan 1999 10:16:18 +0200 

Please help me,
I'm using 2 sets of incremental file handles in my script and it seems I
get
wierd error messages, like:

Use of uninitialized value at test3.pl line 43,<protein0153> chunk 96.
Use of uninitialized value at test3.pl line 43, <protein0163> chunk 60

... and lots and lots of messages like this on my screen.


Protein0000 is the name of the incremental file handle.
Line 43  is the line in which I use "while($loopfiles[$j]){" to read from
the new incremental filehandle.
And after that the screen is filled with messages like these:

Read on closed filehandle <protein0199> at test3.pl line 85. 
Read on closed filehandle <protein0200> at test3.pl line 85. 
Read on closed filehandle <protein0201> at test3.pl line 85. 
Read on closed filehandle <protein0202> at test3.pl line 30.
Read on closed filehandle <protein0203> at test3.pl line 85.

Eventhough I don't use the close statement to close the file handle
proteinXXXX.

If I haven't managed to clear myself, here's a copy of the script.

Thank you,

Yael.

p.s.
the script:
	
#!/usr/bin/perl -w # program for finding something in file
$model=$ARGV[0]; #model is the name of the model/wanted protein and also
the directory of all the loop sequence #files. %score=();
$place="/usr/people/ysofer/3d_proteins"; opendir PROTEINS, $place or die
"can\'t open directory!"; @allfiles=grep -T, map "$place/$_", readdir
PROTEINS; closedir PROTEINS; $i=1; #because first file is rubbish opendir
LOOPS, $place or die "can\'t open directory!"; @loopfiles=grep -T, map
"$model/$_", readdir LOOPS; closedir LOOPS; @n=(); $protein='protein0000';
#incremental fileHandle while($allfiles[$i]){
	print "File number: ",$i,"\n";
	print "File name: $allfiles[$i] \n";
	$counter=1;
	$protein++;
	print "file handle = $protein \n";
	#Read files from directory, searching for the begining of the
sequence
	@n=split /\./,$allfiles[$i];
	print "extension: ",$n[1], "\n";
	# look for ".." only in swissprot, owl, pir, genpept files.
	if(($n[1] eq "swissprot") or ($n[1] eq "genpept") or ($n[1] eq
"owl")
		or($n[1] eq "sp_plant") or($n[1]=~ /p\w/g)){
		open($protein, "<$allfiles[$i]");
		$line=<$protein>;
		while($line){
		if($line=~/\.\./g){
				# maybe better to send to subroutine (from
other if, too)
				@sequence=<$protein>;
				$sequence="@sequence";
				chop($sequence);
				$sequence=~ s/\d*//g;
        			$sequence=~ s/\s+//g;
				$loops='loop0000'; #incremental fileHandle
				$j=1;
				$loops++;
				open($loops, "<$loopfiles[$j]");
				while($loopfiles[$j]){
					print $model."seq";
					if($loopfiles[$j] ne
($model.".seq")){
						# don't search in original
seq file
						$peptide=<$loops>;
						$k=1; #counter for number
of matches
						#searchin'
						
while(length($peptide)>3){
							#cutoff for length
to look for
							if($sequence=~
m/($peptide)/g){

$score{$sequence}[$k]=pos($sequence)+1-length($peptide);

$prot=$sequence;
								$k++;
							}

&MoreSearch($sequence,$peptide);
							$peptide=substr
$peptide,1;
						}
						sub MoreSearch{
							print "In here!!
\n";
							my
$peptide=$peptide;
							$peptide=substr
$peptide,0,-1;

while(length($peptide)>3){

if($sequence=~ m/($peptide)/g){

$score{$sequence}[$k]=pos($sequence)+1-length($peptide);

$k++;
								}

$peptide=substr $peptide,0,-1;
							}
						}
						#close($loops);
						$j++;
						open($loops,
"<$loopfiles[$j]");
					}
				}
		}
		$line=<$protein>;
		}
	}
	# look for "gb_ro, gb_vi, gb_ov, gb_om" and em
	if (($n[1]=~ /gb\w/g) or ($n[1]=~ /em\w/g)){
		open($protein, "<$allfiles[$i]");
		$line=<$protein>;
		while($line){
			if($line=~/translation/g){
					print "At file: $allfiles[$i] \n";
					print "I found the bastard at line
no. ",$counter,"\n";
			}
				else{
					$counter++;
				}
		$line=<$protein>;
		}
	}
	$i++;
	for($j=0; $j<$#n; $j++) {
			$n[$j]="";
				} } print "and now: \n"; print
"$score{$prot}[1]";
	foreach $prot(keys %score){
		print "\n At file= $prot \n";
		foreach $z(1..$#{$score{$prot}}){
			print "Res. number: $score{$prot}[$z]";
		}
	}