match loop failure

Anonymous Monk has asked for the wisdom of the Perl Monks concerning the following question:

I am trying to match an array with the related value in the hash. Hash and array are opened and print fine but I can only get the match for one line not the complete array. Please help, I'm completely stuck and I keep hitting the same problem no matter how I write the rest.

    my $Start_rank;
    my @b;
    my $line2;
    my %hash;
    my $Rank;
    my $info;

while (<INFILE>) {
    my $line=$_;
    $line=~s/\s$//;
    chomp($line);
    my @a;
    #my @a=split/\t/,$line;
    ($Rank, my $id, my $C, my $Position) = split /\t/, $line;
    next unless $Rank=~/\d+/;
    $info = $id . "\t" . $C . "\t" . $Position;
    $hash{$Rank}= $info;
    }
    while (<INFILE2>) {
    $line2=$_;
    $line2=~s/\s$//;
    chomp($line2);
    my @b=split/\t/,$line2;
     next unless $b[0]=~/\d+/;
    $Start_rank = $b[1];
    
    while (($Rank, $SNP_info) = each (%hash))    { 
    foreach ($line2) {
    if ($Start_rank eq $Rank ) {
print "$Start_rank\t$info\t$b[2]\t$b[3]\t$b[4]\t$b[5]\t$b[6]\t$b[7]\t$
+b[8]\t$b[9]\n";    }
else {print "no match\n";    }        } }}
[download]

I should get ~60 matches, instead I get one. Thank you for anything you can suggest.

Comment on match loop failure Download Code

Replies are listed 'Best First'.
Re: match loop failure by toolic (Bishop) on Jun 08, 2011 at 17:09 UTC
Without you showing any input data, actual output data and expected data, it is hard to give specific advice. After neatening up your code with perltidy, one really suspicious line is: `foreach ($line2) {` [download] Since `$line2` is a scalar, the foreach loop will only loop (at most) once. Generic advice: use strict and warnings Start debugging your code by adding more prints (Basic debugging checklist)	[reply] [d/l] [select]
Re^2: match loop failure by Anonymous Monk on Jun 08, 2011 at 17:23 UTC
Apologies it was a first post. You were correct about the scalar. Thanks for your help.	[reply]
Re: match loop failure by jwkrahn (Abbot) on Jun 08, 2011 at 18:23 UTC
It looks like you want something like this: `my %hash; while ( <INFILE> ) { ( my $line = $_ ) =~ s/\s+$//; my ( $Rank, $id, $C, $Position ) = split /\t/, $line; next unless $Rank =~ /\d/; $hash{ $Rank } = "$id\t$C\t$Position"; } while ( <INFILE2> ) { ( my $line = $_ ) =~ s/\s+$//; my @b = split /\t/, $line; next unless $b[ 0 ] =~ /\d/; my $Start_rank = $b[ 1 ]; if ( exists $hash{ $Start_rank } ) { print join( "\t", $Start_rank, $hash{ $Start_rank }, @b[ 2 .. +9 ] ), "\n"; } else { print "no match\n"; } }` [download]	[reply] [d/l]
Re^2: match loop failure by Anonymous Monk on Jun 10, 2011 at 08:22 UTC
After correcting the foreach scalar to @b I was going through each of the 200,000 keys in my hash (creating a 20GB output file). Using your exist correction makes the script much quicker! Thank you!	[reply]