First I have some questions.
Why is ALIGNMENT not a hash ? It seems perfect for what you are need. If
you use ALIGNMENT as a hash, then you can do away with the ID array.
Also you are checking for existence in alignment not ALIGNMENT, this will
be causing problems.
Simplify like this:
mine:
[snip]
#my @ID; # you don't really need this
my %ALIGNMENT; # a hash would work much better, look it up if you
need more info
read_alignment($FILE);
foreach my $key ( keys $ALIGNMENT ) #defines key for each key in your
hash
{
printf "%-15s %s\n", $key, $ALIGNMENT{$key);
}
sub read_alignment {
my ($file) = @_;
my ($line);
local (*TMP);
open(TMP, "< $file") or die "can't open file '$file'\n";
while ( $line = <TMP> )
{
my $key; #something better perhaps
next if $line =~ /^CLUSTAL/;
( $key, $sequence ) = $line =~ /[\w\-]+/;
#This should grab the key and the sequence, basically you want to
match any word character and the dash
# the first match is returned to key and the long sequence is
returned to sequence
if ( !exists $ALIGNMENT{$key} )
{
$ALIGNMENT{$key} = "$sequence";
}
}
close TMP
}
Any questions ?
-----------------------------------------
Craig Moynes
Internship Student
netCC Development
IBM Global Services, Canada
Tel: (905) 316-3486
[EMAIL PROTECTED]
