On Sun, 24 Apr 2011 18:14:52 -0400, galeb abu-ali wrote:
> I revised the code to the following:
[...]
> for my $file( @ARGV ) {
> open( my $IN, "<", $file ) or die "Failed to open: $!\n";
>
> my( %cog_cat, %cog_id, @cogs, $oid, $locus, $source, $cluster_info
> );
>
> while( my $line = <$IN> ) {
> chomp $line;
>
> if( $line=~ /COG_category/ ) {
> ( $oid, $locus, $source, $cluster_info ) = split /\t/,
> $line;
>
> push @{ $cog_cat{ $locus } }, $cluster_info if(
> $cluster_info );
>
> } elsif ( $line=~ /COG\d+/ ) {
> ( $oid, $locus, $source, $cluster_info ) = split /\t/,
> $line; push @{ $cog_id{ $locus } }, $source if( $source );
> push @{ $cog_id{ $locus } }, $cluster_info if( $cluster_info
> );
> }
> }
Be ruthless about removing duplication. The more unnecessary code you
can prune, the more what's left reveals its true intention, like
chiseling away everything that is not David from a block of marble :-)
So in the above, you can take the line
( $oid, $locus, $source, $cluster_info ) = split /\t/, $line;
from both clauses and put it before the if statement. Also, Perl's topic
variable allows you to eliminate the use of certain variables that
otherwise serve no purpose, like $line in your code is only there to get
at its contents. So instead you can say
while (<$IN>) {
chomp;
if ( /COG_CATEGORY/ ) {
my ( $oid, $locus, $source, $cluster_info ) = split /\t/;
See also how I declared those four variables right there? Remove their
declaration from before the while loop now and you've gotten rid of some
more duplication and unnecessarily wide scoping.
> Many thanks again! Must've spent ~ 4 days on this. I've been flirting
> with Perl less than a year, it's so seductive I find myself debating
> whether to go back to school.
Heh, camels can be like that :-)
--
Peter Scott
http://www.perlmedic.com/ http://www.perldebugged.com/
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