Saurabh Singhvi wrote:
> Hi all,
Hello,
> The following code block
>
> foreach $protein (@pdbs) {
> $rmsd[$i] = 0;
> foreach $protein2 (@pdbs2) {
> system("./TMalign $protein $protein2 | cgrep -i rmsd >
What is cgrep? I don't have that on my system.
> temp") == 0 or die $?;
> open(TEMP,'temp') or die $?;
If open fails there will be nothing useful in $?, you want to use the $!
variable instead.
> chomp($line = <TEMP>);
> close TEMP;
> ($length,$rmsd,$tm_score,$id) = split(/\,/,$line);
> $rmsd =~ s/RMSD\=//;
> $rmsd =~ s/\s//g;
> $rmsd[$i] += $rmsd;
> }
> $i++;
> }
Perhaps this will work better:
for my $protein ( @pdbs ) {
my $temp;
for my $protein2 ( @pdbs2 ) {
open my $TEMP, "./TMalign $protein $protein2 |"
or die "Cannot open pipe from 'TMalign' $!":
while ( <$TEMP> ) {
next unless /RMSD \s* = \s* ( \d+ )/ix;
$temp += $1;
last;
}
close $TEMP or warn $! ? "Error closing 'TMalign' pipe: $!"
: "Exit status $? from 'TMalign'";
}
push @rmsd, $temp;
}
> is giving error :
>
> open: null file name
> apparent state: unit 10 named
> last format: (A100)
> lately reading sequential formatted external IO
I searched through perldiag but I couldn't find that error message.
John
--
use Perl;
program
fulfillment
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