Substitution Error in pal2nal perl script
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3.6 years ago
apulunuj ▴ 30

I need some help in understanding how to work, the pal2nal.pl script. The program can be obtained from the website, http://www.bork.embl.de/pal2nal/.

Whenever I run the script I get an error message at the line, (the line of interest has a comment beside it). THe error message says 'Substitution loop at line 338, which is the line of interest'. I don't see why the script should work.

The part of the script with the line:

undef(@nucid);

undef(%id2nucseq);

$nseq = -1;

foreach $i (0..$#nucfiles) {

   open(NUCFILE, "< $nucfiles[$i]") || die "Can't open $nucfiles[$i]"; ##Line of Interest

    $nucfiledata = <NUCFILE>;

    close(NUCFILE);

    $nucfiledata =~ s/\x0D\x0A|\x0D|\x0A/\n/g;

    foreach (split(/\n/, $nucfiledata)) {

        if (!/^#/ && /\S+/) {

            if (/^>(\S+)/) {

                ++$nseq;

                $tmpnucid = $1;

                push(@nucid, $tmpnucid);

            } else {

                s/[^a-zA-Z]//g;

                $id2nucseq{$tmpnucid} .= $_;

            }

        }

    }

}
alignment nucleotide seq perl script • 868 views
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It seems you are trying pal2nal on a massive file - see here. What is it? What is your version of perl?

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perl 5.10.1 is what I am using/

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