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/