Need Emergency PERL help!

surrealitycheck

Sorry for the title, but this is for my dissertation and is a matter of some urgency. I am using a PERL script to look for repeat sequences in various pathogenic and nonpathogenic bacteria, and it is throwing out errors at me. This script has worked for others, but also others have had this error (although I do not know how they resolved it). The error is

print() on closed filehandle OUT at 1-DirectRepeatfinder.pl line 344

The line in question is

print OUT "FT repeat_unit ", "$START", "..", "$STOP", "\n", "FT

This line is also causing issues:

print OUT "$WORD\t$START\n";

Anybody have any ideas what is going on?

Apothe0sis

I think we'd need more information - sample data and the script in question?

The issue is that the handle OUT is being closed somewhere, but it's hard to see how or why without more context.

surrealitycheck

One sec, let me upload them somewhere.

http://www.megaupload.com/?d=RONKLTMT

To run this script you'll need:

Activeperl 5.10 - http://www.activestate.com/activeperl/

BioPerl - http://bioperl.open-bio.org/wiki/Installing_Bioperl_on_Windows (follow the "GUI Installation" further down the page)

I googled around and some people have had this problem before, but no solutions.

surrealitycheck

That file is a truncated fasta sequence, should take 30 secs to 1 minute to run. The genomes I'm running this on take 1-2 hours per genome then at the end refuse to dump the output files, it's driving me insane. In theory it should produce 2 output files.

Apothe0sis

It sounds a lot like the format of the files are confusing it somewhat and it's falling into a big loop or group of loops and then crashing and burning. I'll take a look now.

I'm not the best perl guy there is though, a few of the guys in the Programming thread are probably greatly my superior.

Apothe0sis

I haven't had a chance to try this yet as I've not had a chance to much around in my environment but I'd add

unless ( open( OUT, ">>$REPEAT_FT" ) ) {
die "Could not open out file "$REPEAT_FT"\n";
}

or add an "or die "Could not open out file "$REPEAT_FT"\n";" etc etc at the end of the lines in question. Take a look at what they're saying. From the way it works it shouldn't be able to get to the printing lines without first trying to open the OUT handle so it should only appear closed when that fails. I think. If I had to put money on it, now that I've seen it, I'd probably check out whether the arguments you're passing are appropriately formed. There doesn't seem to be a lot of error checking on the args.

surrealitycheck

Any help would be hugely appreciated, I'm running on a brutally tight schedule here and the bioperl website is down, so I'm having difficulty running the scripts on other pcs.

dmit

The script takes the first 15 characters of the input file and uses them in the filenames for output files, that's why it failed - '|' is not a valid filename character.

To fix this, change line 127 from

$HANDLE =~ s/\s/_/g;

to

$HANDLE =~ s/\W/_/g;

surrealitycheck

dmit you are a GOD

I thank you

You have 3 internet points. Spend them wisely.

EDIT: Out of interest what does that change actually do, explicitly?

Gdiguy

dmit wrote: »

The script takes the first 15 characters of the input file and uses them in the filenames for output files, that's why it failed - '|' is not a valid filename character.

To fix this, change line 127 from

$HANDLE =~ s/\s/_/g;

to

$HANDLE =~ s/\W/_/g;

Perl regular expressions: http://perldoc.perl.org/perlretut.html

\d matches a digit, not just [0-9] but also digits from non-roman scripts
\s matches a whitespace character, the set [\ \t\r\n\f] and others
\w matches a word character (alphanumeric or _), not just [0-9a-zA-Z_] but also digits and characters from non-roman scripts
\D is a negated \d; it represents any other character than a digit, or [^\d]
\S is a negated \s; it represents any non-whitespace character [^\s]
\W is a negated \w; it represents any non-word character [^\w]

So when you use \s in the first one, you're deleting anything that's a space; that leaves all sorts of weird characters (| \ / ; : etc etc)... if you match \W instead, you'll delete anything that's not a digit or character

surrealitycheck

Thank you, handy to know.