[32056] in Perl-Users-Digest
Perl-Users Digest, Issue: 3320 Volume: 11
daemon@ATHENA.MIT.EDU (Perl-Users Digest)
Tue Mar 15 06:09:24 2011
Date: Tue, 15 Mar 2011 03:09:08 -0700 (PDT)
From: Perl-Users Digest <Perl-Users-Request@ruby.OCE.ORST.EDU>
To: Perl-Users@ruby.OCE.ORST.EDU (Perl-Users Digest)
Perl-Users Digest Tue, 15 Mar 2011 Volume: 11 Number: 3320
Today's topics:
Re: convenient module to take statistics for hashed str <jwkrahn@example.com>
Re: convenient module to take statistics for hashed str <nospam.gravitalsun@hotmail.com>
Re: convenient module to take statistics for hashed str <uri@StemSystems.com>
Re: convenient module to take statistics for hashed str <ela@yantai.org>
Re: convenient module to take statistics for hashed str <nospam.gravitalsun@hotmail.com.nospam>
Re: convenient module to take statistics for hashed str <nospam.gravitalsun@hotmail.com.nospam>
Re: convenient module to take statistics for hashed str <ela@yantai.org>
Re: DBD::mysql used to take octets into the utf8 texts <peter@vereshagin.org>
Re: How to suppress non fatal messages <arjenbax@googlemail.com>
Re: Ok, simpler..... <tzz@lifelogs.com>
Re: Ok, simpler..... <bugbear@trim_papermule.co.uk_trim>
Posting Guidelines for comp.lang.perl.misc ($Revision: tadmc@seesig.invalid
Digest Administrivia (Last modified: 6 Apr 01) (Perl-Users-Digest Admin)
----------------------------------------------------------------------
Date: Mon, 14 Mar 2011 15:13:31 -0700
From: "John W. Krahn" <jwkrahn@example.com>
Subject: Re: convenient module to take statistics for hashed structures?
Message-Id: <gqwfp.59406$Ye1.36627@newsfe20.iad>
George Mpouras wrote:
> Sorry for the silly joke at the comment.
>
>
> [ snip ]
>
>
>> @col{1..$#a} #array of hash?
> This is called hash slice;
Correct.
> used to create a hash
Only my() can create a hash.
Used to add keys and values to a hash.
> from an array
from a LIST of keys and a LIST of values.
John
--
Any intelligent fool can make things bigger and
more complex... It takes a touch of genius -
and a lot of courage to move in the opposite
direction. -- Albert Einstein
------------------------------
Date: Tue, 15 Mar 2011 01:12:10 +0200
From: "news.ntua.gr" <nospam.gravitalsun@hotmail.com>
Subject: Re: convenient module to take statistics for hashed structures?
Message-Id: <ilm7cd$gqc$1@news.ntua.gr>
Ο "John W. Krahn" έγραψε στο μήνυμα
news:gqwfp.59406$Ye1.36627@newsfe20.iad...
>
>> @col{1..$#a} #array of hash?
> This is called hash slice;
Correct.
> used to create a hash
Only my() can create a hash.
I thought that local, our, state, could also do the job
------------------------------
Date: Mon, 14 Mar 2011 19:25:09 -0400
From: "Uri Guttman" <uri@StemSystems.com>
Subject: Re: convenient module to take statistics for hashed structures?
Message-Id: <87r5a9z3my.fsf@quad.sysarch.com>
>>>>> "nng" == news ntua gr <nospam.gravitalsun@hotmail.com> writes:
nng> Ο "John W. Krahn" έγραψε στο μήνυμα
nng> news:gqwfp.59406$Ye1.36627@newsfe20.iad...
>>
>>> @col{1..$#a} #array of hash?
>> This is called hash slice;
nng> Correct.
>> used to create a hash
nng> Only my() can create a hash.
nng> I thought that local, our, state, could also do the job
our doesn't create a variable. it only creates a lexical alias to the
variable of the same name in the current package.
local doesn't create a variable. it pushes the value of a variable and
allows for a new value to be put in its place.
state variables are just like my but they don't get reinitialized when
the enclosing block is entered.
uri
--
Uri Guttman ------ uri@stemsystems.com -------- http://www.sysarch.com --
----- Perl Code Review , Architecture, Development, Training, Support ------
--------- Gourmet Hot Cocoa Mix ---- http://bestfriendscocoa.com ---------
------------------------------
Date: Tue, 15 Mar 2011 15:16:12 -0700
From: "ela" <ela@yantai.org>
Subject: Re: convenient module to take statistics for hashed structures?
Message-Id: <iln04v$ev1$1@ijustice.itsc.cuhk.edu.hk>
While the suggested solution works perfectly for the example data inside the
perl script, it does not work when the data change to:
__DATA__
Identity of query sequence Superkingdom Kingdom Subkingdom
Phylum Class Order Family Genus Species group Species
NODE_124_length_77_cov_13.792208 Bacteria undef undef
Proteobacteria Gammaproteobacteria Enterobacteriales
Enterobacteriaceae Escherichia undef Escherichia coli
NODE_124_length_77_cov_13.792208 Bacteria undef undef
Proteobacteria Gammaproteobacteria Enterobacteriales
Enterobacteriaceae Escherichia undef Escherichia coli
even though I changed
my @a = split /\s+/; to my @a = split /\t/;
Moreover, the current implementation is hard-coding a rank instead of
surpassing a threshold so if I input 10 (i.e. incident abundance exceed 10%
is ok) instead of 100, no result will return at all. Even if I use "100",
the result returned still differs from my expectation.
I expect the program gives the result
id=NODE_124_length_77_cov_13.792208, thr=100% ->
Field=Species,Value=Escherichia coli
but it gives me:
id=NODE_124_length_77_cov_13.792208, thr=100% ->
Field=Order,Value=Enterobacteriales
this statement:
push @{ $data{$id}->{field}->{$field}->{rank}->{
100*($data{$id}->{field}->{$field}->{data}->{$item} /
$data{$id}->{lines} ) } } , $item}
looks very new to me, and can anybody further tell me what it is for?
usually I use push like:
push @array, $element;
and the above code even does not have the symbol ";" but no runtime error
.....
------------------------------
Date: Tue, 15 Mar 2011 08:45:59 +0200
From: "George Mpouras" <nospam.gravitalsun@hotmail.com.nospam>
Subject: Re: convenient module to take statistics for hashed structures?
Message-Id: <iln1tt$1sv$1@news.ntua.gr>
>
> our doesn't create a variable. it only creates a lexical alias to the
> variable of the same name in the current package.
Alias of what if our is only the definition ;
#!/usr/bin/perl
our $var=1;
print $var;
exit 0
------------------------------
Date: Tue, 15 Mar 2011 09:20:11 +0200
From: "George Mpouras" <nospam.gravitalsun@hotmail.com.nospam>
Subject: Re: convenient module to take statistics for hashed structures?
Message-Id: <iln3u2$93e$1@news.ntua.gr>
"ela" <ela@yantai.org> wrote in message
news:iln04v$ev1$1@ijustice.itsc.cuhk.edu.hk...
>
> While the suggested solution works perfectly for the example data inside
> the perl script, it does not work when the data change to:
>
> __DATA__
> Identity of query sequence Superkingdom Kingdom Subkingdom Phylum
> Class Order Family Genus Species group Species
> NODE_124_length_77_cov_13.792208 Bacteria undef undef
> Proteobacteria Gammaproteobacteria Enterobacteriales
> Enterobacteriaceae Escherichia undef Escherichia coli
> NODE_124_length_77_cov_13.792208 Bacteria undef undef
> Proteobacteria Gammaproteobacteria Enterobacteriales
> Enterobacteriaceae Escherichia undef Escherichia coli
Garbage in, garbage out.
Your data are completely inconsistent. You have to solve your input data
problem first.
Make sure that your data contain the same number of columns, and each column
is separated from the other with exactly the same string.
Are you sure the first line will always describe your column names ;
For a start, separated your data using the | no comma , so tabs , no
spaces.
Make sure that you have the same number of | at every line.
change the split to my @a = split /\|/, $_, -1;
So after your data looks like the following, try again
ID|C1|C2|C3
1|a1|b1|c1
2|a2|b2|c2
3|a3|b3|c3
------------------------------
Date: Tue, 15 Mar 2011 17:55:29 -0700
From: "ela" <ela@yantai.org>
Subject: Re: convenient module to take statistics for hashed structures?
Message-Id: <iln9fk$ibv$1@ijustice.itsc.cuhk.edu.hk>
The problem arises due to the number of fields. Since there are more than 9
fields, and the sort has to do in this way:
foreach my $field (reverse sort {$a<=>$b} keys %col) {
so perl treats 10 as bigger than 9.
Now the remaining problem is how to solve the threshold problem cleverly.
Originally, George's solution makes use of hash for fast access and in fact
progressive test, 100,99,98, ..., $threshold can be performed. However, when
the data is large (>1 million rows with a lot of ID's), this may not be a
good idea......
------------------------------
Date: Tue, 15 Mar 2011 02:54:26 +0300
From: Peter Vereshagin <peter@vereshagin.org>
Subject: Re: DBD::mysql used to take octets into the utf8 texts but no more in mariadb
Message-Id: <20110314235426.GA14674@external.screwed.box>
Oh Dr.Ruud want you buy me a mersedes benz?
2011/03/13 17:51:56 +0100 "Dr.Ruud" <rvtol+usenet@xs4all.nl> => comp.lang.perl.misc:
DR> > - mariadb revealed this bug, but it may be not of their's in the C API. It can be because of DBD::mysql's XS.
DR> > - DBD::mysql was hiding this bug, but they stated clear in their test that octets should use blob-fields only. Despite I remember the times when mysql did no difference between text and blob fields.
DR> > - applications writers may need to rewrite their code taking care on utf8 flag before their scalar to fit the DBI placeholders. But it just may not sound real as there is too much of their too long spaghetti code.
DR> >
DR> > As a workaround, I use the mysql_enable_utf8 attribute included into the dsn whet connect but authors of those apps don't do that in their code supposing that setting this as a dbh property later by the code runs is enough. But it doesn't dwim.
DR>
DR> It could also just be that you had a C<SET NAME 'utf8'> done initially
DR> for every session.
DR> This is configurable on the host.
It's not a silver bullet to me.
There are circumstances:
- There are several Cyrillic encodings while utf8 is a one preferable at the application level the cp1251 improves mysql speed as it's an 8-bit one. So it's still a typical use: you send and receive data to mysql as utf8 but mysql converts them to/from cp1251 for storage.
- While mariadb was converting my databases, the default character set in the database definition was reset by conversion process ( myisam to aria or so ). Any tables created anew had that strange behavior as I said on topic start.
- Typically application's authors never care about utf flag on a variable before to put it on a DBI placeholder.
- I did some tricks that made me a thing after some deeper learning about. But I'm still in confusion ( see below ).
Here is the test to try-it-yourself:
Environment is:
> show create database test\G
Create Database: CREATE DATABASE `test` /*!40100 DEFAULT CHARACTER SET latin1 */
Code is:
#!/usr/bin/perl
use strict;
use warnings;
use DBI;
use Devel::Peek;
my( $dsn, $db, ) = ( "dbi:mysql:host=127.0.0.1;database=test", "test", );
my $blob = "\x{d1}\x{84}dam";
my $pwd = 'OLBPVCtEirwJMwE0';
sub getPushPop{
my $dbh = shift;
foreach(
[ "drop table if exists test02" ],
[ "create table test02 ( test02 mediumtext character set cp1251 ) " ],
[ "insert into test02 values ( ? ) ", {}, $blob ],
){
$dbh->do( @$_ ) or die;
}
}
foreach my $db_sub (
sub{ DBI->connect( $dsn, $db, $pwd ) or die $!; },
sub{ my $dbh = DBI->connect( $dsn, $db, $pwd ) or die $!;
$dbh->{mysql_enable_utf8}=1; $dbh;
},
sub{ DBI->connect( $dsn.';mysql_enable_utf8=1', $db, $pwd ) or die $! },
sub{ my $dbh = DBI->connect( $dsn, $db, $pwd ) or die $!;
foreach(
'set character set utf8',
){
$dbh->do( $_ ) or die $!;
}
$dbh;
},
){
my $dbh = &$db_sub;
getPushPop $dbh;
print Devel::Peek::Dump $dbh->selectall_arrayref( "select * from test02" )->[0]->[0];
$dbh -> disconnect;
}
The output is:
SV = PV(0x2870194c) at 0x287fb37c
REFCNT = 1
FLAGS = (POK,pPOK)
PV = 0x2865fc2c "?\204dam"\0
CUR = 5
LEN = 8
SV = PV(0x2870194c) at 0x287fb368
REFCNT = 1
FLAGS = (POK,pPOK)
PV = 0x2865fcec "?\204dam"\0
CUR = 5
LEN = 8
SV = PV(0x2881e554) at 0x287fb368
REFCNT = 1
FLAGS = (POK,pPOK)
PV = 0x2865fccc "\321\204dam"\0
CUR = 5
LEN = 8
SV = PV(0x2881e554) at 0x287fb32c
REFCNT = 1
FLAGS = (POK,pPOK)
PV = 0x2865fcac "?dam"\0
CUR = 4
LEN = 8
Output coming 3rd is my solution and the 4th is yours ( and not only yours ).
but it's enough to put a magic spell on it:
> alter database test character set utf8;
and voila:
SV = PV(0x2870194c) at 0x287fb37c
REFCNT = 1
FLAGS = (POK,pPOK)
PV = 0x2865fc2c "?\204dam"\0
CUR = 5
LEN = 8
SV = PV(0x2870194c) at 0x287fb368
REFCNT = 1
FLAGS = (POK,pPOK)
PV = 0x2865fcec "?\204dam"\0
CUR = 5
LEN = 8
SV = PV(0x2881e554) at 0x287fb368
REFCNT = 1
FLAGS = (POK,pPOK)
PV = 0x2865fccc "\321\204dam"\0
CUR = 5
LEN = 8
SV = PV(0x2881e554) at 0x287fb32c
REFCNT = 1
FLAGS = (POK,pPOK)
PV = 0x2865fcac "\321\204dam"\0
CUR = 5
LEN = 8
we can see the cyrillic letter with 'set names utf8'.
What I see is: cyrillic data can be pushed and popped from the mysql storage despite default set of database is latin1.
But this depends very implicitly on a feature that they shouldn't be dependent of.
Actually, not on a feature itself but on a way this feature is used.
Yes, I found a solution for myself, but the questions aforequoted remain: whom of software authors should I ask about that strange behavior?
73! Peter pgp: A0E26627 (4A42 6841 2871 5EA7 52AB 12F8 0CE1 4AAC A0E2 6627)
--
http://vereshagin.org
------------------------------
Date: Tue, 15 Mar 2011 02:32:06 -0700 (PDT)
From: ilovelinux <arjenbax@googlemail.com>
Subject: Re: How to suppress non fatal messages
Message-Id: <5806d2f5-3b09-46d8-acbb-b3212a5fa441@r6g2000vbo.googlegroups.com>
On 11 mrt, 15:04, Nene <rodbas...@gmail.com> wrote:
> Hi,
> The modules works but it prints out some nonfatal message to the
> screen, how do I suppress that?
>
> pty_allocate(nonfatal): posix_openpt(): Success at /usr/lib/perl5/
> site_perl/5.8.8/i686-linux/IO/Pty.pm line 24.
I could not test it, but try enclosing the offending statement in a do-
block with "no warnings":
my $pty = do { no warnings; IO::Pty->new() };
This will suppress other, useful warnings as well, so I think this is
a bug in IO/Tty/Tty.xs, see http://cpansearch.perl.org/src/TODDR/IO-Tty-1.10/Tty.xs,
near line 464.
------------------------------
Date: Mon, 14 Mar 2011 17:10:05 -0500
From: Ted Zlatanov <tzz@lifelogs.com>
Subject: Re: Ok, simpler.....
Message-Id: <87wrk173r6.fsf@lifelogs.com>
On Mon, 14 Mar 2011 22:00:18 +0100 "Peter J. Holzer" <hjp-usenet2@hjp.at> wrote:
PJH> On 2011-03-14 19:32, Ted Zlatanov <tzz@lifelogs.com> wrote:
>> These are very convincing arguments. Please send them to Mr. Terry
>> Pratchett so he can revise _Discworld_ in the next edition:
>>
>> http://www.quotationspage.com/quote/23897.html
PJH> That seems to be a rather vague quotation. Discworld is a series
PJH> comprising of 39 novels and 6 short stories. AFAIK there is no novel or
PJH> story of this title.
Sorry, it's from _Jingo_ in the _Discworld_ series.
http://www.lspace.org/books/pqf/jingo.html
Ted
------------------------------
Date: Tue, 15 Mar 2011 09:23:13 +0000
From: bugbear <bugbear@trim_papermule.co.uk_trim>
Subject: Re: Ok, simpler.....
Message-Id: <SLCdnSn9RNKZreLQnZ2dnUVZ8mGdnZ2d@brightview.co.uk>
Jim Gibson wrote:
> In article<_cWdnaeaBskLv-TQnZ2dnUVZ_q-dnZ2d@polarcomm.com>, WhoDare
> <nobody@nowhere.com> wrote:
>
>> I need to produce a 'tree'
>>
>> Sessions
>> / \
>> / \
>> NOC-CO NOC-INT
>> / \ / \
>
> You will want to use references for this. If all of your "branches"
> have unique names (e.g., 'NOC-CO', 'NOC-INT'), you can use a hash:
>
> my $tree = { 'Sessions' => {'NOC-CO' => {...}, 'NOC-INT' => {...}}};
>
> to whatever level you need.
>
> If any of your sub-trees do not have unique names, you can use a
> reference to an anonymous array.
This is recursive (and untested); it might be simple enough
to turn into an interative solution too.
sub mktree {
my ($hash, $keys) = @_;
if(scalar(@$keys) == 0) {
return;
} else {
my $key = shift @$keys;
if(!exists($hash->{$key})) {
$hash->{$key} = {};
}
mktree($hash->{$key}, $keys);
}
}
(coded, not tested)
BugBear
------------------------------
Date: Tue, 15 Mar 2011 02:15:04 -0500
From: tadmc@seesig.invalid
Subject: Posting Guidelines for comp.lang.perl.misc ($Revision: 1.9 $)
Message-Id: <wK2dnTLlwLtljOLQnZ2dnUVZ5jCdnZ2d@giganews.com>
Outline
Before posting to comp.lang.perl.misc
Must
- Check the Perl Frequently Asked Questions (FAQ)
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Really Really Should
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If You Like
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Posting to comp.lang.perl.misc
Is there a better place to ask your question?
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How to participate (post) in the clpmisc community
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Social faux pas to avoid
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Be extra cautious when you get upset
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-----------------------------------------------------------------
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For more information on quoting style, see:
http://web.presby.edu/~nnqadmin/nnq/nquote.html
Speak Perl rather than English, when possible
Perl is much more precise than natural language. Saying it in Perl
instead will avoid misunderstanding your question or problem.
Do not say: I have variable with "foo\tbar" in it.
Instead say: I have $var = "foo\tbar", or I have $var = 'foo\tbar',
or I have $var = <DATA> (and show the data line).
Ask perl to help you
You can ask perl itself to help you find common programming mistakes
by doing two things: enable warnings (perldoc warnings) and enable
"strict"ures (perldoc strict).
You should not bother the hundreds/thousands of readers of the
newsgroup without first seeing if a machine can help you find your
problem. It is demeaning to be asked to do the work of a machine. It
will annoy the readers of your article.
You can look up any of the messages that perl might issue to find
out what the message means and how to resolve the potential mistake
(perldoc perldiag). If you would like perl to look them up for you,
you can put "use diagnostics;" near the top of your program.
Do not re-type Perl code
Use copy/paste or your editor's "import" function rather than
attempting to type in your code. If you make a typo you will get
followups about your typos instead of about the question you are
trying to get answered.
Provide enough information
If you do the things in this item, you will have an Extremely Good
chance of getting people to try and help you with your problem!
These features are a really big bonus toward your question winning
out over all of the other posts that you are competing with.
First make a short (less than 20-30 lines) and *complete* program
that illustrates the problem you are having. People should be able
to run your program by copy/pasting the code from your article. (You
will find that doing this step very often reveals your problem
directly. Leading to an answer much more quickly and reliably than
posting to Usenet.)
Describe *precisely* the input to your program. Also provide example
input data for your program. If you need to show file input, use the
__DATA__ token (perldata.pod) to provide the file contents inside of
your Perl program.
Show the output (including the verbatim text of any messages) of
your program.
Describe how you want the output to be different from what you are
getting.
If you have no idea at all of how to code up your situation, be sure
to at least describe the 2 things that you *do* know: input and
desired output.
Do not provide too much information
Do not just post your entire program for debugging. Most especially
do not post someone *else's* entire program.
Do not post binaries, HTML, or MIME
clpmisc is a text only newsgroup. If you have images or binaries
that explain your question, put them in a publically accessible
place (like a Web server) and provide a pointer to that location. If
you include code, cut and paste it directly in the message body.
Don't attach anything to the message. Don't post vcards or HTML.
Many people (and even some Usenet servers) will automatically filter
out such messages. Many people will not be able to easily read your
post. Plain text is something everyone can read.
Social faux pas to avoid
The first two below are symptoms of lots of FAQ asking here in clpmisc.
It happens so often that folks will assume that it is happening yet
again. If you have looked but not found, or found but didn't understand
the docs, say so in your article.
Asking a Frequently Asked Question
It should be understood that you may have missed the applicable FAQ
when you checked, which is not a big deal. But if the Frequently
Asked Question is worded similar to your question, folks will assume
that you did not look at all. Don't become indignant at pointers to
the FAQ, particularly if it solves your problem.
Asking a question easily answered by a cursory doc search
If folks think you have not even tried the obvious step of reading
the docs applicable to your problem, they are likely to become
annoyed.
If you are flamed for not checking when you *did* check, then just
shrug it off (and take the answer that you got).
Asking for emailed answers
Emailed answers benefit one person. Posted answers benefit the
entire community. If folks can take the time to answer your
question, then you can take the time to go get the answer in the
same place where you asked the question.
It is OK to ask for a *copy* of the answer to be emailed, but many
will ignore such requests anyway. If you munge your address, you
should never expect (or ask) to get email in response to a Usenet
post.
Ask the question here, get the answer here (maybe).
Beware of saying "doesn't work"
This is a "red flag" phrase. If you find yourself writing that,
pause and see if you can't describe what is not working without
saying "doesn't work". That is, describe how it is not what you
want.
Sending a "stealth" Cc copy
A "stealth Cc" is when you both email and post a reply without
indicating *in the body* that you are doing so.
Be extra cautious when you get upset
Count to ten before composing a followup when you are upset
This is recommended in all Usenet newsgroups. Here in clpmisc, most
flaming sub-threads are not about any feature of Perl at all! They
are most often for what was seen as a breach of netiquette. If you
have lurked for a bit, then you will know what is expected and won't
make such posts in the first place.
But if you get upset, wait a while before writing your followup. I
recommend waiting at least 30 minutes.
Count to ten after composing and before posting when you are upset
After you have written your followup, wait *another* 30 minutes
before committing yourself by posting it. You cannot take it back
once it has been said.
AUTHOR
Tad McClellan and many others on the comp.lang.perl.misc newsgroup.
--
Tad McClellan
email: perl -le "print scalar reverse qq/moc.liamg\100cm.j.dat/"
The above message is a Usenet post.
I don't recall having given anyone permission to use it on a Web site.
------------------------------
Date: 6 Apr 2001 21:33:47 GMT (Last modified)
From: Perl-Users-Request@ruby.oce.orst.edu (Perl-Users-Digest Admin)
Subject: Digest Administrivia (Last modified: 6 Apr 01)
Message-Id: <null>
Administrivia:
To submit articles to comp.lang.perl.announce, send your article to
clpa@perl.com.
Back issues are available via anonymous ftp from
ftp://cil-www.oce.orst.edu/pub/perl/old-digests.
#For other requests pertaining to the digest, send mail to
#perl-users-request@ruby.oce.orst.edu. Do not waste your time or mine
#sending perl questions to the -request address, I don't have time to
#answer them even if I did know the answer.
------------------------------
End of Perl-Users Digest V11 Issue 3320
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