[32038] in Perl-Users-Digest
Perl-Users Digest, Issue: 3302 Volume: 11
daemon@ATHENA.MIT.EDU (Perl-Users Digest)
Mon Feb 28 06:09:29 2011
Date: Mon, 28 Feb 2011 03:09:11 -0800 (PST)
From: Perl-Users Digest <Perl-Users-Request@ruby.OCE.ORST.EDU>
To: Perl-Users@ruby.OCE.ORST.EDU (Perl-Users Digest)
Perl-Users Digest Mon, 28 Feb 2011 Volume: 11 Number: 3302
Today's topics:
going from CPAN to RPM <agw@dsm.fordham.edu>
Hash array with variable size? <ela@yantai.org>
Re: Hash array with variable size? <jurgenex@hotmail.com>
Introduction to Signal Processing by Sophocles J. Orfan (ronald2000)
Re: Introduction to Signal Processing by Sophocles J. O <uri@StemSystems.com>
Re: matching '?' in a string ending with digits <derykus@gmail.com>
Digest Administrivia (Last modified: 6 Apr 01) (Perl-Users-Digest Admin)
----------------------------------------------------------------------
Date: Sun, 27 Feb 2011 19:05:40 -0500
From: Art Werschulz <agw@dsm.fordham.edu>
Subject: going from CPAN to RPM
Message-Id: <2m1v2thvl7.fsf@sobolev.dsm.fordham.edu>
Hi all.
Although we have used the CPAN shell to install Perl modules on our
Linux systems, we would like to use the RPM versions of same instead.
This means that we need to find out which Perl modules were installed
via the CPAN shell, nuke same, and then install the RPM versions (say,
via yum).
How can we find out which Perl modules were installed via the CPAN
shell?
Thanks.
--
Art Werschulz (8-{)} "Metaphors be with you." -- bumper sticker
GCS/M (GAT): d? -p+ c++ l++ u+ P++ e--- m* s n+ h f g+ w+ t+ r-
Net: agw@dsm.fordham.edu http://www.dsm.fordham.edu/~agw
Phone: Fordham U. (212) 636-6325, Columbia U. (646) 775-6035
------------------------------
Date: Mon, 28 Feb 2011 13:37:38 -0800
From: "ela" <ela@yantai.org>
Subject: Hash array with variable size?
Message-Id: <ikfc8r$301$1@ijustice.itsc.cuhk.edu.hk>
I have a flatfile containing many rows (maybe up to 10 million) like the
following lines, with each cell separated by the delimiter "\t",
2794438 dnaA-1 chromosomal replication initiator protein DnaA 2794971 dnaN
DNA polymerase III subunit beta
2794438 dnaA-1 chromosomal replication initiator protein DnaA 2794972 gyrB
DNA gyrase subunit B
2794438 dnaA-1 chromosomal replication initiator protein DnaA 2794973 gyrA
DNA gyrase subunit A
the first cell of each row is to look up, i.e. 2794438 in the above example,
and to print something like:
dnaA-1 dnaN
dnaA-1 gyrB
dnaA-1 gyrA
....
how to make this lookup process more efficient? I don't know whether it is
due to array size difference for each key, i.e. 2794438 here, it takes a
long time (actually never finish) for a query file of about 100,000 rows.
Any better implementation suggestions are highly welcomed.
------------------------------
Date: Mon, 28 Feb 2011 00:28:05 -0800
From: Jürgen Exner <jurgenex@hotmail.com>
Subject: Re: Hash array with variable size?
Message-Id: <nolmm6h16tun1bvc1m494o4pfolfaiirsh@4ax.com>
"ela" <ela@yantai.org> wrote:
[Subject: Hash array with variable size?]
So what is it? A hash or an array?
And yes, Perl hashes as well as arrays are variable size. Where is the
problem with that?
>I have a flatfile containing many rows (maybe up to 10 million) like the
>following lines, with each cell separated by the delimiter "\t",
>
>2794438 dnaA-1 chromosomal replication initiator protein DnaA 2794971 dnaN
>DNA polymerase III subunit beta
>2794438 dnaA-1 chromosomal replication initiator protein DnaA 2794972 gyrB
>DNA gyrase subunit B
>2794438 dnaA-1 chromosomal replication initiator protein DnaA 2794973 gyrA
>DNA gyrase subunit A
>
>the first cell of each row is to look up, i.e. 2794438 in the above example,
>and to print something like:
So, it is what is commonly called a key, is it?
>dnaA-1 dnaN
>dnaA-1 gyrB
>dnaA-1 gyrA
>....
>
>how to make this lookup process more efficient?
More efficient than what? Show us your code, then we can try to optimize
it.
As far as I can tell from your description it is a simple linear scan
through the file and the most time spent should be in reading the file
line by line:
while ($line = <$F>) {
($key, @others) = split ("\t", $line)
if ($key eq $wanted) {
print_from_data_whatever_you_want(@others)
}
}
>I don't know whether it is
>due to array size difference for each key, i.e. 2794438 here, it takes a
What do you mean by "array size difference for each key"?
>long time (actually never finish) for a query file of about 100,000 rows.
10 million lines, each maybe 100 characters (based on your sample data
above), means at least 1GB of data in theory. In reality probably
several times this amount, maybe (but this is just a guess) poorly
designed code or poorly programmed so that data structures are copied
repeatedly, yeah, I can see how this could easily lead to swapping and a
thrashing system, even with several GB of RAM.
>Any better implementation suggestions are highly welcomed.
But you didn't show us any implemention. How could we possibly suggest
improvements to something that we have never seen?
In general:
Use a database. Databases are designed to handle large amounts of data
and to provide fast queries.
Use a disk-based algorithm instead of a RAM based algorithm. Optimize
your code for RAM size instead of for programming convenience or speed
of operations.
You may also benefit from reviewing old algorithms that were developed
decades ago specifically for problems where RAM-size was the restricting
factor.
jue
------------------------------
Date: Sun, 27 Feb 2011 21:07:40 +0000
From: ronaldmanualsea_at_gmail_dot_com@foo.com (ronald2000)
Subject: Introduction to Signal Processing by Sophocles J. Orfanidis
Message-Id: <532d7$4d6abd1c$cf3aab60$14678@news.flashnewsgroups.com>
I have solutions manuals to all problems and exercises in these textbooks.
To get one in an electronic format contact me at:
ronaldmanualsea(at)gmail(dot)com and let me know its title, author and
edition. Please this service is NOT free.
instructor's solutions manual for Mechanical Engineering Design, 7th Ed.
by Mischke, Shigley
instructor's solutions manual for Mechanical Measurements (6th Ed.,
Beckwith, Marangoni & Lienhard)
instructor's solutions manual for Mechanical Vibrations ( Vol.1) 4th Ed.,
Rao
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instructor's solutions manual for Mechanics of Aircraft Structures, 2nd Ed
by Sun
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------------------------------
Date: Sun, 27 Feb 2011 17:28:54 -0500
From: "Uri Guttman" <uri@StemSystems.com>
Subject: Re: Introduction to Signal Processing by Sophocles J. Orfanidis
Message-Id: <87fwr9gli1.fsf@quad.sysarch.com>
>>>>> "r" == ronald2000 <ronaldmanualsea_at_gmail_dot_com@foo.com> writes:
r> edition. Please this service is NOT free.
you are just a stupid spammer. that IS free advice.
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: Sat, 26 Feb 2011 12:11:13 -0800 (PST)
From: "C.DeRykus" <derykus@gmail.com>
Subject: Re: matching '?' in a string ending with digits
Message-Id: <434e5fcf-7201-447c-aa40-63e3f9c7cabe@o30g2000pra.googlegroups.com>
On Feb 26, 12:42=A0am, "ReMo..." <ram...@gmail.com> wrote:
> #!/usr/bin/perl
>
> use strict;
> use warnings;
>
> my @arr =3D ('third1000', 'third1000', 'third?1000', '1000third?', 'third=
{}1000');
> for my $item (@arr) {
> =A0 =A0 my $targ =3D $item;
> =A0 =A0 print "$targ and $item ";
> =A0 =A0 print "do not " if ($item !~ /$targ/);
> =A0 =A0 print "match\n"
>
> }
>
> The output is:
> third1000 and third1000 match
> third1000 and third1000 match
> third?1000 and third?1000 do not match << I don't understand this
> 1000third? and 1000third? match
> third{}1000 and third{}1000 match
>
> In the above, the nondigits represent arbitrary text that digits are
> added to for a multi-array sort in a module I'm making, because there
> may be otherwise-identical text items.
>
> /\Q...\E/ seems to make it go away, but then two characters ('$' and '@')
> would apparently need to be accounted for.
>
> So my question is, what other characters will fail to match in a string
> ending with digits? =A0I assume there are more clues in perlre and perlop=
s,
> but I can't find them. =A0I've got to be missing something really element=
ary
> here.
>
See perldoc perlretut for a quick intro about meta-
characters. Various metacharacters will cause the
regex to fail as mentioned.
One problem is that there must be a literal '?' in
the regex in order to match the '?' in the string
being matched. Since '?' is a regex metacharacter
with special meaning to the regex compilation and
not a literal '?', the match would fail.
The 're' pragma can be helpful in seeing what
happens:
perl -Mre=3Ddebug -wle "print 'not'
if 'third?1000' !~ /third?1000/"
Compiling REx "third?1000"
Final program:
1: EXACT <thir> (3)
3: CURLY {0,1} (7)
5: EXACT <d> (0)
7: EXACT <1000> (9)
9: END (0)
anchored "thir" at 0 floating "1000" at 4..5 (checking
floating) minlen 8
Guessing start of match in sv for REx "third?1000"
against "third?1000"
Found floating substr "1000" at offset 6...
Contradicts anchored substr "thir", giving up...
Match rejected by optimizer
As it turns out though, the debug looks to me as
if the compilation fails for another reason when
the optimizer determines "1000" will occurs at
offset 4 or 5 in the pattern which won't match its
position at offset 6 in the string being matched.
--
Charles DeRykus
------------------------------
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:
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End of Perl-Users Digest V11 Issue 3302
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