[29354] in Perl-Users-Digest
Perl-Users Digest, Issue: 598 Volume: 11
daemon@ATHENA.MIT.EDU (Perl-Users Digest)
Thu Jun 28 21:14:24 2007
Date: Thu, 28 Jun 2007 18:14:11 -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 Thu, 28 Jun 2007 Volume: 11 Number: 598
Today's topics:
Re: Oh great gurus of the list, I need help with a regu <tadmc@seesig.invalid>
Re: Oh great gurus of the list, I need help with a regu <paduille.4061.mumia.w+nospam@earthlink.net>
Re: PERL and Active DIrectory QoS@domain.invalid
Re: Perl Standard for Remote Objects. <glex_no-spam@qwest-spam-no.invalid>
Re: Problem with PERL function <mzhao1@gmail.com>
Re: Problem with PERL function <jurgenex@hotmail.com>
Re: Problem with PERL function <mzhao1@gmail.com>
Re: Problem with PERL function <wahab-mail@gmx.de>
Re: Problem with PERL function <wahab-mail@gmx.de>
Re: Problem with PERL function <tadmc@seesig.invalid>
Digest Administrivia (Last modified: 6 Apr 01) (Perl-Users-Digest Admin)
----------------------------------------------------------------------
Date: Fri, 29 Jun 2007 00:04:34 GMT
From: Tad McClellan <tadmc@seesig.invalid>
Subject: Re: Oh great gurus of the list, I need help with a regular expression please
Message-Id: <slrnf88fsg.o52.tadmc@tadmc30.sbcglobal.net>
Mumia W. <paduille.4061.mumia.w+nospam@earthlink.net> wrote:
> On 06/28/2007 11:24 AM, Clenna Lumina wrote:
>> Tad McClellan wrote:
>>> Clenna Lumina <savagebeaste@yahoo.com> wrote:
>>>
>>>> I think the usefulness it would
>>>> represent would of made it a shoe in?
>>> ^^^^^^^^
>>> ^^^^^^^^ heh. So it's a case of mistaken identity huh?
> Now I'm beginning to think you're a troll. Clenna,
Just now beginning?
You're way behind everybody who was here in 2002 when it was
here last...
> I advise you do just
> drop it.
That won't happen as long as people keep following up to its posts.
> (My spidey sense tells me that you're a morph of PG,
Gurl is most definitely not the Jsut Troll, she is a more
"honorable" person, if that can be said of any troll, than
Jsut is.
She only displays 2 of the 6 Jsut telltales, while we have now
seen all 6 of them with Clenna Lumina and friends.
> but my killfile
> won't care.)
If you are willing to go through the captcha, you can get a couple
dozen of the addresses it has used in the past:
http://groups.google.com/group/comp.lang.perl.misc/msg/52eedd87f97ff558
--
Tad McClellan
email: perl -le "print scalar reverse qq/moc.noitatibaher\100cmdat/"
------------------------------
Date: Thu, 28 Jun 2007 22:16:28 GMT
From: "Mumia W." <paduille.4061.mumia.w+nospam@earthlink.net>
Subject: Re: Oh great gurus of the list, I need help with a regular expression please
Message-Id: <0rWgi.1912$tj6.1863@newsread4.news.pas.earthlink.net>
On 06/28/2007 11:24 AM, Clenna Lumina wrote:
> Tad McClellan wrote:
>> Clenna Lumina <savagebeaste@yahoo.com> wrote:
>>
>>> I think the usefulness it would
>>> represent would of made it a shoe in?
>> ^^^^^^^^
>> ^^^^^^^^ heh. So it's a case of mistaken identity huh?
>
> Oh, so now I'm the only one on the planet who doesn't know the correct
> spelling of "shoo-in", heh.. brilliant detective work once again...
> (note the sarcasm.)
>
>> http://en.wiktionary.org/wiki/shoo-in
>
> And you're called me a troll in another thread? You're the one who KEEPS
> "flame-baiting" and quite frankly [...]
Now I'm beginning to think you're a troll. Clenna, I advise you do just
drop it.
(My spidey sense tells me that you're a morph of PG, but my killfile
won't care.)
------------------------------
Date: Thu, 28 Jun 2007 22:41:18 GMT
From: QoS@domain.invalid
Subject: Re: PERL and Active DIrectory
Message-Id: <iOWgi.4791$%w5.4331@trndny04>
gaz_5_m@yahoo.co.uk wrote in message-id: <1183058740.045092.304550@k79g2000hse.googlegroups.com>
>
> Hi folks,
>
> I was just wondering if anyone was using PERL to any great effect to
> query Active DIrectory.
>
> I'm in the middle of a fairly large project at work that requires
> getting (constantly changing) info from AD. I was doing the same
> things on a daily basis so thought it best to try and script it.
>
> Is there any way to directly interrogate AD from within PERL. At the
> moment, the only way I have been able to figure out is to use the
> Windows Admin Pak to call:
>
> open query, "dsquery group -name "x" | dsget group -members |";
>
> from within the script and then use the piped output of the open
> command to strip out the data that I want.
>
> It works OK, just takes a hell of a long time!
>
> The other issue I get is the default return size that is set in our AD
> environment, 1000, so groups with any larger than 1000 users return
> nothing.
>
> I know you can get round this with VB, but PERL is my language of
> choice! :-)
>
> Anyone with any tips?
Yeah you probably want to use Net::LDAP
it is part of the perl-ldap package
btw this will work with all major directory services
Netscape, AD, NDS, and Solaris Directory
------------------------------
Date: Thu, 28 Jun 2007 16:02:30 -0500
From: "J. Gleixner" <glex_no-spam@qwest-spam-no.invalid>
Subject: Re: Perl Standard for Remote Objects.
Message-Id: <468421e6$0$10307$815e3792@news.qwest.net>
Ilias Lazaridis wrote:
> Is there any standard library to deal with remote objects on perl?
Well, what did you find on CPAN?
------------------------------
Date: Thu, 28 Jun 2007 14:21:14 -0700
From: michaelzhao <mzhao1@gmail.com>
Subject: Re: Problem with PERL function
Message-Id: <1183065674.583722.135460@o61g2000hsh.googlegroups.com>
Here is my code. Keep in mind that this is like my 2nd week on Perl so
it probably is pretty crappy ;). Try not to give me too much flak
about it.
The DNA File is called "verified.fa". It is a FASTA file, a common
file format for storing DNA strings.
#!/usr/bin/perl -w
#The filename of the file containing the e-coli sequence data
$fastadata = 'verified.fa';
#This step is to open the file, if the file cannot be opened, an error
message is printed and the program exits
unless ( open(FASTAFILE,$fastadata) ) {
print "Could not open file $fastadata!\n";
exit;
}
#Read the protein sequence into an array. This array will be used to
generate the Markov Transitional Matrices
@fasta = <FASTAFILE>;
#Close the FASTA data now as all the data has been read into the array
close FASTAFILE;
#Extracting the FASTA file from the array and putting it into a
sequence data
sub extract_sequence_from_fasta_data {
my(@fasta) =@_;
use strict;
use warnings;
#declaing the variables
my $fastasequence = '';
foreach my $line (@fasta) {
#Discard blank line
if ($line =~ /^\s*$/) {
next;
#Discard comment line
} elsif($line =~ /^\s*#/) {
next;
#Discard fasta header line
} elsif($line =~ /^>/) {
next;
#Keep line, add to sequence string
} else {
$fastasequence .= $line;
}
}
#remove non-sequence data from the $sequence string
$fastasequence =~ s/\s//g;
return $fastasequence;
}
$fastasequence = extract_sequence_from_fasta_data (@fasta);
#Split up the FASTA sequence into individual elements
@fastasequence = split( '' , $fastasequence);
#Initialize the tally
$tally_of_Adenosine = 0;
$tally_of_Thymine = 0;
$tally_of_Guanine = 0;
$tally_of_Cytosine = 0;
$errors = 0;
#Initialize a loop so it can tally the nucleotides
foreach $base (@fastasequence) {
if ( $base eq 'A') {
++$tally_of_Adenosine;
} elsif ( $base eq 'T') {
++$tally_of_Thymine;
} elsif ( $base eq 'G') {
++$tally_of_Guanine;
} elsif ( $base eq 'C') {
++$tally_of_Cytosine;
} else {
print "!!!!!! Error - Base not recognized: $base\n";
++$errors;
}
}
#Now that we have a tally of the bases, we have have to calculate the
zero-order Markov Transitional Matrice
print "$tally_of_Adenosine\n";
print "$tally_of_Thymine\n";
print "$tally_of_Guanine\n";
print "$tally_of_Cytosine\n";
unless ($errors eq '0') {
print "$errors\n";
}
------------------------------
Date: Thu, 28 Jun 2007 21:52:52 GMT
From: "Jürgen Exner" <jurgenex@hotmail.com>
Subject: Re: Problem with PERL function
Message-Id: <U4Wgi.2312$t95.1447@trndny01>
michaelzhao wrote:
> Here is my code.
I won't pretend to understand all of your code, but in this part below it
appears as if all you are doing is counting how often a specific character
appears in the given string $fastasequence.
> #Split up the FASTA sequence into individual elements
> @fastasequence = split( '' , $fastasequence);
>
> #Initialize the tally
> $tally_of_Adenosine = 0;
> $tally_of_Thymine = 0;
> $tally_of_Guanine = 0;
> $tally_of_Cytosine = 0;
> $errors = 0;
>
>
> #Initialize a loop so it can tally the nucleotides
> foreach $base (@fastasequence) {
>
> if ( $base eq 'A') {
> ++$tally_of_Adenosine;
> } elsif ( $base eq 'T') {
> ++$tally_of_Thymine;
> } elsif ( $base eq 'G') {
> ++$tally_of_Guanine;
> } elsif ( $base eq 'C') {
> ++$tally_of_Cytosine;
> } else {
> print "!!!!!! Error - Base not recognized: $base\n";
> ++$errors;
> }
If my guess is correct, then this whole section can be replaces with a
simple
$tally_of_Adenosine = tr/A/A/;
$tally_of_Thymine = tr/T/T/;
$tally_of_Guanine = tr/G/G/;
$tally_of_Cytosine = tr/C/C/;
The tr// operator returns the number of replacements it has performed and
thus tells you how many A's it has replaced with A's.
From "perldoc perlop"
tr/SEARCHLIST/REPLACEMENTLIST/cds
Transliterates all occurrences of the characters found in the
search list with the corresponding character in the replacement
list. It returns the number of characters replaced or deleted.
[...]
jue
------------------------------
Date: Thu, 28 Jun 2007 15:03:37 -0700
From: michaelzhao <mzhao1@gmail.com>
Subject: Re: Problem with PERL function
Message-Id: <1183068217.468743.242080@g4g2000hsf.googlegroups.com>
On Jun 26, 5:23 pm, jgra...@ti.com wrote:
> use...@DavidFilmer.com writes:
> > On Jun 26, 12:15 pm, michaelzhao <mzh...@gmail.com> wrote:
>
> > > Basically, I need the frequencies of the 4 bases, Adenosine (A),
> > > Thymine (T), Cytosine (C), and Guanine (G).
>
> > > However, here is my problem. Instead of doing it globally. I need to
> > > be able to specify an arbitrary start and stop position
>
> > I don't know bioperl (and there are LOTS of modules related to
> > bioperl; maybe one does exactly what/how you want) but if all you want
> > to do is basic frequency analysis on an array (assuming your bases are
> > in an array) then there are several statistics packages that will do
> > this for you. Consider:
>
> snip example of use Statistics::Frequency;
>
> > If you want to specify an arbitrary range, just slice the array, such
> > as:
> > my $freq = Statistics::Frequency->new( @dna[4..9] );
> > (remember arrays start numbering at zero, so this will get the fifth-
> > tenth items)
>
> I don't know bioperl either, but it seems like the DNA strings of ATCG
> might be represented as long strings because dna people might like to
> use regexp to search for subsets.
>
> In that case, here are some idioms
> for counting characters in a scalar using tr///,
> and for accessing a subset of a string with substr; (pasted and tested)
> # 0123456789.12345678
> $dna = 'TCTCTCGGGAAGAGATTGA';
> $Tcount = $dna =~ tr/T/T/; # tr returns number of T->T replacements
> $start = 3; # inclusive, based at 0
> $stop = 9; # inclusive
> $len = $stop-$start+1
> $Tcountss = substr($dna,$start,$len) =~ tr/T/T/; # access subset of $dna
> print "dna = '$dna' has $Tcount T's,\n";
> print " but only $Tcountss T's in $start to $stop, inclusive\n",
> printf " for a relative frequency of %f\n", $Tcountss/$len;
>
> -- output is
>
> dna = 'TCTCTCGGGAAGAGATTGA' has 5 T's,
> but only 1 T's in 3 to 9, inclusive
> for a relative frequency of 0.142857
>
> As mentioned before, posting short example datastructures from your code
> shows you are paying attention, and enable more appropriate assistance.
>
> --
> Joel
Wow Joel! Thanks a lot for your help. Your suggestion really hit the
spot. I was able to learn quite a bit from the code you put up and
succesfully modified it to fit my needs.
To everyone else: Thanks for the suggestions and the help! With the
exception of the jerkoff who wrote the first response.
------------------------------
Date: Thu, 28 Jun 2007 23:49:21 +0200
From: Mirco Wahab <wahab-mail@gmx.de>
Subject: Re: Problem with PERL function
Message-Id: <f61f1i$1lc$1@mlucom4.urz.uni-halle.de>
michaelzhao wrote:
> Here is my code. Keep in mind that this is like my 2nd week on Perl so
> it probably is pretty crappy ;). Try not to give me too much flak
> about it.
Thats really good! It works.
> The DNA File is called "verified.fa". It is a FASTA file, a common
> file format for storing DNA strings.
> #!/usr/bin/perl -w
> #The filename of the file containing the e-coli sequence data
> $fastadata = 'verified.fa';
I'd guess all your program does or intends to do is the following:
...
my $fastasequence = '';
my %Tally;
open my $fh, '<', 'verified.fa' or die "can't open file!$!";
while (<$fh>) {
/([ATCG]+)(?{ $fastasequence .= $1 })/g unless /^[>#]/
}
close $fh;
1 while $fastasequence =~ /(.)(?{ ++$Tally{$1} })/g;
print
map "$_: $Tally{$_} " . (100. * $Tally{$_}/length $fastasequence) . "%\n",
keys %Tally;
...
(Please correct me if I'm wrong)
Please have also a look at:
http://www.perl.com/pub/a/2003/09/10/bioinformatics.html
Regards
M.
------------------------------
Date: Thu, 28 Jun 2007 23:57:22 +0200
From: Mirco Wahab <wahab-mail@gmx.de>
Subject: Re: Problem with PERL function
Message-Id: <f61gvs$2ba$1@mlucom4.urz.uni-halle.de>
Mirco Wahab wrote:
> 1 while $fastasequence =~ /(.)(?{ ++$Tally{$1} })/g;
Oh, I forgot: if you need defined ranges in the nucleotide
string, you could use the 'substr' function directly,
($st and $nn denote sequence start/seqence count)
...
my ($fastasequence, $st, $nn) = ('', 1, 444);
open my $fh, '<', 'verified.fa' or die "can't open file!$!";
while (<$fh>) { /([ATCG]+)(?{ $fastasequence .= $1 })/g unless /^[>#]/ }
close $fh;
my %Tally;
1 while substr($fastasequence, $st, $nn) =~ /(.)(?{ ++$Tally{$^N} })/g;
print
map "$_: $Tally{$_} ".(100*$Tally{$_}/length substr $fastasequence, $st, $nn)."%\n",
keys %Tally;
...
Regards
M.
------------------------------
Date: Fri, 29 Jun 2007 00:04:34 GMT
From: Tad McClellan <tadmc@seesig.invalid>
Subject: Re: Problem with PERL function
Message-Id: <slrnf88i62.o52.tadmc@tadmc30.sbcglobal.net>
michaelzhao <mzhao1@gmail.com> wrote:
> On Jun 26, 5:23 pm, jgra...@ti.com wrote:
>> As mentioned before,
Who mentioned it before?
>> posting short example datastructures from your code
>> shows you are paying attention, and enable more appropriate assistance.
> To everyone else: Thanks for the suggestions and the help! With the
> exception of the jerkoff who wrote the first response.
Oh. It was the "jerkoff" who mentioned how to get help with your problem.
Calling the regulars names will have a negative effect on your ability
to get quality help here in the future. I suggest you try to refrain
from doing that anymore.
--
Tad McClellan
email: perl -le "print scalar reverse qq/moc.noitatibaher\100cmdat/"
------------------------------
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>
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------------------------------
End of Perl-Users Digest V11 Issue 598
**************************************
