Overlapping substitution

/,\.,/ or is there something I missed? Thank you, Kevin Kevin Viel, PhD Post-doctoral fellow Department of Genetics Southwest Foundation for Biomedical Research San Antonio, TX 78227 -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED

RE: Overlapping substitution

rom my naïve view, I don't think I would have attempted to include the alternation within the zero-width positive look-ahead assertion without seeing your example. As you correctly pointed out, I had forgotten to check the last variable, too. Kind regards, Kevin Kevin Viel, PhD Post-doctoral

RE: Overlapping substitution

ithout the /x? What part of this is saved in $1? Do you qualify the use of chomp since you used \z? Thank you, Kevin Kevin Viel, PhD Post-doctoral fellow Department of Genetics Southwest Foundation for Biomedical Research San Antonio, TX 78227 -- To unsubscribe, e-mail: [EMAIL PROTECTED

RE: Overlapping substitution

. Are these character classes that have single elements? In other words: [.] matches . [?] matches ? [*] matches * Can they be combined? [.*] Thanks, Kevin Kevin Viel, PhD Post-doctoral fellow Department of Genetics Southwest Foundation for Biomedical Research San Antonio, TX 78227 -

Hash of array

intended to INDEX the array: my $index ; if ( ~ exists $subjects{ $ID }{ $var } ) { $index = 0 ; } else { $index = $subjects{ $ID }{ $var } ) $subjects{ $ID }{ $var }[ $index ] = $var1 ; I would appreciate any comments or suggestions concerning this approach. Thank you, Kevin Kevin Viel

RE: Hash Variables

s that the last comma is "harmless, but convenient". I might be inclined to avoid it (but I need to test it): my %fruit_color = ( apple => "red" , banana => "yellow" ) ; HTH, Kevin Kevin Viel, PhD Post-doctoral fellow Department of Genetics Southwest Foundation for Biomedical Research San Antonio, TX 78227 -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED] http://learn.perl.org/

RE: Pragmas use strict and use warnings

lexical of that name ^^^ How else might one describe a lexical? A short variable name (or assignment to a symbol table) specific to the current package? Sometimes, this term seems clear, then not... Thanks, Kevin Kevin Viel, PhD Post-doctoral fellow Department of Genetics Sou

RE: Hash Variables

perl code style, so perhaps these are not advantages. However, if including the last comma is really more conventional (useful), then I can easily adopt that with little effort. Kind regards, Kevin Kevin Viel, PhD Post-doctoral fellow Department of Genetics Southwest Foundation for Biome

split then match, regex better?

ch or offer a better one? Thank you, Kevin Kevin Viel, PhD Post-doctoral fellow Department of Genetics Southwest Foundation for Biomedical Research San Antonio, TX 78227 -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED] http://learn.perl.org/

open and close a filehandle

# cycled through all of the fields After I print the mod( $_ , 3000 ) = 0 field to the file, I close that filehandle and reset $cnt to zero. I am not sure, but it seems that the open function is not openning the subsequent filehandles. I would appreciate any corrections or suggestions. Kind re

RE: open and close a filehandle

> -Original Message- > From: John W. Krahn [mailto:[EMAIL PROTECTED] > Sent: Thursday, January 10, 2008 8:26 AM > To: Perl Beginners > Subject: Re: open and close a filehandle > > Kevin Viel wrote: > > I have a file with thousands of fields, but a subsequent

references to complex data structures

f bracers with the appropriate symbol ($, @, %) the default? If so, how does perl select the correct symbol? I realize that it is seemingly moot, but it may help my understanding of more complex structures, like hash of arrays or hash of hases. Thanks, Kevin Kevin Viel, PhD Post-doctoral

RE: references to complex data structures

> -Original Message- > From: Rob Dixon [mailto:[EMAIL PROTECTED] > Sent: Monday, January 14, 2008 8:59 PM > To: beginners@perl.org > Cc: Kevin Viel > Subject: Re: references to complex data structures > > Kevin Viel wrote: > > Consider the following anony

while and last

Hello, If I only want the data on the first line of a file, can I use "last" to exit the loop or should I consider another tool? Thank you, Kevin Kevin Viel, PhD Post-doctoral fellow Department of Genetics Southwest Foundation for Biomedical Research San Antonio, TX 78227

RE: while and last

> -Original Message- > From: John W. Krahn [mailto:[EMAIL PROTECTED] > Sent: Tuesday, January 15, 2008 1:39 PM > To: Perl Beginners > Subject: Re: while and last > my $data = ; # Grap one line from file Doh! Thanks :) Kevin Viel, PhD Post-doctoral fellow Depa

Hash of hashes?

Perl for Bioinformatics", "Perl for C Programmers", and the Llama book. Thank you, Kevin Kevin Viel, PhD Post-doctoral fellow Department of Genetics Southwest Foundation for Biomedical Research San Antonio, TX 78227 -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e

Clear a hash

Is there a way to empty/clear a hash in mass? For instance: %hash = {} ; Might the above create an reference? Thank you, Kevin Kevin Viel, PhD Post-doctoral fellow Department of Genetics Southwest Foundation for Biomedical Research San Antonio, TX 78227 -- To unsubscribe, e-mail: [EMAIL

RE: Hash of hashes?

> -Original Message- > From: Chas. Owens [mailto:[EMAIL PROTECTED] > Sent: Friday, January 18, 2008 9:07 PM > To: Kevin Viel > Cc: beginners@perl.org > Subject: Re: Hash of hashes? > > On Jan 18, 2008 6:06 PM, Kevin Viel <[EMAIL PROTECTED]> wrote: > &

RE: Hash of hashes?

> -Original Message- > From: Chas. Owens [mailto:[EMAIL PROTECTED] > Sent: Monday, January 21, 2008 1:11 PM > To: Kevin Viel > Cc: beginners@perl.org > Subject: Re: Hash of hashes? > #! /usr/bin/perl > > use strict; > use warnings; > > use Dat

!system and output

t;feed" them to STDIN. I could write them to a temporary file, read them after the child process has returned control to the perl program, and then delete them, but it seems like I might find a "better" way. I would appreciate any suggestions or references. Thank you, Kevin Kevin

Re: regex one liner

BTW, out here in the real world (that would be UNIX), *.pl stands for Perl Library file, not a script. What extension do you suggest using, if any, in the real world? Thanks, Kevin -- Kevin Viel Department of Genetics

Citing perl

Is there a standard citation of perl, for instance a paper in a journal describing the language, that I might use for a publication? Thanks, Kevin -- Kevin Viel Department of Genetics e-mail: [EMAIL PROTECTED

Re: Citing perl

Tom Phoenix wrote: On 4/26/06, Kevin Viel <[EMAIL PROTECTED]> wrote: Is there a standard citation of perl, for instance a paper in a journal describing the language, that I might use for a publication? Well, just to be certain, are you talking about Perl the programming language? O

Re: Stealing vs buying Was: Print

n.com. -Kevin -- Kevin Viel Department of Genetics e-mail: [EMAIL PROTECTED] Southwest Foundationphone: (210)258-9884 P.O. Box 760549 fax:(210)258-9444 San Antoni

Providing STDIN to a PIPEd call to perl

text file containing the file name, but this is wasteful. I appreciate any comments. Thanks, Kevin ------ Kevin Viel Department of Genetics e-mail: [EMAIL PROTECTED] Southwest Foundationphone:

Re: Providing STDIN to a PIPEd call to perl

Mr. Shawn H. Corey wrote: Kevin Viel wrote: I call a perl script from SAS using a pipe. The file on which the script acts changes. Is there a way to provide the file name to the script using STDIN on the command line? The SAS call looks like: filename ABI pipe "perl C:/base.ps"

Re: Providing STDIN to a PIPEd call to perl

Chad Perrin wrote: On Wed, Jul 05, 2006 at 11:31:55AM -0500, Kevin Viel wrote: Mr. Shawn H. Corey wrote: Kevin Viel wrote: I call a perl script from SAS using a pipe. The file on which the script acts changes. Is there a way to provide the file name to the script using STDIN on the

Hide code and user interfaces

seems lengthy to implement and I do not want them opening my script and altering (on accident). Thanks, Kevin PS Yes, I realize that I should hire an experienced programmer, but I have no budget at this point in my career. -- Kevin Viel Department of Genetics [EMAIL

regex help

=~ /^[a-zA-Z0-9]+_A|a[0-9](F|R)[0-9](1-4)$/ I am unsure if I need to group the relevant parts using (). Could anyone advise or is the use of the anchor sufficient? Thanks in advance, Kevin -- Kevin Viel Department of Genetics [EMAIL PROTECTED] Southwest Foundation for

Perl on external hard drive

-- Kevin Viel Department of Genetics [EMAIL PROTECTED] Southwest Foundation for Biomedical Research phone: (210)258-9884 P.O. Box 760549 fax:(210)258-9444 San Antonio, TX 78245-0549 Kevin Viel PhD Candidate Department of Epidemiology Rollins

Re: Perl on external hard drive

Kevin Viel wrote: Is it possible to install perl and modules on an external hard drive that I could take from computer to computer? It seems a simple as installing it onto that drive, but I do not know whether I can use PPM to install CPAN modules there or whether I can use it successfully

CPAN installs

I am attempting to install modules on a Solaris v10 computer for which I do not have root privileges. I see in MyConfig.pm that the build directory is local: 'build_dir' => q[/home/kviel/.cpan/build] Where does it install the (built) module? Thank you, Kevin -- Kevin Viel

Re: CPAN installs

Wiggins d'Anconia wrote: Kevin Viel wrote: I am attempting to install modules on a Solaris v10 computer for which I do not have root privileges. I see in MyConfig.pm that the build directory is local: 'build_dir' => q[/home/kviel/.cpan/build] Where does it install

substituting one variable, assign to another

How can take the value of one variable, substitute say its suffix, and assign it to another? I have only figured out how to do it using an intermediate variable: if ( $code eq "" ){ my $base = $out ; $base =~ s/\.out$/\.cde/ ; $code = $base ; } Many thanks, Kevin --

Re: C language and bioinformatics

resequencing (3 billion data points per subject X 3 bits minimum), you can bet that such a suite will be the standard; noone is going to expect a technician to review the data. Kind regards, Kevin -- Kevin Viel Department of Genetics [EMAIL PROTECTED] Southwest Foundation for

Re: substituting one variable, assign to another

Tom Phoenix wrote: On 1/24/07, Kevin Viel <[EMAIL PROTECTED]> wrote: How can take the value of one variable, substitute say its suffix, and assign it to another? I have only figured out how to do it using an intermediate variable: if ( $code eq "" ){ my $base = $out ;

parsing XML

icial 9606 190080 I would like search for certain keywords and abstract all gene in this query that meet the criteria. Can someone recommend a module? I looked at XML::Simple::DTDReader. I would be grateful for any help or suggestion. Thank you, Kevin -- Kevin Viel Depa

Re: parsing XML

From: Kevin Viel <[EMAIL PROTECTED]> I have obtain results of a query in XML format: http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSummary_041029.dtd";> 4609 MYC v-myc myelocytomatosis viral oncogene homolog (avian) Homo sapiens

Re: C language and bioinformatics

have lots of modules available from Bio* projects http://bioperl.org http://biopython.org thats my 2 cents !!! Can you describe *why* python might be preferred? What does it offer that is an advantage compared to perl? Thanks, Kevin -- Kevin Viel Department of Genetics

Compound variable names

Greetings, I have been struggling with this one for a while. How can I create a variable name composed of two or more variables? I suspect I have to I have to use a reference: my $var1 = "part" ; my $var2 = "2"; my $compound = $var1_$var2 ; Thanks, Kevin -- K

unix date for perl time calculation

ful reference (while I begin to RTFM). Thank you, Kevin -- Kevin Viel Department of Genetics [EMAIL PROTECTED] Southwest Foundation for Biomedical Research phone: (210)258-9884 P.O. Box 760549 fax:(210)258-9444 San Antonio, TX 78245-0549 Ke

Re: Perl error

this problem? Thank you, Kevin -- Kevin Viel Department of Genetics [EMAIL PROTECTED] Southwest Foundation for Biomedical Research phone: (210)258-9884 P.O. Box 760549 fax:(210)258-9444 San Antonio, TX 78245-0549 Kevin Viel PhD Cand

Re: Perl error

, I'd like to say over a year, but I am not sure. So, could it be that somehow the environment path variable relating to perl had been changed? Otherwise, I cannot account for the difference. Thanks, Kevin -- Kevin Viel Department of Genetics [EMAIL PROTECTED] Sout

Installing CPANPLUS

place for it? Thanks in advance, Kevin -- Kevin Viel Department of Genetics e-mail: [EMAIL PROTECTED] Southwest Foundationphone: (210)258-9884 P.O. Box 760549 fax