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  • How to create a matrix format in perl

    - by shaq
    I have an array of array in which each array is like: clusterA gene1 1 clusterA gene2 0 clusterB gene1 1 clusterB gene2 0 I want to produce a file like: name gene1 gene2 clusterA 1 0 clusterB 1 0 Current attempt: if (condition) { @array = ($cluster, $genes, "1"); } elsif (not condition) { @array = ($cluster, $genes, "0"); } push @AoA, [ @array ]; @A0A is my array of array.

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  • perl Date::Manip array problem

    - by medalto
    im using Date::Manip http://search.cpan.org/~sbeck/Date-Manip-6.11/lib/Date/Manip.pod for a variety of things and want to create an array of days of the month i think I need @date = &ParseRecur("2010:4:0:0:0:0:0"); but it doesnt do it . ive read & reread the man page but cant get the syntax. @date = &ParseRecur("2010:4:0:1:0:0:0"); @date = &ParseRecur("2010:4:0:1*:0:0:0"); dont work either !

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  • running jar file with multiple arguments in perl

    - by compiler9999
    Hi All, Im trying to run a jar file. this jar file will output multiple question in console manner, i want to eliminate the console and i need to input a value in order to proceed. e.g : A. Choose value 1 : [1] Windows [2] Unix Input : 2 B. Choose value 2 : [1] Oracle [2] DB2 Input : 1 Im trying : "java -jar program.jar < abc.txt" where abc.txt has a value of : 2 1 3 etc. but its not working its only getting the first value. please help. thanks. btw, ive also try : OPEN PIPE, "| java -jar program.jar"; open (FH, /abc.txt) print PIPE "$res"; close FH; close PIPE; Regards

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  • Perl regular expression question

    - by user368311
    Suppose I have variables $x1 = 'XX a b XX c d XX'; $x2 = 'XX a b XX c d XX e f XX'; I want a regular expression that will find each instance of letters between XX. I'm looking for a general solution, because I don't know how many XX's there are. I tried using /XX(.*?)XX/g but this only matches "a b" for x1 and "a b", "e f" for x2 because once the first match is found, the engine has already read the second "XX". Thanks for any help.

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  • Reading another packages symbol table in Perl

    - by justintime
    I am trying to read a global symbol from another package. I have the package name as a string. I am using qualify_to_ref from Symbol module my $ref = qualify_to_ref ( 'myarray', 'Mypackage' ) ; my @array = @$ref ; gives me Not an ARRAY reference at ...... I presume I am getting the format of the dereference wrong. Here is a complete example program. use strict; use Symbol ; package Mypackage ; our @myarray = qw/a b/ ; package main ; my $ref = qualify_to_ref ( 'myarray', 'Mypackage' ) ; my @array = @$ref ;

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  • selecting delimiter in regex while selecting portion between lines in case of perl

    - by Gaurav S
    The message has detection report: <detection_report> Test 1 Test 2 Test 3 </detection_report> --------------------------------------------- Have a nice day I want to select portion between <detection_report> tags, including these two tags. I have written following code. The message has detection report\:((.|\n|\r)+)(\<\/detection_report\>) but its not working. Can anyone help me with this.

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  • Perl scraping script not recognising certain characters

    - by user1849286
    I have a script that works fine locally but on the server fails. It displays the non-breaking space symbol &nbsp; as ? when printing to standard output. In the parsing of the page, if I try to get rid of non breaking space symbol with s/&nbsp;//g nothing happens, neither getting rid of the question mark s/?//g It seems to stick no matter what. Bizzarely, this is not an issue when running the script locally. Additionally, question marks within a diamond symbol are inserted everywhere (on both the server script and the local script) instead of apostrophes, although at least that is not causing the parsing of the page to break on the local page. Confused, pls help.

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  • How to determinate file in Perl

    - by rodnower
    Hello, I use File::Find - find(\&f, $directory) for find some file with some content. Relevant part of my delegate looks like: sub f { my $file = $File::Find::name; return unless -f $file; return unless $file =~ /$file_pattern/; etc... but the problem is that, that this code returns every time where $file not exist in current directory. For example for file ./test it fine, but for file ./dir/test this return... Is there some better way to know if $file is file?

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  • Matching elements from 2 arrays in perl

    - by Paul
    Right now I am attempting to synchronize two data files that are listed by date so that i can make comparisons later on. However I can not seem to print out only the lines where the dates match. At this point I have separated out the data for each file into 2 arrays. I need to find only the dates that are in both arrays and print them out. Any suggestions would be much appreciated.

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  • Perl check for the existence of a value in a regular array

    - by Mel
    I am trying to figure out a way of checking for the existence of a value in an array without iterating through the array. I am reading a file for a parameter. I have a long list of parameters I do not want to deal with. I placed these unwanted parameters in an array @badparams I want to read a new parameter and if it does not exist in @badparams, process it. If it does exist in @badparams, go to the next read.

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  • In Perl, how to match several prefixes

    - by xorsyst
    I have 2 input files. One is a list of prefix and lengths, like this: 101xxx 102xxx 30xx 31xx (where x is any number) And another is a list of numbers. I want to iterate through the second file, matching each number against any of the prefix/lengths. This is fairly easy. I build a list of regexps: my @regexps = ('101...', '102...', '30..', '31..'); Then: foreach my $regexp (@regexps) { if (/$regexp/) { # do something But, as you can guess, this is slow for a long list. I could convert this to a single regexp: my $super_regexp = '101...|102...|30..|31..'; ...but, what I need is to know which regexp matched the item, and what the ..s matched. I tried this: my $catching_regexp = '(101)(...)|(102)(...)|(30)(..)|(31)(..)'; but then I don't know whether to look in $1, $3, %5 or $7. Any ideas? How can I match against any of these prefix/lengths and know which prefix, and what the remaining digits where?

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  • Perform regular expression on a PERL PDL variable

    - by Ahdee
    is it possible to perform a regular expression on a n-dimension PDL variable? For example I can add 100 to all the element by doing $a1 = pdl [1,2]; print $a1+100; However what if my array was a bunch of string that I would like to perform some task on, for example this fails. $a = pdl ['suze','david']; $a =~ s/suze/female/; print $a; not sure if this is even possible but thanks in advance. Ahdee

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  • How can I run Devel::Cover under mod_perl2?

    - by codeholic
    Unfortunately, Devel::Cover does not yet work with threads. It doesn't work with prefork either. Being use'd in startup.pl, Devel::Cover issues Not a CODE reference. END failed--call queue aborted. perl 5.8.9, Apache 2.2.13. My OS is FreeBSD, if that matters. The same problem is reported for win32.

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  • mod_perl memory

    - by Pavel Georgiev
    Hi, I have a perl script running in mod_perl that needs to write a large amount of data to the client, possibly over a long period. The behavior that I observe is that once I print and flush something, the buffer memory is not reclaimed even though I rflush (I know this cant be reclaimed back by the OS). Is that how mod_perl operates and is there a way that I can force it to periodically free the buffer memory, so that I can use that for new buffers instead of taking more from the OS?

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  • Is there a way that I can force mod_perl to re-use buffer memory?

    - by Pavel Georgiev
    Hi, I have a Perl script running in mod_perl that needs to write a large amount of data to the client, possibly over a long period. The behavior that I observe is that once I print and flush something, the buffer memory is not reclaimed even though I rflush (I know this can't be reclaimed back by the OS). Is that how mod_perl operates and is there a way that I can force it to periodically free the buffer memory, so that I can use that for new buffers instead of taking more from the OS?

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  • Can a Perl subroutine return data but keep processing?

    - by Perl QuestionAsker
    Is there any way to have a subroutine send data back while still processing? For instance (this example used simply to illustrate) - a subroutine reads a file. While it is reading through the file, if some condition is met, then "return" that line and keep processing. I know there are those that will answer - why would you want to do that? and why don't you just ...?, but I really would like to know if this is possible. Thank you so much in advance.

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  • BugZilla XML RPC Interface

    - by Damo
    I am attempting to setup BugZilla to receive but reports from another system using the XML-RPC interface. BugZilla works fine on its own with its own interface. When I attempt to test the XML-RPC functionality by accessing "xmlrpc.cgi" in my browser I get the error: The XML-RPC Interface feature is not available in this Bugzilla at C:\BugZilla\xmlrpc.cgi line 27 main::BEGIN(...) called at C:\BugZilla\xmlrpc.cgi line 29 eval {...} called at C:\BugZilla\xmlrpc.cgi line 29 Following this I install test-taint package from the default perl repository, this installs version 1.04. Re-running "xmlrpc.cgi" gives me an IIS error: 502 - Web server received an invalid response while acting as a gateway or proxy server. There is a problem with the page you are looking for, and it cannot be displayed. When the Web server (while acting as a gateway or proxy) contacted the upstream content server, it received an invalid response from the content server. So I run the checksetup.pl which inform me that: Use of uninitialized value in open at C:/Perl/site/lib/Test/Taint.pm line 334, <DATA> line 558. Installing Test-Taint from CPAN is the same. I assume XML-RPC is relent on Test-Taint, but Test-Taint doesn't seem to run correctly. If I ignore this error and attempt to invoke "bz_webservice_demo.pl" to add an entry the script times out. How can I get the XML-RPC / Test-Taint function working ? Current Setup: IIS7.5 on Windows Server 2008 Bugzilla 4.2.2 Perl 5.14.2 C:\BugZilla>perl checksetup.pl Set up gcc environment - 3.4.5 (mingw-vista special r3) * This is Bugzilla 4.2.2 on perl 5.14.2 * Running on Win2008 Build 6002 (Service Pack 2) Checking perl modules... Checking for CGI.pm (v3.51) ok: found v3.59 Checking for Digest-SHA (any) ok: found v5.62 Checking for TimeDate (v2.21) ok: found v2.24 Checking for DateTime (v0.28) ok: found v0.76 Checking for DateTime-TimeZone (v0.79) ok: found v1.48 Checking for DBI (v1.614) ok: found v1.622 Checking for Template-Toolkit (v2.22) ok: found v2.24 Checking for Email-Send (v2.16) ok: found v2.198 Checking for Email-MIME (v1.904) ok: found v1.911 Checking for URI (v1.37) ok: found v1.59 Checking for List-MoreUtils (v0.22) ok: found v0.33 Checking for Math-Random-ISAAC (v1.0.1) ok: found v1.004 Checking for Win32 (v0.35) ok: found v0.44 Checking for Win32-API (v0.55) ok: found v0.64 Checking available perl DBD modules... Checking for DBD-Pg (v1.45) ok: found v2.18.1 Checking for DBD-mysql (v4.001) ok: found v4.021 Checking for DBD-SQLite (v1.29) ok: found v1.33 Checking for DBD-Oracle (v1.19) ok: found v1.30 The following Perl modules are optional: Checking for GD (v1.20) ok: found v2.46 Checking for Chart (v2.1) ok: found v2.4.5 Checking for Template-GD (any) ok: found v1.56 Checking for GDTextUtil (any) ok: found v0.86 Checking for GDGraph (any) ok: found v1.44 Checking for MIME-tools (v5.406) ok: found v5.503 Checking for libwww-perl (any) ok: found v6.02 Checking for XML-Twig (any) ok: found v3.41 Checking for PatchReader (v0.9.6) ok: found v0.9.6 Checking for perl-ldap (any) ok: found v0.44 Checking for Authen-SASL (any) ok: found v2.15 Checking for RadiusPerl (any) ok: found v0.20 Checking for SOAP-Lite (v0.712) ok: found v0.715 Checking for JSON-RPC (any) ok: found v0.96 Checking for JSON-XS (v2.0) ok: found v2.32 Use of uninitialized value in open at C:/Perl/site/lib/Test/Taint.pm line 334, <DATA> line 558. Checking for Test-Taint (any) ok: found v1.04 Checking for HTML-Parser (v3.67) ok: found v3.68 Checking for HTML-Scrubber (any) ok: found v0.09 Checking for Encode (v2.21) ok: found v2.44 Checking for Encode-Detect (any) not found Checking for Email-MIME-Attachment-Stripper (any) ok: found v1.316 Checking for Email-Reply (any) ok: found v1.202 Checking for TheSchwartz (any) not found Checking for Daemon-Generic (any) not found Checking for mod_perl (v1.999022) not found Checking for Apache-SizeLimit (v0.96) not found *********************************************************************** * OPTIONAL MODULES * *********************************************************************** * Certain Perl modules are not required by Bugzilla, but by * * installing the latest version you gain access to additional * * features. * * * * The optional modules you do not have installed are listed below, * * with the name of the feature they enable. Below that table are the * * commands to install each module. * *********************************************************************** * MODULE NAME * ENABLES FEATURE(S) * *********************************************************************** * Encode-Detect * Automatic charset detection for text attachments * * TheSchwartz * Mail Queueing * * Daemon-Generic * Mail Queueing * * mod_perl * mod_perl * * Apache-SizeLimit * mod_perl * *********************************************************************** COMMANDS TO INSTALL OPTIONAL MODULES: Encode-Detect: ppm install Encode-Detect TheSchwartz: ppm install TheSchwartz Daemon-Generic: ppm install Daemon-Generic mod_perl: ppm install mod_perl Apache-SizeLimit: ppm install Apache-SizeLimit Reading ./localconfig... OPTIONAL NOTE: If you want to be able to use the 'difference between two patches' feature of Bugzilla (which requires the PatchReader Perl module as well), you should install patchutils from: http://cyberelk.net/tim/patchutils/ Checking for DBD-mysql (v4.001) ok: found v4.021 Checking for MySQL (v5.0.15) ok: found v5.5.27 WARNING: You need to set the max_allowed_packet parameter in your MySQL configuration to at least 3276750. Currently it is set to 3275776. You can set this parameter in the [mysqld] section of your MySQL configuration file. Removing existing compiled templates... Precompiling templates...done. checksetup.pl complete.

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  • How can I check the location of perl and CPAN files?

    - by Rob
    I constantly have to set up new servers for an employer of mine for an exact purpose of his, and as such they all have to be set up in exactly the same way. So I've created a script in PHP that I run from my own box to automatically send over all the relevant files, compile everything, run updates, and everything else. However, for some reason these brand new servers come with perl, which is fine, but they have perl installed in different locations. This makes it a pain for me to copy over Config.pm for CPAN without going in and finding the location manually. Is there perhaps some command I'm unaware of that will hunt down the precise location? If it helps, usually the servers are CentOS 5

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  • Why doesn't Apache2::SubProcess spawn my subprocess?

    - by codeholic
    The following script works without errors, but /tmp/test.touch is not being created (even being checked later in the command line). It seems to me as if $r->spawn_proc_prog doesn't spawn a process. What may cause the problem? #!/usr/bin/perl use strict; use warnings; use Apache2::RequestUtil; use Apache2::SubProcess (); my $r = Apache2::RequestUtil->request; print "Content-Type: text/plain\n\n"; print eval { $r->spawn_proc_prog('/usr/bin/touch', ['/tmp/test.touch']) } ? `ls -l /tmp/test.touch` : $@;

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  • How can I properly use environment variables encoded as Windows-1251 in Perl?

    - by Kartlee
    I have an environment variable set in Windows as TEST=abc£ which uses Windows-1252 code page. Now, when I run a Perl program test.pl this environment value comes properly. When I call another Perl code - test2.pl from test1.pl either by system(..) or Win32::Process, the environment comes garbled. Can someone provide information why this could be and way to resolve it? The version of perl I am using is 5.8. If my understanding is right, perl internally uses utf-8, so the initial process - test1.pl received it right from Windows-1252 → utf-8. When we call another process, should we convert back to Windows-1252 code page?

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  • What does the status code of the Perl interpreter mean?

    - by futureelite7
    Hi, This might sound slightly confusing, but please bear with me. I'm trying to execute a copy of the Perl interpreter using Java's Runtime.exec(). However, it returned error code 9. After running the file a few times, the perl interpreter mysteriously started to return code 253 with no changes in my command at all. What does code 253 / code 9 mean? A google search for perl interpreter's exit codes turned up nothing. Where can I find a list of exit codes for the Perl interpreter? Thanks!

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  • How can I test when a feature was added to Perl?

    - by Eric Strom
    Are there any services similar to codepad that will allow you to test Perl constructs on old versions of perl? Ideally, a system where you could enter an expression and it will tell you the oldest version of perl that it will work with. Of course it's possible to use CPANTS for this, but that seems like an abuse of the service (if only for making the BackPan bigger). And it could take several days/weeks to get decent test coverage on old versions.

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  • Why doesn't Perl file glob() work outside of a loop in scalar context?

    - by Rob
    According to the Perl documentation on file globbing, the <*> operator or glob() function, when used in a scalar context, should iterate through the list of files matching the specified pattern, returning the next file name each time it is called or undef when there are no more files. But, the iterating process only seems to work from within a loop. If it isn't in a loop, then it seems to start over immediately before all values have been read. From the Perl docs: In scalar context, glob iterates through such filename expansions, returning undef when the list is exhausted. http://perldoc.perl.org/functions/glob.html However, in scalar context the operator returns the next value each time it's called, or undef when the list has run out. http://perldoc.perl.org/perlop.html#I/O-Operators Example code: use warnings; use strict; my $filename; # in scalar context, <*> should return the next file name # each time it is called or undef when the list has run out $filename = <*>; print "$filename\n"; $filename = <*>; # doesn't work as documented, starts over and print "$filename\n"; # always returns the same file name $filename = <*>; print "$filename\n"; print "\n"; print "$filename\n" while $filename = <*>; # works in a loop, returns next file # each time it is called In a directory with 3 files...file1.txt, file2.txt, and file3.txt, the above code will output: file1.txt file1.txt file1.txt file1.txt file2.txt file3.txt Note: The actual perl script should be outside the test directory, or you will see the file name of the script in the output as well. Am I doing something wrong here, or is this how it is supposed to work?

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