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• Why does File::Slurp return a scalar when it should return a list?

  - by BrianH

  I am new to the File::Slurp module, and on my first test with it, it was not giving the results I was expecting. It took me a while to figure it out, so now I am interested in why I was seeing this certain behavior. My call to File::Slurp looked like this: my @array = read_file( $file ) || die "Cannot read $file\n"; I included the "die" part because I am used to doing that when opening files. My @array would always end up with the entire contents of the file in the first element of the array. Finally I took out the "|| die" section, and it started working as I expected. Here is an example to illustrate: perl -de0 Loading DB routines from perl5db.pl version 1.22 Editor support available. Enter h or `h h' for help, or `man perldebug' for more help. main::(-e:1): 0 DB<1> use File::Slurp DB<2> $file = '/usr/java6_64/copyright' DB<3> x @array1 = read_file( $file ) 0 'Licensed material - Property of IBM.' 1 'IBM(R) SDK, Java(TM) Technology Edition, Version 6' 2 'IBM(R) Runtime Environment, Java(TM) Technology Edition, Version 6' 3 '' 4 'Copyright Sun Microsystems Inc, 1992, 2008. All rights reserved.' 5 'Copyright IBM Corporation, 1998, 2009. All rights reserved.' 6 '' 7 'The Apache Software License, Version 1.1 and Version 2.0' 8 'Copyright 1999-2007 The Apache Software Foundation. All rights reserved.' 9 '' 10 'Other copyright acknowledgements can be found in the Notices file.' 11 '' 12 'The Java technology is owned and exclusively licensed by Sun Microsystems Inc.' 13 'Java and all Java-based trademarks and logos are trademarks or registered' 14 'trademarks of Sun Microsystems Inc. in the United States and other countries.' 15 '' 16 'US Govt Users Restricted Rights - Use duplication or disclosure' 17 'restricted by GSA ADP Schedule Contract with IBM Corp.' DB<4> x @array2 = read_file( $file ) || die "Cannot read $file\n"; 0 'Licensed material - Property of IBM. IBM(R) SDK, Java(TM) Technology Edition, Version 6 IBM(R) Runtime Environment, Java(TM) Technology Edition, Version 6 Copyright Sun Microsystems Inc, 1992, 2008. All rights reserved. Copyright IBM Corporation, 1998, 2009. All rights reserved. The Apache Software License, Version 1.1 and Version 2.0 Copyright 1999-2007 The Apache Software Foundation. All rights reserved. Other copyright acknowledgements can be found in the Notices file. The Java technology is owned and exclusively licensed by Sun Microsystems Inc. Java and all Java-based trademarks and logos are trademarks or registered trademarks of Sun Microsystems Inc. in the United States and other countries. US Govt Users Restricted Rights - Use duplication or disclosure restricted by GSA ADP Schedule Contract with IBM Corp. ' Why does the || die make a difference? I have a feeling this might be more of a Perl precedence question instead of a File::Slurp question. I looked in the File::Slurp module and it looks like it is set to croak if there is a problem, so I guess the proper way to do it is to allow File::Slurp to croak for you. Now I'm just curious why I was seeing these differences.

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• Perl: Deleting multiple re-occuring lines where a certain criteria is met

  - by george-lule

  Dear all, I have data that looks like below, the actual file is thousands of lines long. Event_time Cease_time Object_of_reference -------------------------- -------------------------- ---------------------------------------------------------------------------------- Apr 5 2010 5:54PM NULL SubNetwork=ONRM_RootMo,SubNetwork=AXE,ManagedElement=BSJN1,BssFunction= BSS_ManagedFunction,BtsSiteMgr=LUGALAMBO_900 Apr 5 2010 5:55PM Apr 5 2010 6:43PM SubNetwork=ONRM_RootMo,SubNetwork=AXE,ManagedElement=BSJN1,BssFunction= BSS_ManagedFunction,BtsSiteMgr=LUGALAMBO_900 Apr 5 2010 5:58PM NULL SubNetwork=ONRM_RootMo,SubNetwork=AXE,ManagedElement=BSCC1,BssFunction= BSS_ManagedFunction,BtsSiteMgr=BULAGA Apr 5 2010 5:58PM Apr 5 2010 6:01PM SubNetwork=ONRM_RootMo,SubNetwork=AXE,ManagedElement=BSCC1,BssFunction= BSS_ManagedFunction,BtsSiteMgr=BULAGA Apr 5 2010 6:01PM NULL SubNetwork=ONRM_RootMo,SubNetwork=AXE,ManagedElement=BSCC1,BssFunction= BSS_ManagedFunction,BtsSiteMgr=BULAGA Apr 5 2010 6:03PM NULL SubNetwork=ONRM_RootMo,SubNetwork=AXE,ManagedElement=BSJN1,BssFunction= BSS_ManagedFunction,BtsSiteMgr=KAPKWAI_900 Apr 5 2010 6:03PM Apr 5 2010 6:04PM SubNetwork=ONRM_RootMo,SubNetwork=AXE,ManagedElement=BSJN1,BssFunction= BSS_ManagedFunction,BtsSiteMgr=KAPKWAI_900 Apr 5 2010 6:04PM NULL SubNetwork=ONRM_RootMo,SubNetwork=AXE,ManagedElement=BSJN1,BssFunction= BSS_ManagedFunction,BtsSiteMgr=KAPKWAI_900 Apr 5 2010 6:03PM Apr 5 2010 6:03PM SubNetwork=ONRM_RootMo,SubNetwork=AXE,ManagedElement=BSCC1,BssFunction= BSS_ManagedFunction,BtsSiteMgr=BULAGA Apr 5 2010 6:03PM NULL SubNetwork=ONRM_RootMo,SubNetwork=AXE,ManagedElement=BSCC1,BssFunction= BSS_ManagedFunction,BtsSiteMgr=BULAGA Apr 5 2010 6:03PM Apr 5 2010 7:01PM SubNetwork=ONRM_RootMo,SubNetwork=AXE,ManagedElement=BSCC1,BssFunction= BSS_ManagedFunction,BtsSiteMgr=BULAGA As you can see, each file has a header which describes what the various fields stand for(event start time, event cease time, affected element). The header is followed by a number of dashes. My issue is that, in the data, you see a number of entries where the cease time is NULL i.e event is still active. All such entries must go i.e for each element where the alarm cease time is NULL, the start time, the cease time(in this case NULL) and the actual element must be deleted from the file. In the remaining data, all the text starting from word SubNetwork upto BtsSiteMgr= must also go. Along with the headers and the dashes. Final output should look like below: Apr 5 2010 5:55PM Apr 5 2010 6:43PM LUGALAMBO_900 Apr 5 2010 5:58PM Apr 5 2010 6:01PM BULAGA Apr 5 2010 6:03PM Apr 5 2010 6:04PM KAPKWAI_900 Apr 5 2010 6:03PM Apr 5 2010 6:03PM BULAGA Apr 5 2010 6:03PM Apr 5 2010 7:01PM BULAGA Below is a Perl script that I have written. It has taken care of the headers, the dashes, the NULL entries but I have failed to delete the lines following the NULL entries so as to produce the above output. #!/usr/bin/perl use strict; use warnings; $^I=".bak" #Backup the file before messing it up. open (DATAIN,"<george_perl.txt")|| die("can't open datafile: $!"); # Read in the data open (DATAOUT,">gen_results.txt")|| die("can't open datafile: $!"); #Prepare for the writing while (<DATAIN>) { s/Event_time//g; s/Cease_time//g; s/Object_of_reference//g; s/\-//g; #Preceding 4 statements are for cleaning out the headers my $theline=$_; if ($theline =~ /NULL/){ next; next if $theline =~ /SubN/; } else{ print DATAOUT $theline; } } close DATAIN; close DATAOUT; Kindly help point out any modifications I need to make on the script to make it produce the necessary output. Will be very glad for your help Kind regards George.

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• Perl MiniWebserver

  - by snikolov

  hey guys i have config this miniwebserver, however i require the server to download a file in the local directory i am getting a problem can you please fix my issue thanks !/usr/bin/perl use strict; use Socket; use IO::Socket; my $buffer; my $file; my $length; my $output; Simple web server in Perl Serves out .html files, echos form data sub parse_form { my $data = $_[0]; my %data; foreach (split /&/, $data) { my ($key, $val) = split /=/; $val =~ s/+/ /g; $val =~ s/%(..)/chr(hex($1))/eg; $data{$key} = $val;} return %data; } Setup and create socket my $port = shift; defined($port) or die "Usage: $0 portno\n"; my $DOCUMENT_ROOT = $ENV{'HOME'} . "public"; my $server = new IO::Socket::INET(Proto = 'tcp', LocalPort = $port, Listen = SOMAXCONN, Reuse = 1); $server or die "Unable to create server socket: $!" ; Await requests and handle them as they arrive while (my $client = $server-accept()) { $client-autoflush(1); my %request = (); my %data; { -------- Read Request --------------- local $/ = Socket::CRLF; while (<$client>) { chomp; # Main http request if (/\s*(\w+)\s*([^\s]+)\s*HTTP\/(\d.\d)/) { $request{METHOD} = uc $1; $request{URL} = $2; $request{HTTP_VERSION} = $3; } # Standard headers elsif (/:/) { (my $type, my $val) = split /:/, $_, 2; $type =~ s/^\s+//; foreach ($type, $val) { s/^\s+//; s/\s+$//; } $request{lc $type} = $val; } # POST data elsif (/^$/) { read($client, $request{CONTENT}, $request{'content-length'}) if defined $request{'content-length'}; last; } } } -------- SORT OUT METHOD --------------- if ($request{METHOD} eq 'GET') { if ($request{URL} =~ /(.*)\?(.*)/) { $request{URL} = $1; $request{CONTENT} = $2; %data = parse_form($request{CONTENT}); } else { %data = (); } $data{"_method"} = "GET"; } elsif ($request{METHOD} eq 'POST') { %data = parse_form($request{CONTENT}); $data{"_method"} = "POST"; } else { $data{"_method"} = "ERROR"; } ------- Serve file ---------------------- my $localfile = $DOCUMENT_ROOT.$request{URL}; Send Response if (open(FILE, "<$localfile")) { print $client "HTTP/1.0 200 OK", Socket::CRLF; print $client "Content-type: text/html", Socket::CRLF; print $client Socket::CRLF; my $buffer; while (read(FILE, $buffer, 4096)) { print $client $buffer; } $data{"_status"} = "200"; } else { $file = 'a.pl'; open(INFILE, $file); while (<INFILE>) { $output .= $_; ##output of the file } $length = length($output); print $client "'HTTP/1.0 200 OK", Socket::CRLF; print $client "Content-type: application/octet-stream", Socket::CRLF; print $client "Content-Length:".$length, Socket::CRLF; print $client "Accept-Ranges: bytes", Socket::CRLF; print $client 'Content-Disposition: attachment; filename="test.zip"', Socket::CRLF; print $client $output, Socket::CRLF; print $client 'Content-Transfer-Encoding: binary"', Socket::CRLF; print $client "Connection: Keep-Alive", Socket::CRLF; # #$data{"_status"} = "404"; # } close(FILE); Log Request print ($DOCUMENT_ROOT.$request{URL},"\n"); foreach (keys(%data)) { print (" $_ = $data{$_}\n"); } ----------- Close Connection and loop ------------------ close $client; } END

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• Issues running python scripts in Command Prompt (Specifically with command line arguments)?

  - by dmanatunga

  I am trying to run my python scripts in DOS without calling python.exe first. I am specifically doing this in relation to running django-admin.py. I have C:\Python26 and C:\Python26\Scripts in my PATH. However, if I try running django-admin.py by doing: django-admin.py startproject helloworld I get the message: Type 'django-admin.py help' for usage. Now, after some experimentation, I realized the problem is that the secondary arguments to these scripts are not being passed for some reason, since I tried it with a some other python scripts I have. I know I could avoid this problem by simply doing: python C:\Python26\Scripts\django-admin.py startproject helloworld But I know it should be possible to run the first command only and get it to work, because I had it working before. I've looked everywhere, and not many places have been helpful so any idea would be useful for me at this point.

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• Why does my Perl CGI script complain about "Can't locate CGI/Simple.pm"?

  - by dexter

  For more information see this Example use strict; use warnings; use CGI::Simple; use DBI; my $cgi = CGI::Simple->new; my $dsn = sprintf( 'DBI:mysql:database=%s;host=%s', 'cdcol', 'localhost' ); my $dbh = DBI->connect($dsn, root => '', { AutoCommit => 0, RaiseError => 0 } ); my $status = $dbh ? 'Connected' : 'Failed to connect'; print $cgi->header, <<HTML; <!DOCTYPE HTML> <html> <head><title>Test</title></head> <body> <h1>Perl CGI Script</h1> <p>$status</p> </body> </html> HTML This code gives me error: The server encountered an internal error and was unable to complete your request. Error message: Can't locate CGI/Simple.pm in @INC (@INC contains: C:/xampp/perl/site/lib/ C:/xampp/perl/lib C:/xampp/perl/site/lib C:/xampp/apache) at C:/xampp/htdocs/perl/index.pl line 4. BEGIN failed--compilation aborted at C:/xampp/htdocs/perl/index.pl line 4. , Error 500 localhost 3/25/2010 11:19:19 AM Apache/2.2.14 (Win32) DAV/2 mod_ssl/2.2.14 OpenSSL/0.9.8l mod_autoindex_color PHP/5.3.1 mod_apreq2-20090110/2.7.1 mod_perl/2.0.4 Perl/v5.10.1 What does this mean and how can I resolve it?

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• Why do I get "Error 6060" when I try to use DBD::Advantage with a 64-bit perl on Linux?

  - by WarheadsSE

  I realize that I am attempting to go beyond the "supported" behavior of the manf's released drivers for Perl, after all they have only released it in package with x86 .so's. However, since I cannot use their package with x64 Perl on a RHEL 5.4 x86_64 box, and maintaining a seperate install of x86 Perl just for this one package, I have made an attempt to get this puppy working thanks to released 64-bit .so's that accompany other driver packages for Advantage. What I have done to this point: download beta 10 DBI drivers, in 32 download beta 10 PHP extension (it contains 32 and x86_64) copy the required DLLs into the ads-lib location (eg /usr/local/ads/lib64) compile the Perl DBI driver with the path to the lib64's .so's Good compilation, good install, good use. The problem is that I always get : failed: [iAnywhere Solutions][Advantage SQL][ASA] Error 6060: Advantage Database Server not available on specified server. axServerConnect (SQL-HY000)(DBD: db_login/SQLConnect err=-1) Does anyone have any ideas? EDIT: fixed package name in post title EDIT: Updated title. It appears that it's not just the x64 perl, but the RHEL 5.4 underneath that may be interfering. As commented below, I managed to shoe-horn a x86 perl onto the system, and compile the DBD::Advantage 9.99, and later replacing that with 9.10, and none of these x86 would connect either. Neither library (9.99 or 9.10) in either bit-edness will connect from this x86_64 server to the windows server's UNC path. I have successfully mounted this share without problems, but still I cannot seem to connect to the 9.1. I have tried: \hostname\PATH \FQDN\PATH \IP\PATH and all of these variations with the port (default) 6262 included. My windows machine connects fine, with both 9.1 and 9.99 from strawberry perl.

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• Need Help getting perl module DBD::mysql installed for bugzilla on RedHat.

  - by Alos Diallo

  Hi everyone I am having some issues getting Bugzilla setup, I have the software on the server and am trying to get the pre-rec's setup. I am using RedHat 4.1.2-42. I have all of the required perl modules save one:DBD::mysql When I try: sudo perl install-module.pl DBD::mysql I get the following response(this is only an excerpt): rm -f blib/arch/auto/DBD/mysql/mysql.so LD_RUN_PATH="/usr/lib64/mysql:/usr/lib64:/lib64" /usr/bin/perl myld gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic dbdimp.o mysql.o -o blib/arch/auto/DBD/mysql/mysql.so \ -L/usr/lib64/mysql -lmysqlclient -lz -lcrypt -lnsl -lm -L/usr/lib64 -lssl -lcrypto \ /usr/bin/ld: skipping incompatible /usr/lib/libssl.so when searching for -lssl /usr/bin/ld: skipping incompatible /usr/lib/libssl.a when searching for -lssl /usr/bin/ld: cannot find -lssl collect2: ld returned 1 exit status make: * [blib/arch/auto/DBD/mysql/mysql.so] Error 1 /usr/bin/make -- NOT OK Running make test Can't test without successful make Running make install make had returned bad status, install seems impossible I then tried the following: CFLAGS="-I/usr/lib64/mysql:/usr/lib64:/lib64" perl install-module.pl DBD::mysql I get the same result. I have also tried to install it using CPAN but also get the same result. Right now I have DBD-mysql v3.0007 but need (v4.00) Also when I try to install open ssl it says I have the latest version. Does anyone know what I have to do to get this to work? Any help would be greatly appreciated. Thank you

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• Cassandra inserts using Net::Cassandra::Easy in Perl

  - by knorv

  When using the Perl module Net::Cassandra::Easy to interface with Cassandra I use the following code to read colums col[123] from rows row[123] in column-family Standard1: my $cassandra = Net::Cassandra::Easy->new(keyspace => 'Keyspace1', server => 'localhost'); $cassandra->connect(); my $result = $cassandra->get(['row1', 'row2', 'row3'], family => 'Standard1', byname => ['col1', 'col2', 'col3']); This works as expected. However, when trying to insert row row1 with .. $result = $cassandra->mutate(['row1'], family => 'Standard1', insertions => { "col1" => "Value to set." }); .. I get the error message Can't use string ("0") as a SCALAR ref while "strict refs" in use at .../Net/GenThrift/Thrift/BinaryProtocol.pm line 376. What am I doing wrong?

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• SHELL OR PERL QUESTION

  - by user150674

  I have a very large file, named 'ColCheckMe', tab-delimited, that you are asked to process. You are told that each line in 'ColCheckMe' has 7 columns, and that the values in the 5th column are integers. Using shell functions indicate how you would verify that these conditions were satisfied in 'ColCheckMe' K got this... nawk ‘ NF != 7 { Printf(“[%d] has invalid [%d] number of fileds\n”, FNR, NF) } $5 !~ /^[0-9]+$/ { Printf(“[%d] 5th field is invalid [%s]\n”, FNR, $5) }’ ColCheckMe Now, 2. In with the similar file, you are told that each value in column 1 is unique. How would I verify that? Also write a shell function that counts the number of occurrences of the word “SpecStr” in the file 'ColCheckMe' Any one can help in SHELL or everything including the first in PERL Scripting.

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• How do i make a system call to tar files(along with exclude tag) in Perl

  - by superstar

  This is the system call, i am making right now in perl to tar the files system("${tarexe} -pcvf $tarname $includepath") which works fine. $tarexe -> location of my tar.exe file $tarname -> myMock.tar $includepath -> ./input/myMockPacketName ./input/myPacket/my2/*.wav ./input/myPacket/my3 ./input/myPacket/in.html Now i want to exclude some files using exclude tag, which doesnot exclude the files system("${tarexe} -pcvf $tarname $includepath --exclude $excludepath") $excludepath -> ./input/myMockPacketName/my3 The same stament ${tarexe} -pcvf $tarname $includepath --exclude $excludepath works fine when i run it in the command line.

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• perl regex groups

  - by Aaron Moodie

  I've currenly trying to pull out dates from a file and feed them directly into an array. My regex is working, but I have 6 groups in it, all of which are being added to the array, when I only want the first one. @dates = (@dates, ($line =~ /((0[1-9]|[12][0-9]|3[01])(\/|\-)(0[1-9]|1[0-2])(\/|\-)([0-9][0-9][0-9][0-9]|[0-9][0-9]))/g )); is there a simple way to grab the $1 group of a perl regex? my output is looking like this: 13/04/2009, 13, /, 04, /, 2009, 14-12-09, 14, -, 12, -, 09

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• Perl :Getting the name of the current subroutine

  - by kiruthika

  Hi all, In perl we can get the name of the current package and current line number Using the predefined variables like _PACKAGE and __LINE . Like this I want to get the name of the current subroutine. Example use strict; use warnings; print __PACKAGE__; sub test() { print __LINE__; } &test(); In the above code I want to get the name of the subroutine inside the function 'test'. Thanks in advance.

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• Running CGI With Perl under Apache Permission Problem

  - by neversaint

  I have the following entry under apache2.conf in my Debian box. AddHandler cgi-script .cgi .pl Options +ExecCGI ScriptAlias /cgi-bin/ /var/www/mychosendir/cgi-bin/ Then I have a perl cgi script stored under these directories and permissions: nvs@somename:/var/www/mychosendir$ ls -lhR .: total 12K drwxr-xr-x 2 nvs nvs 4.0K 2010-04-21 13:42 cgi-bin ./cgi-bin: total 4.0K -rwxr-xr-x 1 nvs nvs 90 2010-04-21 13:40 test.cgi However when I tried to access it in the web browser: http://myhost.com/mychosendir/cgi-bin/test.cgi They gave me this error: Forbidden You don't have permission to access /mychosendir/cgi-bin/test.cgi on this server. What's wrong with it?

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• Switching Timezones in Perl's Template::Toolkit plugin Template::Plugin::Date

  - by aidan

  I have a calendar on my website, generated in Perl using Template::Toolkit and Template::Plugin::Date. It highlights the current day. I achieve this by iterating through all the dates (as I print the calendar) and comparing against the current date. Something like this: [% IF cur_date == date.format(format = '%Y-%m-%d') %] ... [% END %] It all works well until someone in Australia looks at it. (They are in a different timezone to me and my server in the UK). What's the best way to get Template::Plugin::Date to use a different time zone? It accepts a 'locale' parameter, but AFAIK this is only used for formatting.

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• Perl/Tk : Giving alert to the user

  - by kiruthika

  Hi all, I am learning Perl/Tk. I want to give alert to the user whenever he/she receives the mail. I have planned to use message box in Tk,but it is expecting the user to click ok or cancel button. Until user clicked the any one button it wont do any further operations. But I want ,it just needs to give alert to the user and user can continue with the further process. Please help me.. Thanks in advance.

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• Simple Perl script help required.

  - by Umar Siddique

  I'm looking to create a perl script that I will run on a JavaScript file to automatically change ( ' ) that breaks the script. Example: file.js document.writeln('&#187; <a href="/LINK1" TARGET="_blank">Lorem ipsum lorem 1</a><br>'); document.writeln('&#187; <a href="/LINK2" TARGET="_blank">Lorem ipsum lor'em x em 2</a><br>'); document.writeln('&#187; <a href="/LINK3" TARGET="_blank">Lorem ipsum lorem 3</a><br>'); In 2nd line " Lorem ipsum lor'em x em 2 " contains a single quote which will be removed by script. Rest of the single quotes will be there like " document.writeln(' "

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• Can you hep me with my Perl homework?

  - by riya

  Could someone write simple Perl programs for the following scenarios: convert a list from {1,2,3,4,5,7,9,10,11,12,34} to {1-5,7,9-12,34} to sort a list of negative numbers to insert values to hash array there is a file with content: C1 c2 c3 c4 r1 r2 r3 r4 put it into an hash array where keys = {c1,c2,c3,c4} and values = {r1,r2,r3,r4} There are testcases running each testcase runs as a process and has a process ID. The logs are logged in a logfile process ID appended to each line. Prog to find out if the test case has passed or failed. The program shoud be running till the processes are running and display output.

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• Teach Perl as a first language?

  - by yossale

  I need to teach a non-programmer the basics of computer programming + some basic programming skills (- He's going to be in a position between the clients and the programmers , so the company requires him to learn the basic concepts of programming). I thought of Perl - You can teach it without getting into typing and pointers and it's syntax is very close to human (precious "bless" :) ) - but I'm a bit troubled because I feel like I'm going to "spoil" him for other languages in the future (C,C++,Java - What some people call "Real" languages) - exactly because of the reasons mentioned above. What do you think?

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• Convert Chunk of Data into Tabular Format Using Perl

  - by neversaint

  I have a data that looks like this 1:SRX000566 Submitter: WoldLab Study: RNASeq expression profiling for ENCODE project(SRP000228) Sample: Human cell line GM12878(SRS000567) Instrument: Solexa 1G Genome Analyzer Total: 4 runs, 62.7M spots, 2.1G bases Run #1: SRR002055, 11373440 spots, 375323520 bases Run #2: SRR002063, 22995209 spots, 758841897 bases Run #3: SRR005091, 13934766 spots, 459847278 bases Run #4: SRR005096, 14370900 spots, 474239700 bases 2:SRX000565 Submitter: WoldLab Study: RNASeq expression profiling for ENCODE project(SRP000228) Sample: Human cell line GM12878(SRS000567) Instrument: Solexa 1G Genome Analyzer Total: 3 runs, 51.2M spots, 1.7G bases Run #1: SRR002052, 12607931 spots, 416061723 bases Run #2: SRR002054, 12880281 spots, 425049273 bases Run #3: SRR002060, 25740337 spots, 849431121 bases 3:SRX012407 Submitter: GEO Study: GSE17153: Illumina sequencing of small RNAs from C. elegans embryos(SRP001363) Sample: Caenorhabditis elegans(SRS006961) Instrument: Illumina Genome Analyzer II Total: 1 run, 3M spots, 106.8M bases Run #1: SRR029428, 2965597 spots, 106761492 bases Is there a compact way to convert them into tabular format (tab separated). Hence 1 entry/row per chunk. In these case 3 rows. I tried this but doesn't seem to work. perl -laF/\n/ -000ne"print join chr(9),@F" myfile.txt

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• Testing a command from Perl and checking content of a file

  - by justintime

  I want to test a script I have written in Perl and specifically check what output it writes to file. I wrote it some time ago and don't want to modify it to the extent of turning it into a module but would like to regression test it before adding some small functional changes. So far I have use Test::Command tests = 10; exit_is_num($cmd, 0); .... But the command produces some files and I want to check those files are the same as I expect (either equal or match some regexp). Any suggestions

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• Perl system call

  - by claferri

  I'm a beginner in Perl and I have some trouble using the "system" call. Here is a little piece of code where I try to execute 2 shell commands : # First command is : # dot -Tpng $dottmpfile > $pngfile # Second command is : # rm $dottmpfile if (!($pngfile eq "")) { my @args = ("dot", "-Tpng", $dottmpfile, " > ", $pngfile); system (join (' ' , @args )) or die "system @args failed : $!"; unlink $dottmpfile; } EDIT : Here is my code now, and I still get an error : system dot -Tpng toto.dot > toto.png failed : Inappropriate ioctl for device at /home/claferri/bin/fractal.pl line 79. I've used this to produce this piece of code.

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• User input in perl - Issue with running script in KomodoEdit

  - by golwalkar.rohan

  i wrote this tiny code on gedit and ran it :- #/usr/bin/perl print "Enter the radius of circle: \n"; $radius = <>; chomp $radius; print "radius is: $radius\n"; $circumference = (2*3.141592654) * $radius; print "Circumference of circle with radius : $radius = $circumference\n"; Runs fine using command line.Ran the same code on Komodo Edit: facing an issue i expect first line as output as :- Enter the radius of circle: whearas it waits on the screen i.e waiting for an input and after that runs everything in sequence -- can someone tell me why it runs fine with command line but not Komodo?

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• Doing permutation of different arrays in perl

  - by nubie2

  Hello! I want to do permutation in perl. For example I have three arrays. ["big", "tiny", "small"] and then I have ["red", "yellow", "green"] and also ["apple", "pear", "banana"]. How do I get: ["big", "red", "apple"] ["big", "red", "pear"] ..etc.. ["small", "green", "banana"] I understand this is called permutation. But I am not sure how to do it. Also I don't know how many arrays I can have. There may be three or four, so I don't want to do nested loop.

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• Perl file test operator help

  - by Aaron Moodie

  This is a really basic issue, but I'm new to perl and cannot work out what the issue is. I'm just trying to isolate the files in a directory, but the -d operator keeps treating all the folder contents as files ... @contents is my array, and when I run this: foreach $item(@contents) { if (-d $item) { next; } print"$item is a file\n"; } I keep getting both folders and files. Alternatively, if I use -f, I get nothing. edit: this is the output - file01.txt is a file folder 01 is a file folder 02 is a file Screen shot 2010-04-18 at 1.26.17 PM.png is a file I'm running this on OSX

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• Matching n parentheses in perl regex

  - by coding_hero

  Hi, I've got some data that I'm parsing in Perl, and will be adding more and more differently formatted data in the near future. What I would like to do is write an easy-to-use function, that I could pass a string and a regex to, and it would return anything in parentheses. It would work something like this (pseudocode): sub parse { $data = shift; $regex = shift; $data =~ eval ("m/$regex/") foreach $x ($1...$n) { push (@ra, $x); } return \@ra; } Then, I could call it like this: @subs = parse ($data, '^"([0-9]+)",([^:]*):(\W+):([A-Z]{3}[0-9]{5}),ID=([0-9]+)'); As you can see, there's a couple of issues with this code. I don't know if the eval would work, the 'foreach' definitely wouldn't work, and without knowing how many parentheses there are, I don't know how many times to loop. This is too complicated for split, so if there's another function or possibility that I'm overlooking, let me know. Thanks for your help!

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