Perl is a high-level, general-purpose, interpreted, dynamic programming language. It was originally developed by Larry Wall as a general-purpose Unix scripting language to make report processing easier, over a period with support from open source community, it has evolved and matured to be used for ...

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1answer
117 views

How do I reinstall the bioperl modules on Ubuntu?

I am trying to learn bioinformatics the hard way. I have no background in Linux, Ubuntu, bash, Perl, Python, etc. I'm trying to use several programs, mostly the bioperl modules, that have been ...
3
votes
1answer
1k views

Send log messages to a different location

I want to send messages from C program and from Perl script to a file (for example, /var/log/my_log). I don't have access to the syslog daemon configuration, so I think in launch a differente syslog ...
1
vote
1answer
166 views

Perl CPAN module download fails

The download for the 'App-xml_grep2-0.14.tar.gz' perl module continually fails for me. cpan http://search.cpan.org/CPAN/authors/id/M/MI/MIROD/App-xml_grep2-0.14.tar.gz Please login with USER and ...
0
votes
2answers
2k views

Failed dependencies trying to install package 'libxml2'

I am trying to install libxml2, but my system complains about dependencies. The dependent packages exist on system. The ultimate goal is to install xml_grep2, I have been trying various methods ...
2
votes
1answer
97 views

How to list all present optical drivers?

How can I list all the installed optical drivers with udev or any other core-based tool (perl is also very good) ? P.S.: I know about the wodim --devices command, but it's an undesirable ...
0
votes
2answers
6k views

How to use the find command in Perl script?

Could someone tell me why the find command always go to the root directory but not the directory that is specified in $srceDir? my $srceDir = "/mnt/SDrive/SV/Capture Data/"; my $find_cmd = 'find ...
0
votes
1answer
141 views

Error trying to call find from perl

use warnings; use File::Find; my $srceDir = "//mnt/Share_Drive/Verizon PM&T/Capture Files/"; opendir(DIR, $srceDir) or die "Can't open $srceDir: $!"; my @files = (find -type f -newermt "12 Feb ...
4
votes
5answers
5k views

How can I split a text file into multiple text files using Perl?

I have a file ABC_TabDelim.txt that contains the following: 00:00:00:00 00:00:05:00 01SC_001.jpg 00:00:14:29 00:00:19:29 01SC_002.jpg 00:01:07:20 00:01:12:20 01SC_003.jpg 00:00:00:00 00:00:03:25 ...
1
vote
1answer
1k views

Identify text/ascii files in Linux/Solaris

I have a little project to build bash script that search in the OS ( Linux/Solaris ) the current IP address from files and replace them with other IP address. The problem is that IP address could be ...
1
vote
3answers
680 views

linux/solaris + verify duplicate valid IP address from file

what the best way to find duplicate IP from file ( I have ksh script in this script I need to write function that check for duplicate IP ) for example if IP - 192.1926.23.52 exists twice in file - ...
5
votes
2answers
344 views

Getting or cloning the users current terminal?

I have to work with a script that forks and launches an instance of xterm in order to display log output in one window and have an interactive interface in the other. Personally I prefer rxvt-unicode ...
2
votes
5answers
681 views

Replacing lines in files with file contents

I have several files which contain some PHP includes and I want to substitute them with the file contents. The file looks like foo <?php include("file1.php"); ?> bar baz <?php ...
2
votes
2answers
88 views

'tie' [nonexisting] files to programs

Recently, I just had an idea which turned out to be pretty useful under certain circumstances. But first some simple explanation: In Perl, you have the option to tie variables to some functions ...
1
vote
2answers
125 views

No perldoc for POSIX?

On some other systems, like Ubuntu, perldoc POSIX works, but on Arch, %> perldoc POSIX No documentation found for "POSIX". %> perldoc /usr/lib/perl5/core_perl/POSIX.pm No documentation found ...
0
votes
1answer
2k views

Whats the most efficient way of adding milliseconds to this code?

#----------------------------------------------------------------------------- # # Get time string # #----------------------------------------------------------------------------- # sub formatTime ...
1
vote
1answer
756 views

Linux + replace STRING/WORD in file according to rule

My target is to replace any word/string/Any characters in file with new word/string according to the following rules: If numeric characters on the left side of word/string then we not replace the ...
3
votes
1answer
334 views

Use all system memory in Solaris

I am doing server testing and intentionally trying to crash a virtual Solaris server by using all memory. Server has a ulimit of 15 GB (several hundred GB of total system/swap memory). Is there a ...
0
votes
1answer
507 views

linux + perl + replace any WORD in file with special characters with condition

Example1 work fine when I want to replace OLD_TEXT with NEW_TEXT ( its replace also all special characters as $@^%)(_+`:; etc ..) example1 export OLD_TEXT='$$OLD_WORD$$' export ...
0
votes
1answer
261 views

Issue with installing CPAN XML::RSS

I'am running debian on my server and want to install the CPAN module XML::RSS. But I get this error: http://pastebin.com/5syPaQfe (Pastebin because it's really long) I'am trying to install ...
2
votes
1answer
2k views

Email picture attachments as inline along with the email body

I'm right now working with a script for emailing attachment (.png pics). Since I'm using mutt command with -a option, the email is sent as a mail attachment. I want these .png pictures to be mailed ...
2
votes
4answers
2k views

Replace all but a set of characters in a file with newline

how to delete all characters in file except numbers and "." , each word (numbers/dot) should be in new line in file see example2 the solution can be with sed or awk or ksh syntax remark - ...
0
votes
3answers
83 views

Fixing header and print

I have header starting with '>' and I want fix the header by keeping first word and removing other shown as in output.txt and print it input.txt >AGAJ01065549.1 ...
0
votes
3answers
1k views

Split and print

I have tab-demlimted text file with 50,000lines. I want to split the first column and print as shown in output.txt Input.txt rt|371443144|mb|MN556661.1| 2200443 A rt|371443344|mb|MN556645.1| ...
6
votes
2answers
4k views

Replacing missing value blank space with zero

I have input.txt tab-delimited text file around 30K lines, I would like to check each row (s1..s30K lines) for missing value (i.e blank space) and fill the missing value with zero value.See out.txt ...
2
votes
2answers
3k views

Fetch values from plist file on Linux

I have bash script which was written for OS X and now ported to Linux. I don't have access to the Linux box. The bash script would read values from plist files using the defaults read and PlistBuddy ...
0
votes
1answer
1k views

/bin/sh: ./check-dependencies.pl: not found — but check-dependencies.pl exists!

I'm trying to build Moses, but when I run make I get the following output: minakshi@minakshi-Vostro-3500:~/Desktop/working-dir/moses/scripts$ make release # Compile the parts make all make[1]: ...
7
votes
5answers
15k views

invalid SSL_version specified at /usr/share/perl5/IO/Socket/SSL.pm line 332

Since I upgraded my PC from (k)ubuntu 12.04 to 12.10 I receive this error message when trying to send an email using sendemail. Installing an older version of IO::Socket::SSL is not an option. I ...
2
votes
1answer
259 views

Combining files with 4 columns each, into 4 files for each column [closed]

So I have a bunch of text files which look like this: T1 r1 a b c d r2 d e f g ... T2 r1 h i j k r2 l m n o ... And I want to make FOUR different text files in the following ...
1
vote
5answers
232 views

frequency of occurence

I have a tab-delimited text file, that is around 3K lines long. I want to calculate frequency of data appearing in it, in 10,000 ranges. Input.txt Price 500 1500 10001 15000 17000 ...
2
votes
4answers
204 views

Output some sections of a text file [closed]

I have input like the following: >gi|481443199|gb|MH447771.1| 49 0 0 0 1 50 0 0 1 0 >gi|987078004|gb|RTYJ01067061.1| 412 0 0 1 ...
1
vote
1answer
176 views

problem occur during installation of moses scripts [duplicate]

Possible Duplicate: /bin/sh: ./check-dependencies.pl: not found — but check-dependencies.pl exists! I obtain an error when I compile moses-script, which reads as follows: ...
3
votes
3answers
2k views

Average rows with same first column

Given a file with two columns: Id ht 510 69 510 67 510 65 5l0 62 510 59 601 29 601 26 601 21 601 20 I need a way to coalesce all rows with the same ID into one that has an average height. In this ...
3
votes
2answers
274 views

Bash error message on a mac using Perl

I'm trying to run basic functions on Perl (Mac) but I get the same error message all the time. I managed to run programs like the simple 'hello, world' example. They work fine: $ perl -w hello.pl ...
2
votes
4answers
6k views

Extracting column from comma separated text

I have a long comma-separated delimited file with 20K lines. Here's a sample: "","id","number1","number2","number3","number4","number5","number6","number7" ...
0
votes
1answer
95 views

How to get rows between lines?

I have a perl oneliner: echo -e 'sla\ndfjAAAAk\nsaljdfla\nsjdfBBBBsadf\njasdf' | perl -E 'my $_ = do { local $/; <> }; say join qq!\n!, m!\QAAAA\E\K(.*?)(?=\QBBBB\E)!gs' k saljdfla sjdf it ...
10
votes
4answers
2k views

Why is Perl installed by default with most Linux distributions?

Just curious. The title says it all: Why is Perl installed by default with most Linux distributions?
2
votes
3answers
2k views

Debian Wheezy and perl modules installed into /root not system

I have small problem cause everytime i issue cpan YAML or try to install any perl module it install's it inito /root/perl5 and with this any other user cannot use modules that I've installed as a ...
4
votes
6answers
458 views

What is the easiest way to check if column A and B values goes both ways with AWK? [closed]

What is the easiest way to check if column A and B values goes both ways? Output to check: Mike John John Mike Pamela Barbara Barbara Pamela Mike Paul Roger Paul Desired output Mike <-> ...
1
vote
2answers
870 views

What scripting language or platform to use for web page downloads and screen interaction? [duplicate]

Possible Duplicate: Does anybody here have experience in automating some tasks in web applications using curl? Here is what I need to do? Wondering what platform is most suited - easy to ...
2
votes
3answers
123 views

Need to parse a double entry table with two pairs

I have this two-entry table resulting from a program output: Variable1 : Value1 Variable2 : Value2 Variable3 : Value3 Variable4 : Value4 Variable5 : Value5 Variable6 : Value6 ...
6
votes
2answers
371 views

Trying to do arithmetic in Perl rename tool (Debian)

Let's suppose I have five mp3 files: 01-trackfoo.mp3 02-trackbar.mp3 03-trackbaz.mp3 04-trackabc.mp3 05-trackxyz.mp3 Now I give a quick listen to the files (just mplayer on console will do the ...
0
votes
2answers
215 views

Getting data from matching list

list.txt GETID_17049_knownids_1/2_Confidence_0.625_Length_2532 GETID_9248_knownids_6/10_Confidence_0.439_Length_2474 GETID_11084_knownids_3/3_Confidence_0.600_Length_1451 ...
1
vote
4answers
6k views

sed/awk/perl - delete spaces between two strings/words + solaris 10

please advice how to delete the spaces between "=" to the value/string ( after the "=" character) , should be implemented by awk or sed or perl command and command must to fit for solaris OS , ( ...
4
votes
2answers
175 views

Column mismatch and substituting

input.txt (tab-delimted) TTTTOTTT00000000008 RTTTT899 5.00E-28 TTTTOTTT00000000046 RTTTWRR 3.00E-31 TTTTOTTT00000000051 2.00E-11 TTTTOTTT00000000051 7.00E-12 TTTTOTTT00000000054 ...
2
votes
2answers
384 views

Get row data for non-matching column values

I want to read the file (1600 rows) and get rows only the columns have different values (sno1, sno2, sno3 & sno4-should be not be equal value) and it should be above 50%.The example of output ...
3
votes
2answers
435 views

Print row contain maximum and minimum value

I need to read the file (contains 16K rows)and print the entire row if any of columns and all columns contains max value (100) and all columns contain min value (0).The ouput example is given ...
0
votes
1answer
216 views

Bugzilla email_in.pl script will take 111 hours to complete - how can I change that?

I have an old Bug tracking system, with about 20k bugs. We have installed a new bugzilla system, and part of the initiation will be to import all the bugs from the old system to the new. I am able to ...
3
votes
2answers
2k views

Where are the command-line options to perl documented?

On StackExchange I came across a command that looked like this: perl -pe ... Curious what the -pe options meant, I did man perl. This is the synopsis of that man page: perl [ -sTtuUWX ] [ ...
2
votes
1answer
236 views

Why does this simple Perl client not work?

I am fairly new to IPC with sockets and expect this issue is a simple one to resolve. I'm trying to understand why I cannot get this example script from perldoc perlipc to run on my Ubuntu setup: ...
0
votes
1answer
137 views

How do I get bcvi installed and working (with Cygwin and Perl 5.8.8)?

I'm trying to install bcvi (under Cygwin), and there are apparently no directions that apply to this setup. The directions at http://sshmenu.sourceforge.net/articles/bcvi/#installation state that ...