Questions tagged [perl]

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 graphics programming, system administration, network programming, finance, bioinformatics, and other engineering applications.

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2
votes
1answer
316 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 ...
2
votes
5answers
304 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
232 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 ...
3
votes
2answers
398 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 ...
0
votes
1answer
107 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 ...
4
votes
6answers
996 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 <-> John ...
0
votes
2answers
553 views

Linux - get shared memory values from Perl script

I'm trying to get shared memory information from a linux box. I'm looking for shmmax, shmmni, shmall, msgmax, msgmni, semmsl, semmns etc. How to get all those values from a Perl script. any help is ...
2
votes
3answers
176 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 ...
0
votes
2answers
261 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 GETID_15916_knownids_10/...
4
votes
2answers
251 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 5.00E-...
3
votes
2answers
752 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 input....
0
votes
1answer
320 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 ...
0
votes
1answer
193 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 ...
0
votes
2answers
782 views

Perl-Minimum & Maximum value [closed]

input file Xm_ABL1 Geneious extracted region 1 168 . + . Name=Extracted region from gi|371443098|gb|JH556762.1|;Extracted interval="3512970000000 -> 3514640000000" Xm_ABL1 Geneious ...
1
vote
2answers
1k views

Perl piping some out of script and some to the screen

How do I pipe some output to screen and some other selected output, out of the Perl script?
2
votes
1answer
214 views

perl-get input, check conditions

cat input1.txt ##gff-version 2 ##source-version geneious 5.6.4 Xm_ABL1 Geneious CDS 1 168 . + . Name=Xm_ABL1;created by=User;modified by=User;ID=...
2
votes
1answer
281 views

Perl- Adding underscore and sorting rows

As I am biologist and new to perl, I would like to get help of perl expert cat input.txt ##gff-version 2 ##source-version geneious 5.6.3 gi371443188gbJH5566721_extraction_reversed Geneious CDS ...
7
votes
2answers
2k views

Installing CPAN dists not in the Arch repos

There's a lot of CPAN distributions in the Arch repositories, but not all of them. How should I handle a situation when I need a dist that is not already in the repos? Should I use the cpan program ...
3
votes
2answers
2k views

Parsing a text-file table and aggregating information

I have long text file with the following columns, space-delimited: Id Pos Ref Var Cn SF:R1 SR He Ho NC cm|371443199 22 G A R Pass:8 0 1 0 0 cm|...
0
votes
1answer
167 views

knock on Scientific Linux 6.1? (perl script for knocking?)

I have an OpenWrt router where I installed knockd: knockd.conf [options] logfile = /var/log/knockd.log [openSSH] sequence = 7000,8000,9000 seq_timeout = 5 command = /usr/...
2
votes
2answers
816 views

find command for the newest 500 files in a directory tree and also be POSIX compliant

I am looking for a single line shell script or unix command to find the newest 500 files in a directory. Major constraints are it should be POSIX complaint and the directory can have tons of files.
1
vote
1answer
3k views

Connect to a remote mysql server with bash php or perl

What is the best and lowest resource way to connect to a remote mysql server (server1.example.com) and execute queries like INSERT into SERVICES (user, id) ($user, $id) from server2.example.com? Is ...
2
votes
1answer
131 views

Solaris “clean” group files (or for that matter any text file)

I am looking to find a way to script a cleaning operation on the /etc/group file on a large number of servers. Looking for users in a particular group more than once. i.e. somegroup::100000:userA, ...
3
votes
1answer
281 views

Is it a good idea to supplement shell script with perl purely for use of regex?

I'm looking for a simple way to utilize regex in a UNIX shell script where not every system will have perl extensions built into grep. What is really helpful about perl regex here is back/forward ...
0
votes
1answer
1k views

install RPM packages using perl

I'm trying to install RPM package using 'yum' through perl. But, the package is prompting to enter 'Y/N' during the install. How can i do a silent install?
2
votes
3answers
1k views

How to move files into newly created directory on condition in shell/perl

It was a mess of music files and directory. It is needed to perform the below operation over multiple directories at once: If the directory contains ".jpg" files, then create a new directory "...
0
votes
1answer
229 views

How to get the filename if particular regexp is present in the file in Perl

In a directory containing many files, if a particular regexp (or format) was found in file, I'd like to get that filename Example: If the word "rama" is found in file called ramayana, print the ...
6
votes
1answer
4k views

Escaping of meta characters in basic/extended posix regex strings in grep

Is it possible to escape all meta characters of a string inside a variable before passing it to grep? I know similar question has been asked before on SE (here) and also a good explanation here, but I ...
4
votes
1answer
2k views

Query DHCP server leases from Perl script

I have a Windows 2003 server and need to poll the DHCP lease information from it with a perl script that is running on a Ubuntu server. Then I need to analyze & store the information in a mysql ...
0
votes
2answers
1k views

Need to install MySQL Client libaries but RPM not installing them

I'm trying install the MySQL Client libraries for the Perl Mod of the same name but when I run sudo rpm --install -v --allfiles MySQL-client-5.5.16-1.linux2.6.i386.rpm and querying the rpm database ...
2
votes
4answers
5k views

Extract IP address from a string

The Linux host command returns: hostA.domain.com has address xx.xxx.xxx.xx How do I get just the IP address and put it in the $ipaddr variable? open(FILE, "hostlist.txt") or die("Unable to open ...
10
votes
6answers
3k views

Delete lines beginning with #

How do I delete lines beginning with a #, given that there can be whitespace on the left and right of the #? # Master socket provides access to userdb information. It's typically
2
votes
1answer
1k views

How do I make a droplet/.app in platypus for my unix command?

This is my sample code from the platypus tutorial. I am trying to make it work with a command named pymol, and I want it to open .pdb files or open just pymol. I know nothing about perl, but I have ...
11
votes
3answers
12k views

Regex & Sed/Perl: Match word that ISN'T preceded by another word

I'd like to use sed or perl to replace all occurrences of a word that doesn't have a certain word in front of it. For example, I have a text file that contains a plot of a movie and I want to replace ...
2
votes
1answer
756 views

How to insert a first column to many files + how to convert unix time to normal time

There are many-many files in a directory that has e.x.: the following content: INPUT: root 1324711901 sshd 1272725792 And I'm searching for a solution how to convert the content of the ...
2
votes
2answers
539 views

perl regex replacing globally when global not selected

I'm using Ubuntu 11.04 and wrote a small script that searches within text files for certain "tokens" and replaces with some a prewritten snippet from a template file of the same name. The text files ...
3
votes
3answers
289 views

What does . match?

In working with regular expressions, I have been told that a dot character . will match everything. Except for newlines \n. Are there any other exceptions? What about the NUL character \0, or the ...
4
votes
1answer
4k views

How race conditions affect reads and writes (that happen at the same time)

Let's say I open a file a for reading. What if an application, let's call it aWriter writes to this file in random intervals. Are there any possibilities of me receiving improper file contents if I ...
2
votes
4answers
6k views

ncurses based menus

How can I build an ncurses based menu? Are there any other solutions for building "menus" for use on the console? I just need an "inter-operating system" (all non-windows :P) solution. Are there any ...
1
vote
1answer
954 views

Need command-line program to download all of http:// https:// scp:// ftp:// style links (on e.g. ubuntu)

I'm writing a perl program where I want to accept all kinds of "file names" from the user, including /home/foo/bar.txt and scp://server/some/file.txt or whatever. And then I thought that if I can find ...
1
vote
1answer
1k views

Find server with small ping latency (my script, but can anyone write it in e.g.: Perl?) [closed]

I want to download OpenBSD with FTP with a script, and I want to download it from a server that is near me. So I want to choose a mirror that has low "ping latency". I wrote a little script, that ...
2
votes
2answers
276 views

Perl find and replace is writing every file

Here's the test script I'm running matt@server:~ $ cat test.sh #!/bin/bash mkdir test cd test echo "has the string foo" > yes.txt echo "hasn't the string" > no.txt ls -l --time-style=full-iso ...
1
vote
4answers
3k views

Using regex to see if a UNIX process is up

In UNIX, I am checking to see if a process is up by executing the following command; E.g. psg dtllst pe99 This returns the following output if the process is running; UID PID PPID C ...

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