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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3answers
3k views

compare two files based on a column and print it

I have two big files of 400,000 lines. I want to compare the column 1 of the second file with column 1 of first file recursively. If they match I would like to print the whole line. It is a sorted ...
3
votes
2answers
2k views

echo test | stty -echo -> stty: standard input: Inappropriate ioctl for device

I was playing with a perl script that takes user input with the following: system( qw( stty -echo ) ); $? == 0 or die "Error unable to disable character printing.\n"; print "$prompt: "; my $input = ...
1
vote
2answers
116 views

Merging two different files with conditions

I have two different files as shown below. Content of a.txt: HDR|1|||||||||| DTL|@||||||||||| TLR||||||||||||| HDR|1|||||||||||| ...
0
votes
2answers
36 views

occurance of a string in multiple file

I have two files 1. input.txt 2. keyword.txt input.txt has contents like .src_ref 0 "call.s" 24 first 0x000000 0x5a80 0x0060 BRA.l 0x60 .src_ref 0 "call.s" 30 first 0x000002 ...
0
votes
2answers
1k 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 ...
3
votes
1answer
38 views

Filter out inconsistent data blocks

I would like to filter out rows that has inconsistent geno values in line-part blocks. In case of duplicate consistent values , I would just keep the first row. As example, 'gf345 part1' has more ...
1
vote
1answer
71 views

Assp won't start

I tried to install ASSP (Anti-Spam SMTP Proxy Server),but when I try to start it I get the following: $ perl assp.pl Perl version 5.012003 (5.12.3) is at least recommended to run ASSP 2.4.3 (14313) ...
1
vote
1answer
1k views

“Requires: perl(:MODULE_COMPAT_5.8.8)”

I use CentOS 6.5 for my server with below repository: IUS epel ces-standard-* base/upgrade/extras When I tried to update today (it's been a while I haven't updated this server), I got the ...
1
vote
1answer
152 views

How to safely move a file to another directory and remove duplicates

I want to move files from Downloads, Documents, Pictures, Music, et al to shared locations. This is for various reasons, including because I want to keep media in a central, shared place. I want to ...
1
vote
1answer
109 views

How to mention rpm to look for dependent perl modules in the system

By default rpm looks for the perl modules inside the rpm itself and throws dependency error if it is not found. For eg., I have a perl script in the rpm that uses Crypt::DES perl module. I have that ...
1
vote
1answer
157 views

Why wouldn't Perl CGI script run

I'm using Apache on CentOS and am trying to run a Perl CGI script as directory index so it will run automatically as a subdomain. I added DirectoryIndex script.cgi and added a Directory stanza noting ...
1
vote
1answer
107 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 ...
0
votes
1answer
16 views

amavisd: Unrecognized character \xBB;

I have a problem to start the amavisd. When I try to start with /etc/init.d/amavis start I get the following error: Starting amavisd: Problem in Amavis::DKIM code: Unrecognized character \xBB; marked ...
0
votes
1answer
326 views

How to convert XML file to CSV using Perl?

I'm looking for some suggestion to convert the .asn1 (CDR Data) to CSV to load to tables. As per current approach I'm using informatica B2B parser to parse the ASN file to XML than using XSD loading ...
0
votes
1answer
58 views

How to split files?

Input.txt: line.....1 line.....2 line.....3 ..... line.....3 line.....4 line.....5 ..... line.....4 line.....5 line.....6 ..... line.....5 line.....6 line.....7 ..... Condition for output file ...
2
votes
0answers
33 views

Perl failed set locale on AIX 7.1

After setting user language to Chinese with GB18030 encoding in SMIT, following env variable was added in user's .profile: LANG=Zh_CN LC_MESSAGE=%l.%c ...
2
votes
0answers
133 views

How to print the first three lines and last two lines of a file using perl?

Through the command line I draw one or several of the patterns found text.xml file: perl -ln0e 'while(/<PMResult.*?<\/PMResult>/gs) { $x=$&;print $x if $x=~/BCCEL-[1-3]/}' text.xml I ...
1
vote
0answers
10 views

Make a rpm package from the cpan compatible tree?

I always make my perl module following the CPAN-complient tree. I would like to use this tree to create a rpm file I could install on a hundreth servers. Is it possible to make a rpm package with ...
1
vote
0answers
44 views

Neutralisation of data from Windows to Unix

I just noticed that other platforms files (Windows) had to cause me many bugs, like here, in my regexes. Mostly, the line ending ^M. There seems to be many ways to do dos2unix, like here described. ...
1
vote
0answers
118 views

How can I send email without using uuencode and mute?

Is it possible to send attachment from unix/AiX without using uuencode and MUTE command? We can write a Perl script which will send email properly but without attachment, can I get the perl code ...
1
vote
0answers
63 views

Some errors have occured when I installed lucene, a perl module!

Some errors have occured when I installed lucene, a perl module: [xlwang@localhost Lucene-0.18]$ make test Running Mkbootstrap for Lucene () chmod 644 Lucene.bs PERL_DL_NONLAZY=1 ...
1
vote
0answers
74 views

Better approach to generating and adding contents to files

I have an input file like below. 1 First one 2 First two 3 First three 3 Second three I am generating 2 output files like below. #FILE1 1 First one 2 First two 3 First three #FILE2 1 ...
1
vote
0answers
93 views

Perl Script to Display Pork Offline Message

I use pork 0.99.8.1 on openSuse 11.4 for my AIM account when I don't want to use irssi + bitlbee. The only problem I have encountered so far is that offline messages are not displayed. I just get a ...
0
votes
0answers
21 views

What “bad list v: No such file or directory at -/usr/libdata/per15/OpenBSD/Pkg_Add.pm line 1115” means?

I recently installed OpenBSD on an old laptop from 2005 and I am trying to install nano and then xfce4 and then a few other programs, but every time I try to use pkg_add, I get the message: Fatal ...
0
votes
0answers
17 views

error for installing Math module CDF in perl

I am trying to install Math::CDF in perl I tried both cpan -i Math::CDP and install from downloaded files both end up in error after enter make install: Running make install make[1]: Nothing to be ...
0
votes
0answers
15 views

capture tmux screen and process with shell command

is there a way to capture text currently on the screen of a tmux session and pipe it into a shell command then display the output? I was hoping to use something like this with Oracles sqlplus to do ...
0
votes
0answers
24 views

Unable to access bugzilla url

Actually I installed bugzilla in one vm. It is using mod_perl and Email configured. Everything working fine. In browser i access the url http://MY_server_IP/bugzilla working fine. In another vm, I ...
0
votes
0answers
28 views

Can't locate Cairo.pm in @INC

I am running prinseq for trimming my data but got this error: Can't locate Cairo.pm in @INC (@INC contains: /home/A/software/vcftools_0.1.11/perl How do I install this?
0
votes
0answers
15 views

Building debian package of Perl module with Module::Build and pbuilder

I have a Perl module that I package for Debian using pbuilder. The module has a Makefile.PL. The debian/rules file is very simple: #!/usr/bin/make -f PACKAGE := $(shell dh_listpackages) %: ...
0
votes
0answers
18 views

To visualise look-behind in this Regex

I am using Regexr to visualise my regexes now. I need look-behind but Javascript does not support it, example code here. The project code base seems to be dependent Javascript (NodeJS) in Github. I ...
0
votes
0answers
91 views

Folding in vimrc does not work as expected

I added these to my vimrc: set foldenable set foldmethod=syntax set foldlevelstart=1 let javaScript_fold=1 " JavaScript let perl_fold=1 " Perl let php_folding=1 ...
0
votes
0answers
136 views

Unable to install Crypt::SSLeay perl module on RHEL 5.7 (x86_64)

Here is the scenario, actually my RHEL 5.7 (x64_86) server don't have internet connection. but I want to install Crypt::SSLeay perl module on that server. So I downloaded it from CPAN & then ...
0
votes
0answers
90 views

zip command is failing during high memory usage

We have several perl scripts, which generates and emails reports. The script that emails the files expects a .zip extension. The report scripts generates a .txt or .xls file and then runs the ...
0
votes
0answers
70 views

Install application on barebone linux board without internet

I'm kind of new to using linux for hardware development. I made a C program which uses ExifTool, and it works fine on the desktop. The ExifTool have to be installed and runs on Perl. I can cross ...
0
votes
0answers
50 views

Hit “sasl_decode error=-1” while sending mail via sendmail server on RHEL

Having installed sendmail and openwebmail on RHEL workstation 6.3, I can send email through webmail(cgi-bin/openwebmail/openwebmail.pl), but failed to interact with sendmail server in Perl script as ...
0
votes
0answers
62 views

replacement script multiple targets

I have this input file Name=code_229633_138;isoforms=1 Name=code_229633_138 Name=code_229633_138;Target=R77_09738T0 Name=code_230519_1;isoforms=1 ...
-2
votes
0answers
24 views

Extracting soft clipped sequences

I have a file like this SRR959756.2011 256 20S24M GCCGGGCGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAG SRR959756.2011 256 19S22M3S GCCGGGCGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAG SRR959756.2011 256 ...