BOL: Related items

Machine learning in Perl

Jit — Sun, 16 Feb 2020 15:32:03 -0600

this is a fourth blog post in the Machine learning in Perl series, focusing on the AI::MXNet, a Perl interface to Apache MXNet, a modern and powerful machine learning library.

If you're interested in refreshing your memory or just new to the series, please check previous entries over here: 1 2 3

https://metacpan.org/pod/AI::MXNet

Address of the bookmark: http://blogs.perl.org/users/sergey_kolychev/2018/07/machine-learning-in-perl-kyuubi-goes-to-a-modelzoo-during-the-starry-night.html

Download mutliple fasta file from NCBI in one GO!!

Rahul Agarwal — Wed, 21 Aug 2013 08:13:30 -0500

if you have less time, then use three ways mentioned in bookmark link to extract/download all fasta sequences in single click given that you already have a list of GIs or accession IDs .

Alternatively, use one liner perl script:

perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @ARGV' GIs.txt >sequence.fasta

where GIs.txt contains a list of GIs or accession IDs.

(from :http://edwards.sdsu.edu/labsite/index.php/robert?start=5)

Address of the bookmark: http://edwards.sdsu.edu/labsite/index.php/robert/380-ncbi-sequence-or-fasta-batch-download-using-entrez

Awesome perl frameworks, libraries and software - PART 5

Neel — Fri, 07 Jul 2017 04:12:47 -0500

robelix/sub2srt - subtitle converter
reyjrar/graphite-scripts - A Collections of Scripts for Working with Graphite
regilero/check_nginx_status - Nagios check for nginx status report
omniti-labs/resmon - resmon
motemen/App-htmlcat - redirect stdin to web browser
moose/Moo - Minimalist Object Orientation (with Moose compatibility)
miyagawa/fastpass - Tiny, XS free, standalone and preforking FastCGI daemon for PSGI
miyagawa/Filesys-Notify-Simple - Simple and dumb file system watcher
mhop/fhem-mirror - Branch 'master' is a read-only-mirror of svn://svn.code.sf.net/p/fhem/code which is updated once a day. On branch 'enocean' I am going to add some Enocean-Devices
lopnor/Plack-App-DAV - simple DAV server for Plack
kazuho/url_compress - a static PPM-based URL compressor / decompressor
jnthn/6model - Just a place that I'm keeping some meta-model prototyping; anything that matters will make it to another repo (e.g. nqp-rx one or Rakudo one) at some point.
jasonhancock/nagios-puppetdb - Nagios plugins and pnp4nagios templates related to Puppetlab's PuppetDB project.
goccy/p5-Compiler-Parser - Create Abstract Syntax Tree for Perl5
cgutteridge/Grinder - Create RDF data from spreadsheets or CSV
c9s/Plack-Middleware-OAuth - Plack Middleware for OAuth1 and OAuth2
bzip2-cuda/bzip2-cuda - Parallel implementation of bzip2 using cuda
alanstevens/ChocoPackages - Chocolatey Nuget Packages
SoylentNews/slashcode - The slashcode repository for SoylentNews. The initial code base was uploaded as it appeared on Sourceforge as of the last commit in September 2009
Miserlou/XSS-Harvest - XSS Weaponization

getopts.pl file

Jit — Fri, 15 Jun 2018 04:43:03 -0500

SSPACE_longread complain for getopts.pl file.

To resolve this, download and have in SSPACED-Longreads folder.

Cheers :)

Computational, but a Biologist !

LEGE — Thu, 09 Apr 2026 00:44:46 -0500

There was a time when doing biology
meant working only with your hands—
and that alone was seen
as “real science.”

People using computers were often seen
as helpers, not leaders—
useful, but not essential.

Sometimes, the criticism was direct.
Sometimes subtle.
But the message was the same—
this work doesn’t really count.

Then biology changed.
The questions became bigger,
and experiments alone
were no longer enough.

Organizing knowledge by hand worked once.
Now it needs computers—
to handle scale, speed, and complexity.

Some patterns are simply invisible
if you look at one sample.
You need many—
and the right tools to understand them.

So we started building maps—
of genomes, cells, and systems.
Not perfect,
but extremely useful.

Ideas also had to become clearer.
It’s no longer enough to say something sounds right—
you have to measure it.

The divide between “types” of biologists
never really made sense.
We are solving the same problems—
just in different ways.

Progress didn’t wait for agreement.
It moved forward with data,
with code,
and with careful analysis.

What matters now is simple:
• Biology depends on computation
• Coding is an important skill
• Statistics helps us think clearly
• And the people building these tools
are shaping the future of science

How to install Perl modules manually, using CPAN command, and other quick ways

Jit — Fri, 12 Jul 2013 07:20:24 -0500

As a bioinformatics programmer, and crunchy data analyser you need to install several perl modules and dependencies. Installing Perl modules manually by resolving all the dependencies is tedious and annoying process. Some of the packages like GD is the real pain.

However, Installing Perl modules using CPAN is a better solution, as it resolves all the dependencies automatically. In this article, let us review how to install Perl modules on Linux ( which is prefereced amonst bioinformatician) using both manual and CPAN method.

When a Perl module is not installed, application will display the following error message. In this example, XML::Parser Perl module is missing.

Can't locate XML/parser.pm in @INC (@INC contains:
/usr/lib/perl5/5.10.0/i386-linux-thread-multi
/usr/lib/perl5/5.10.0
/usr/local/lib/perl5/site_perl/5.10.0/i386-linux-thread-multi
/usr/local/lib/perl5/site_perl/5.10.0
/usr/lib/perl5/vendor_perl/5.10.0/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.10.0 /usr/lib/perl5/vendor_perl
/usr/lib/perl5/site_perl/5.10.0 .)

Manual Method of Perl Module Installation

Install Perl Modules Manually

This manual method is very useful when your computer or server is not connected to the Internet.

Download Perl module:
Go to CPAN Search website and search for the module that you wish to download. In this example, let us search, download and install XML::Parser Perl module. I have downloaded the XML-Parser-2.36.tar.gz to /home/download

# cd /home/download
# gzip -d XML-Parser-2.36.tar.gz
# tar xvf XML-Parser-2.36.tar
# cd XML-Parser-2.36

Build the perl module:
Build by running Makefile.PL, remember the case sensitivity, make and make test.

# perl Makefile.PL
Checking if your kit is complete...
Looks good
Writing Makefile for XML::Parser::Expat
Writing Makefile for XML::Parser
# make
# make test

Install the perl module:
Now your package is ready to install.

# make install

As a newbie it looks pretty simple, and one go. But, luckily this is a very simple one module with no dependencies. Typically, Perl modules will be dependent on several other modules. Just imagine chasing all these dependencies one-by-one, thinking ... oh ye I got it. That will be very painful and annoying task. I recommend the CPAN method of installation as shown below.

Install Perl Modules using CPAN automatically

Logically, you should must have the CPAN perl module installed in your server or computer before you can install any other Perl modules using CPAN. I know you are laughing, "to install a perl module you need another perl module" ;)

Lets verify whether CPAN is already installed:

To install Perl modules using CPAN, make sure the cpan command is working. Following are the error message when CPAN module is not installed.

# cpan
-bash: cpan: command not found

# perl -MCPAN -e shell
Can't locate CPAN.pm in @INC (@INC contains:
/usr/lib/perl5/5.10.0/i386-linux-thread-multi
/usr/lib/perl5/5.10.0
/usr/local/lib/perl5/site_perl/5.10.0/i386-linux-thread-multi
/usr/local/lib/perl5/site_perl/5.10.0
/usr/lib/perl5/vendor_perl/5.10.0/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.10.0
/usr/lib/perl5/vendor_perl /usr/lib/perl5/site_perl/5.10.0 .).
BEGIN failed--compilation aborted.

Install the CPAN module using yum:
If CPAN in not installed in your system, you can use "yum" for the rescue. Dont worry biological data cruncher, this is true we are now dependent all these tiny magicians :).

# yum install perl-CPAN

Output of yum install perl-CPAN command:

Loaded plugins: refresh-packagekit
updates-newkey                       | 2.3 kB     00:00
primary.sqlite.bz2                   | 2.4 MB     00:00
Setting up Install Process
Parsing package install arguments

Resolving Dependencies
Transaction Summary
=============================================================================
Install      5 Package(s)
Update       0 Package(s)
Remove       0 Package(s)

Total download size: 1.0 M
Is this ok [y/N]: y
Downloading Packages:
(1/5): perl-ExtUtils-ParseXS-2.18-31.fc9.i386.rpm     | 30 kB     00:00
(2/5): perl-Test-Harness-2.64-31.fc9.i386.rpm         | 70 kB     00:00
(3/5): perl-CPAN-1.9205-31.fc9.i386.rpm               | 217 kB     00:00
(4/5): perl-ExtUtils-MakeMaker-6.36-31.fc9.i386.rpm   | 284 kB     00:00
(5/5): perl-devel-5.10.0-31.fc9.i386.rpm              | 408 kB     00:00

Installing     : perl-ExtUtils-ParseXS                             [1/5]
Installing     : perl-devel                                        [2/5]
Installing     : perl-Test-Harness                                 [3/5]
Installing     : perl-ExtUtils-MakeMaker                           [4/5]
Installing     : perl-CPAN                                         [5/5]

Installed: perl-CPAN.i386 0:1.9205-31.fc9
Dependency Installed:
perl-ExtUtils-MakeMaker.i386 0:6.36-31.fc9
perl-ExtUtils-ParseXS.i386 1:2.18-31.fc9
perl-Test-Harness.i386 0:2.64-31.fc9
perl-devel.i386 4:5.10.0-31.fc9
Complete!

Configure cpan the first time:
Once the CPAN is installed, you need to configure it by executing cpan, you should set some configuration parameters as shown below. I have shown only the important configuration parameters below. Accept all the default values by pressing enter.

Note: Make sure to execute “o conf commit” in the cpan prompt after the configuration to save the settings.

# cpan

Sorry, we have to rerun the configuration dialog for CPAN.pm due
to some missing parameters...

CPAN build and cache directory? [/root/.cpan]
Download target directory? [/root/.cpan/sources]
Directory where the build process takes place? [/root/.cpan/build]

Always commit changes to config variables to disk? [no]
Cache size for build directory (in MB)? [100]
Let the index expire after how many days? [1]

Perform cache scanning (atstart or never)? [atstart]
Cache metadata (yes/no)? [yes]
Policy on building prerequisites (follow, ask or ignore)? [ask]

Parameters for the 'perl Makefile.PL' command? []
Parameters for the 'perl Build.PL' command? []

Your ftp_proxy? []
Your http_proxy? []
Your no_proxy? []
Is it OK to try to connect to the Internet? [yes]

First, pick a nearby continent and country by typing in the number(s)
(1) Africa
(2) Asia
(3) Central America
(4) Europe
(5) North America
(6) Oceania
(7) South America
Select your continent (or several nearby continents) [] 5

(1) Bahamas
(2) Canada
(3) Mexico
(4) United States
Select your country (or several nearby countries) [] 4

(2) ftp://carroll.cac.psu.edu/pub/CPAN/
(3) ftp://cpan-du.viaverio.com/pub/CPAN/
(4) ftp://cpan-sj.viaverio.com/pub/CPAN/
(5) ftp://cpan.calvin.edu/pub/CPAN
(6) ftp://cpan.cs.utah.edu/pub/CPAN/
e.g. '1 4 5' or '7 1-4 8' [] 2-16

cpan[1]> o conf commit
commit: wrote '/usr/lib/perl5/5.10.0/CPAN/Config.pm'

cpan[2]> quit
No history written (no histfile specified).
Lockfile removed.

Install Perl Modules using CPAN

Hey smile please, now you are ready with CPAN and can download modules in one line command.

You can use one of the following method to install a Perl module using cpan:

# perl -MCPAN -e 'install Bundle::BioPerl'

(or)

# cpan
cpan shell -- CPAN exploration and modules installation (v1.9205)
ReadLine support available (maybe install Bundle::CPAN or Bundle::CPANxxl?)

cpan[1]> install "Bundle::BioPerl"

In the example above, CPAN will check for Bundle::BioPerl dependencies and automatically resolves and installs Bundle::BioPerl with all the dependent Perl modules.

Quick Ways

Oh, look at your face.. smily hmm :). This is what your are looking for, a quick and best way to install Perl modules, Bioperl. Following are the the steps to download BioPerl in your server/computer.

# sudo apt-cache search perl BioPerl

Output will be like as follows:

bioperl - Perl tools for computational molecular biology
bioperl-run - BioPerl wrappers: scripts
libbio-perl-perl - BioPerl core perl modules
libbio-perl-run-perl - BioPerl wrappers: modules
libbio-samtools-perl - Perl interface to SamTools library for DNA sequencing
libbiojava-java - Java API to biological data and applications (default version)
libbiojava3-java - Java API to biological data and applications (default version)
python-biopython-sql - Biopython support for the BioSQL database schema
libbtlib-perl - library for basic sequence manipulation

# sudo apt-get install bioperl

If it is installed then flash the following message:

Reading package lists... Done
Building dependency tree
Reading state information... Done
bioperl is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.

In it is found not installed in your server or system them install all with dependencies.

You can use the same approach to install all the modules, and packages if required.

Thanks for reading. Best of luck for your research.

Perl Maven tutorial by Gabor Szabo

Jitendra Narayan — Fri, 09 Aug 2013 05:43:10 -0500

I personally reccoment this tutorial for Perl users.

More detail http://perlmaven.com/

Which Perl distribution should I choose for bioinformatics study : ActivePerl, Strawberry Perl, DWIM Perl, Citrus Perl ?

Manshi Raghubanshi — Wed, 14 Aug 2013 15:43:06 -0500

I'm new to bioinformatics and recently started learning Perl. I found several rival distributions available for Windows platform, which confuse me at the begining.

I google it and found that Strawberry comes with additional dev tools to compile CPAN modules if necessary. Whereas ActivePerl has a lot of prepackaged modules which are easier to install with PPM. In addition, DWIM Perl contains the standard Perl and a lot of extension and Citrus Perl is a binary distribution of Perl created for GUI application developers.

Now, I wonder what should I pick to get started?

Note: I am going to use BioPerl in near future.

http://dwimperl.com/

http://www.activestate.com/activeperl

http://www.citrusperl.com/

http://strawberryperl.com/

Clean the FASTA file

Jit — Thu, 03 Oct 2013 14:19:14 -0500

Mostly FASTA file contain NNN characters, which can be replace by random A T G C character with this perl script. It also print the FASTA sequence name, N's counts, nucleotide count and percentage details at command prompt/standard output.

Perl One liner basics !!

Abhimanyu Singh — Sun, 24 May 2015 09:28:33 -0500

Perl has a ton of command line switches (see perldoc perlrun), but I'm just going to cover the ones you'll commonly need to debug code. The most important switch is -e, for execute (or maybe "engage" :) ). The -e switch takes a quoted string of Perl code and executes it. For example:

$ perl -e 'print "Hello, World!\n"'
Hello, World!

It's important that you use single-quotes to quote the code for -e. This usually means you can't use single-quotes within the one liner code. If you're using Windows cmd.exe or PowerShell, you must use double-quotes instead.

I'm always forgetting what Perl's predefined special variables do, and often test them at the command line with a one liner to see what they contain. For instance do you remember what $^O is?

$ perl -e 'print "$^O\n"'
linux

It's the operating system name. With that cleared up, let's see what else we can do. If you're using a relatively new Perl (5.10.0 or higher) you can use the -E switch instead of -e. This turns on some of Perl's newer features, like say, which prints a string and appends a newline to it. This saves typing and makes the code cleaner:

$ perl -E 'say "$^O"'
linux

Pretty handy! say is a nifty feature that you'll use again and again.