Group activity

  • BioStar commented on a page titled Benchmarking Perl Module ! 616 days ago
    Benchmarking a Perl module involves measuring the performance of the module in terms of its execution time and memory usage. This can be done using the Perl Benchmark module, which provides a simple and standardized way to measure and compare the...
  • If using conda conda create --name perlENV perlconda activate perlENV conda install -c bioconda perl-bundle-bioperl conda install -c bioconda perl-bioperl
  • Installing in CONDA env You can check using which perl - it should give you the perl that's located within your conda environment. In this case, it should install things into your conda-directory. When you install packages via cpan...
  • To install BioPerl on a macOS system, you can follow these steps: Open the Terminal app on your macOS system. Install Homebrew if you haven't already installed it by entering the following command: /bin/bash -c "$(curl -fsSL...
  • If you are on Ubuntu https://packages.ubuntu.com/bionic/bioperl sudo apt-get install <name_mentioned_in_list>
  • If you are on Conda, you can try installing cpamn  https://anaconda.org/bioconda/perl-app-cpanminus and then cpanm install <name>  
  • # envname is the name of your (existing) conda env conda activate envname # cpanm is available on either conda-forge or # bioconda, so add conda-forge (or look up # how to set up bioconda if you need tools # for bioinformatics) conda config...
  • Check the perl module  Test if dependencies are met by running this perl one-liner: perl -e "use JSON::XS;"
  • #To install perl modules perl -MCPAN -e shell # go to CPAN install modeinstall Bundle::CPAN # update CPANreload cpaninstall Set::Scalar
  • Jit published a blog post List of perl special symbols ! 1760 days ago
    Perl is know for symbols !
  • Jit commented on a page titled Perl one-liner for bioinformatician !!! 2156 days ago
    This tutorial is useful https://blogs.oracle.com/linux/the-top-10-tricks-of-perl-one-liners-v2
  • Rahul Nayak created a page Benchmarking Perl Module ! 2280 days ago
    The benchmark module is a great tool to know the time the code takes to run. The output is usually in terms of CPU time. This module provides us with a way to optimize our code. With the advent of petascale computing and other multicore processor it...
    Comments
    • BioStar 616 days ago

      Benchmarking a Perl module involves measuring the performance of the module in terms of its execution time and memory usage. This can be done using the Perl Benchmark module, which provides a simple and standardized way to measure and compare the performance of Perl code.

      Here is a quick guide to benchmarking a Perl module using the Benchmark module:

      1. Install the Benchmark module: If you don't already have the Benchmark module installed, you can install it using the following command:

        cpan Benchmark

      2. Write benchmark code: Write a simple benchmark program that exercises the functionality of your Perl module. This program should take the form of a subroutine that runs the code you want to benchmark. Here's an example of a benchmark subroutine that calls a function from a hypothetical module named "MyModule":

        use MyModule; use Benchmark qw(:hireswallclock); sub benchmark_my_module { my $result = MyModule::my_function(); }
      3. Run the benchmark: Call the timethese function from the Benchmark module to run the benchmark. The timethese function takes two arguments: the number of iterations to run and a reference to the benchmark subroutine. Here's an example of how to call the timethese function to run the benchmark for 100 iterations:

        timethese(100, { 'MyModule' => \&benchmark_my_module, });
      4. Analyze the results: The timethese function will output the results of the benchmark, including the number of iterations, the total time taken, and the average time per iteration. You can use these results to compare the performance of your Perl module to other modules or to previous versions of your own module. You can also use other functions from the Benchmark module, such as cmpthese, to compare the performance of multiple modules or subroutines.

      In summary, benchmarking a Perl module involves writing a benchmark program that exercises the functionality of the module, running the benchmark using the timethese function from the Benchmark module, and analyzing the results to compare the performance of the module. The Benchmark module provides a simple and standardized way to measure and compare the performance of Perl code.

  • Jit commented on a page titled Perl one-liner for bioinformatician !!! 2414 days ago
    Convert file to lowercase dd $ dd if=input.txt of=output.txt conv=lcase tr $ tr '[:upper:]' '[:lower:]' < input.txt > output.txt awk $ awk '{ print tolower($0) }' input.txt > output.txt perl $ perl -pe '$_= lc($_)' input.txt >...
  • Install cpanm to make installing other modules easier (you'll thank us later). You need to type these commands into a Terminal emulator (Mac OS X, Win32, Linux) cpan App::cpanminus Now install any module you...
  • BioStar commented on a bookmark Perl and BioPerl Tutorials 2509 days ago
    Learn Perl module basic http://mathforum.org/ken/perl_modules.html
  • Check of array contain a string or number in it
  • Martin Jones commented on a bookmark Perl and BioPerl Tutorials 2816 days ago
    Perl books http://perltraining.com.au/notes.html https://github.com/vhf/free-programming-books/blob/master/free-programming-books.md#perl
  • $_ The default or implicit variable. @_ Subroutine parameters. $a$b sort comparison routine variables. @ARGV The command-line args. Regular Expressions $<digit> Regexp parenthetical capture...
  • Jit bookmarked Perl6 2849 days ago
    The official documentation of the Perl 6 programming language is now published! Besides online browsing and searching, you can also view everything in one file or contribute by reporting mistakes or sending patches. Language Reference &...
  • Jit commented on a bookmark Perl and BioPerl Tutorials 3053 days ago
    Learn perl in 2 hour https://qntm.org/files/perl/perl.html