NAME

Alien::SeqAlignment::cutadapt - Find or install cutadapt

VERSION

version 0.05

SYNOPSIS

Command line tool:

system 'cutadapt' (list of arguments and options);
system "cutadapt  (list of argumentns and options)"; # less safe

or you can even do this to maintain compatibility with the Alien tool API

system Alien::SeqAlignment::cutadapt->cutadapt (list of arguments and options)

DESCRIPTION

This distribution provides the python tool cutadapt so that it can be used by other Perl distributions that are on CPAN. It does this by first trying to detect an existing install of cutadapt on your system. If found it will use that. If it cannot be found, it will use the Python package installer pipx to download and install cutadapt in an isolated environment for each user. Note that after installation one ends up with a tool that can be used from the shell (i.e. no need for Perl), hence uninstalling the Perl module will not uninstall cutadapt or pipx. If you would like to uninstall cutadapt, then you should use pipx to uninstall it as in:

pipx uninstall cutadapt.

Note that the installation method of pipx varies by operating system. MacOS and Windows users should have working installations of homebrew and scoop respectively to use this Perl Alien module.

METHODS

cutadapt

Alien::SeqAlignment::cutadapt->cutadapt

Returns the command name for running the CLI version of the cutadapt CLI.

SEE ALSO

• cutadapt

  Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

  Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the 3' sequencing adapter because the read is longer than the molecule that is sequenced. Amplicon reads start with a primer sequence. Poly-A tails are useful for pulling out RNA from your sample, but often you don't want them to be in your reads.

  Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter single-end and paired-end reads in various ways. Adapter sequences can contain IUPAC wildcard characters. Cutadapt can also demultiplex your reads.

• pipx

  pipx is a tool to help you install and run end-user applications written in Python. It's roughly similar to macOS's brew, JavaScript's npx, and Linux's apt.

  It's closely related to pip. In fact, it uses pip, but is focused on installing and managing Python packages that can be run from the command line directly as applications.

  How is it Different from pip?

  pip is a general-purpose package installer for both libraries and apps with no environment isolation. pipx is made specifically for application installation, as it adds isolation yet still makes the apps available in your shell: pipx creates an isolated environment for each application and its associated packages.

  pipx does not ship with pip, but installing it is often an important part of bootstrapping your system.

• Homebrew

  Homebrew installs the stuff you need that Apple (or your Linux system) didn't.

• Scoop

  Scoop is a command-line installer for Windows that: *Eliminates permission popup windows *Hides GUI wizard-style installers *Prevents PATH pollution from installing lots of programs *Avoids unexpected side-effects from installing and uninstalling programs *Finds and installs dependencies automatically *Performs all the extra setup steps itself to get a working program

• Alien

  Documentation on the Alien concept itself.

• Alien::Base

  The base class for this Alien.

• Alien::Build::Manual::AlienUser

  Detailed manual for users of Alien classes.

• Bio::SeqAlignment

  A collection of tools and libraries for aligning biological sequences from within Perl.

AUTHOR

Christos Argyropoulos <chrisarg@gmail.com>

COPYRIGHT AND LICENSE

This software is copyright (c) 2024 by Christos Argyropoulos.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.