Description

Here we have command-line utilities for popular Bio::Perl classes.

Specifically:

• bioaln: Bio::SimpleAlign with additional methods
• biopop: Bio::PopGen which can be converted from Bio::SimpleAlign; and additional methods
• bioseq: Bio::Seq with additional methods
• biotree: Bio::Tree with additional methods

The motivation is to allow BioPerl users from writing full-blown scripts for routine manipulations of sequences, alignments, trees, and others. For common operations of sequences and alignments, Bio::BPWrapper makes it easy to create workflows with a single BASH script containing a combination command-line calls: no Perl or BioPerl coding is necessary.

Internally, the programs follow a "Wrap, don't Write" design principle. That is, we have full faith in the robustness of the BioPerl development framework. As such, methods here should all be wrappers to BioPerl methods so that exceptions can be handled properly by BioPerl.

The Bio::BPWrapper module also include some useful methods which are not part of Bio::Perl.

Install & Test from git:

You need Perl 5.010 or later. There are other Perl dependencies, but the package will check and install that.

    $ git clone https://github.com/bioperl/p5-bpwrapper
    $ cd p5-bpwrapper
    $ cpan Module::Build  # may need sudo
    $ perl ./Build.PL
    $ ./Build installdeps
    $ ./Build
    $ make check
    $ ./Build install # may require sudo or root access

Get Help

Each script, bioaln, biopop, bioseq and biotree give shorter usage help when given command-line option --help. Manual-page help is also giving the option --man.

Documentation is maintained in this project's wiki.

A help file with use cases is maintained at: http://diverge.hunter.cuny.edu/labwiki/Bioutils

Developers, Contact, Citation

• Yözen Hernández
• Pedro Pagan
• Girish Ramrattan
• Weigang Qiu, City University of New York, Hunter College (Correspondence: weigang@genectr.hunter.cuny.edu))
• If you find the tools useful, please cite: Y. Hernández, P. Pagan, G. Ramrattan, & W.-G. Qiu. (2015). Bp-utils (Release 1.0): BioPerl-based command-line utilities for manipulating sequences, alignments, and phylogenetic trees. URL: https://github.com/bioperl/bp-utils.