Name: p5-bpwrapper
Owner: BioPerl
Description: BioPerl scripts and utilities
Created: 2014-12-14 21:09:22.0
Updated: 2017-09-14 17:18:40.0
Pushed: 2017-10-27 17:51:08.0
Homepage: null
Size: 5685
Language: Perl
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Here we have command-line utilities for popular Bio::Perl classes.
Specifically:
Bio::SimpleAlign
with additional methodsBio::PopGen
which can be converted from Bio::SimpleAlign
; and additional methodsBio::Seq
with additional methodsBio::Tree
with additional methodsThe motivation is to allow users to perform routine BioPerl manipulations of sequences, alignments, and trees without having to write full-blown scripts. 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.
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
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
The git code generally has the newest code. If git is not your thing, you can also install the last release from CPAN:
cpan install Bio::BPWrapper
cpanm --sudo Bio::BPWrapper