Simple Bio Data

Bio::NEXUS::TaxaBlock is a Perl module that represents TAXA block of a NEXUS file. SYNOPSIS if ( $type =~ /taxa/i ) { $block_object = new Bio::NEXUS::TaxaBlock($type, $block, $verbose); } If a NEXUS block is a taxa block, this module parses the block and stores the taxonomic data....

Bio::NEXUS::TreesBlock is a Perl module that represents TREES block of a NEXUS file. SYNOPSIS if ( $type =~ /trees/i ) { $block_object = new Bio::NEXUS::TreesBlock( $block_type, $block, $verbose ); } If a NEXUS block is a Trees Block, this module parses the block and stores the tree data....

Bio::Root::Object is a core Perl 5 object. SYNOPSIS # Use this module as the root of your inheritance tree. Object Creation require Bio::Root::Object; $dad = new Bio::Root::Object(); $son = new Bio::Root::Object(-name => Junior, -parent => $dad, -make => full); See the new() method...


Platforms: *nix

Bio::Tools::Run::PiseApplication::charge is a Perl module. Bio::Tools::Run::PiseApplication::charge Bioperl class for: CHARGE Protein charge plot (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/charge.html for available values): charge (String) init...


Platforms: *nix

Data::Stag is a Perl module with structured tags datastructures. SYNOPSIS # PROCEDURAL USAGE use Data::Stag qw(:all); $doc = stag_parse($file); @persons = stag_find($doc, "person"); foreach $p (@persons) { printf "%s, %s phone: %sn", stag_sget($p, "family_name"), stag_sget($p,...


Platforms: *nix

Regression mAKEr project is a simple modular application for data investigation. This is an application to help user (mathematician) to make regression between series of data, draw grpahics, and export them into various formats by means of common graphics packages (i.e., gnuplot, plotutils). It...


Platforms: *nix

Bio::ConnectDots::ConnectDots is a top level class for connect-the-dots. SYNOPSIS use Bio::ConnectDots::DB; use Bio::ConnectDots::ConnectDots; my $db=new Bio::ConnectDots::DB(-database=>test, -host=>computername, -user=>usename, -password=>secret); my $cd=my $cd=new...


Platforms: *nix

Template::Plugin::Data::HTMLDumper is a template toolkit plugin interface to Data::HTMLDumper. SYNOPSIS [% USE Data.HTMLDumper %] [% Data.HTMLDumper.dump(myvar) %] A very simple Template Toolkit Plugin Interface to the Data::HTMLDumper module. The Data::HTMLDumper module displays output...


Platforms: *nix

Data::Diff is a data structure comparison module. SYNOPSIS use Data::Diff qw(diff); # simple procedural interface to raw difference output $out = diff( $a, $b ); # OO usage $diff = Data::Diff->new( $a, $b ); $new = $diff->apply(); $changes = $diff->diff_a(); Data::Diff computes the...


Platforms: *nix

Data::Region Perl module can define hierarchical areas with behaviors. SYNOPSIS use Data::Region; $r = Data::Region->new( 8.5, 11, { data => PageObj->new() } ); $r->data( PageObj->new() ); foreach my $c ( $r->subdivide(2.5,3) ) { $a = $c->area(0.25,0.25, 2.25,2.75); $a2 =...


Platforms: *nix

JDatabaseImport is a simple tool created to import data between different databases. How does it work? You can work with it in two ways, either using a configuration file or accessing its api using Java. Example: The following code show an example of a file called *export.xml*: < export...


Platforms: *nix

Data::Dumper module contains stringified perl data structures, suitable for both printing and eval. SYNOPSIS use Data::Dumper; # simple procedural interface print Dumper($foo, $bar); # extended usage with names print Data::Dumper->Dump([$foo, $bar], [qw(foo *ary)]); # configuration...


Platforms: *nix

Bio::Map::CytoMap is a Bio::MapI compliant map implementation handling cytogenic bands. SYNOPSIS use Bio::Map::CytoMap; my $map = new Bio::Map::CytoMap(-name => human1, -species => $human); foreach my $marker ( @markers ) { # get a list of markers somewhere $map->add_element($marker); }...


Platforms: *nix

Bio::Location::CoordinatePolicyI is an abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location. SYNOPSIS # get a location, e.g., from a SeqFeature $location = $feature->location(); # examine its coordinate computation policy print...


Platforms: *nix

Bio::PopGen::IO contains input individual,marker,allele information. SYNOPSIS use Bio::PopGen::IO; my $io = new Bio::PopGen::IO(-format => csv, -file => data.csv); # Some IO might support reading in a population at a time my @population; while( my $ind = $io->next_individual ) { push...


Platforms: *nix

Bio::Index::Blast is a Perl module with indexes Blast reports and supports retrieval based on query accession(s). SYNOPSIS use strict; use Bio::Index::Blast; my ($indexfile,$file1, $file2); my $index = new Bio::Index::Blast(-filename => $indexfile, -write_flag => 1);...


Platforms: *nix

RDF::Simple::Parser is a simple RDF/XML parser that reads a string containing RDF in XML. SYNOPSIS my $uri = http://www.zooleika.org.uk/bio/foaf.rdf; my $rdf = LWP::Simple::get($uri); my $parser = RDF::Simple::Parser->new(base => $uri) my @triples = $parser->parse_rdf($rdf); # returns...


Platforms: *nix

A Simple TimeSheet (ASTS) allows a group of people to record the hours spent working on a variety of projects. For each project, the hours can be divided into a number of different tasks. There are global projects and tasks but also personal projects and tasks for each user. The main aim is to...


Platforms: *nix

Simple Multitrack contains a set of programs that allows the simultaneous recording of an audio track while listening to a monitor mix of other tracks. This software uses the OSS audio drivers found in the Linux kernel or the CoreAudio API on Mac OS X. It has been tested on Linux 2.4.20 on a...


Platforms: *nix

GD::Simple module is a simplified interface to GD library. SYNOPSIS use GD::Simple; # create a new image $img = GD::Simple->new(400,250); # draw a red rectangle with blue borders $img->bgcolor(red); $img->fgcolor(blue); $img->rectangle(10,10,50,50); # draw an empty rectangle with...


Platforms: *nix