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Bio::PrimarySeqI is a Perl Interface definition for a Bio::PrimarySeq. SYNOPSIS # Bio::PrimarySeqI is the interface class for sequences. # If you are a newcomer to bioperl, you should # start with Bio::Seq documentation. This # documentation is mainly for developers using # Bioperl. #...
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Bio::Tools::CodonTable is a bioperl codon table object. SYNOPSIS # This is a read-only class for all known codon tables. The IDs are # the ones used by nucleotide sequence databases. All common IUPAC # ambiguity codes for DNA, RNA and animo acids are recognized. # to use use...
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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); }...
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Bio::Biblio::Patent is a representation of a patent. SYNOPSIS $obj = new Bio::Biblio::Patent (-doc_number => 1-2-3-4-5); #--- OR --- $obj = new Bio::Biblio::Patent; $obj->doc_number (1-2-3-4-5); A storage object for a patent. See its place in the class hierarchy in...
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Bio::Ontology::Ontology is a standard implementation of an Ontology. SYNOPSIS use Bio::Ontology::Ontology; # create ontology object my $ont = Bio::Ontology::Ontology->new(-name => "OBF"); # add terms, relationships ... my $bp = Bio::Ontology::Term->new(-name => "Bioperl"); my $obf =...
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Bio::Factory::SeqAnalysisParserFactoryI is a Perl interface describing objects capable of creating SeqAnalysisParserI compliant parsers. SYNOPSIS # initialize an object implementing this interface, e.g. $factory = Bio::Factory::SeqAnalysisParserFactory->new(); # obtain a parser object...
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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...
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Bio::Tools::Run::PiseApplication::freak is a Perl module. Bio::Tools::Run::PiseApplication::freak Bioperl class for: FREAK Residue/base frequency table or plot (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/freak.html for available values): freak...
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Bio::MAGE::Protocol::SoftwareApplication is a Perl module. SYNOPSIS use Bio::MAGE::Protocol::SoftwareApplication; # creating an empty instance my $softwareapplication = Bio::MAGE::Protocol::SoftwareApplication->new(); # creating an already populated instance my $softwareapplication =...
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Bio::MAGE::Protocol::Software - Software represents the software used. SYNOPSIS use Bio::MAGE::Protocol::Software; # creating an empty instance my $software = Bio::MAGE::Protocol::Software->new(); # creating an already populated instance my $software =...
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Bio::Genex::Software is Perl module with methods for processing data from the GeneX DB table: Software. SYNOPSIS use Bio::Genex::Software; # instantiating an instance my $Software = Bio::Genex::Software->new(id=>47); # retrieve data from the DB for all columns $Software->fetch(); #...
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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...
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Bio::Tree::DistanceFactory is a Perl module to construct a tree using distance based methods. SYNOPSIS use Bio::Tree::DistanceFactory; use Bio::AlignIO; use Bio::Align::DNAStatistics; my $tfactory = Bio::Tree::DistanceFactory->new(-method => "NJ"); my $stats =...
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Bio::Index::Blast is a Perl module with indexes Blast reports and supports retrieval based on query accession(s). SYNOPSIS use strict; use Bio::Index::Blast; my ($indexfile,$file1, $file2); my $index = new Bio::Index::Blast(-filename => $indexfile, -write_flag => 1);...
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Bio::Map::MappableI is an object that can be placed in a map. SYNOPSIS # get a Bio::Map::MappableI somehow my $position = $element->map_position(); # these methods will be important for building sorted lists if( $position->equals($p2) ) { # do something } elsif( $position->less_tha($p2)...
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Bio::Tree::Tree is an implementation of TreeI interface. SYNOPSIS # like from a TreeIO my $treeio = new Bio::TreeIO(-format => newick, -file => treefile.dnd); my $tree = $treeio->next_tree; my @nodes = $tree->get_nodes; my $root = $tree->get_root_node; This object holds handles to Nodes...
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Bio::Factory::SequenceFactoryI is a Perl interface that allows for generic building of sequences in factories which create sequences (like SeqIO). SYNOPSIS # do not use this object directly it is an interface # get a Bio::Factory::SequenceFactoryI object like use Bio::Seq::SeqFactory; my...
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Bio::LiveSeq::Translation is a translation class for LiveSeq. This stores informations about aminoacids translations of transcripts. The implementation is that a Translation object is the translation of a Transcript object, with different possibilities of manipulation, different coordinate...
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Bio::Tools::Run::JavaRunner is a Perl module that can run java programs. SYNOPSIS my $runner = Bio::Tools::Run::JavaRunner->new(-jar => $jar); $runner->run(); This module is probably incomplete. It is intended to be a wrapper for running java programs..
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Bio::Graphics::Glyph::cds module contains the "cds" glyph. SYNOPSIS See L< Bio::Graphics::Panel > and L< Bio::Graphics::Glyph >. This glyph draws features that are associated with a protein coding region. At high magnifications, draws a series of boxes that are color-coded to indicate the...
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