Rose Mcgowan Bio
Bio::Index::Swissprot is a Perl Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format). SYNOPSIS # Complete code for making an index for several # Swissprot files use Bio::Index::Swissprot; use strict; my $Index_File_Name = shift; my $inx =...
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Bio::Graphics::Feature is a simple feature object for use with Bio::Graphics::Panel. SYNOPSIS use Bio::Graphics::Feature; # create a simple feature with no internal structure $f = Bio::Graphics::Feature->new(-start => 1000, -stop => 2000, -type => transcript, -name => alpha-1...
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License: Freeware | Size: 4.7 MB | Download (100): Bio::Graphics::Feature Download |
Bio::Graphics::Glyph::alignment is the "alignment" glyph. SYNOPSIS See L< Bio::Graphics::Panel > and L< Bio::Graphics::Glyph >. This is identical to the "graded_segments" glyph, and is used for drawing features that consist of discontinuous segments. The color intensity of each segment is...
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Bio::NEXUS::HistoryBlock is a Perl module that represents a HISTORY block of a NEXUS file. SYNOPSIS $block_object = new Bio::NEXUS::HistoryBlock(history, $block, $verbose); This is a class representing a history block in NEXUS file METHODS new Title : new Usage : block_object = new...
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Rose::URI is a standalone URI class allowing easy and efficient manipulation of query parameters and other URI components. SYNOPSIS use Rose::URI; $uri = Rose::URI->new(http://un:pw@foo.com/bar/baz?a=1&b=two+3); $scheme = $uri->scheme; $user = $uri->username; $pass = $uri->password;...
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Rose::HTML::Objects is a Perl object-oriented interfaces for HTML. SYNOPSIS use Rose::HTML::Form; $form = Rose::HTML::Form->new(action => /foo, method => post); $form->add_fields ( name => { type => text, size => 20, required => 1 }, height => { type => text, size => 5, maxlength => 5...
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Bio::Graphics::Panel is a Perl module to generate GD images of Bio::Seq objects. SYNOPSIS # This script parses a GenBank or EMBL file named on the command # line and produces a PNG rendering of it. Call it like this: # render.pl my_file.embl | display - use strict; use Bio::Graphics;...
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License: Freeware | Size: 5.7 MB | Download (99): Bio::Graphics::Panel 1.5.2_005 Download |
Bio::Graphics::FeatureFile is a set of Bio::Graphics features, stored in a file. SYNOPSIS use Bio::Graphics::FeatureFile; my $data = Bio::Graphics::FeatureFile->new(-file => features.txt); # create a new panel and render contents of the file onto it my $panel = $data->new_panel; my...
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License: Freeware | Size: 4.7 MB | Download (99): Bio::Graphics::FeatureFile Download |
Bio::Phylo::Manual is a Perl module that contains a Bio::Phylo v.0.14 user guide. This is the manual for Bio::Phylo. Bio::Phylo is a perl5 package for phylogenetic analysis. For installation instructions, read the README file in the root directory of the distribution. The stable URL for the...
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Bio::NEXUS::Node is a Perl module that provides functions for manipulating nodes in trees. SYNOPSIS new Bio::NEXUS::Node; METHODS new Title : new Usage : $node = new Bio::NEXUS::Node(); Function: Creates a new Bio::NEXUS::Node object Returns : Bio::NEXUS::Node object Args : none...
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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...
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Bio::Seq is a sequence object, with features. SYNOPSIS # This is the main sequence object in Bioperl # gets a sequence from a file $seqio = Bio::SeqIO->new( -format => embl , -file => myfile.dat); $seqobj = $seqio->next_seq(); # SeqIO can both read and write sequences; see Bio::SeqIO #...
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Rose::DB::Object::Tutorial is a guided tour of the basics of Rose::DB::Object. INTRODUCTION This document provides a step-by-step introduction to the Rose::DB::Object module distribution. It demonstrates all of the important features using a semi-realistic example database. This tutorial does...
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Rose::DateTime is a Perl module with DateTime helper functions and objects. SYNOPSIS use Rose::DateTime::Util qw(:all); $now = parse_date(now); $then = parse_date(12/25/2001 6pm); $date_text = format_date($then, "%D at %T %p"); ... use Rose::DateTime::Parser; $parser =...
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Bio::Tools::Run::PiseWorkflow is a class to create a Pise workflow using Pise application objects as methods. A workflow is defined by a set of methods which all instanciate the class PiseApplication. SYNOPSIS # First, create a Bio::Tools::Run::AnalysisFactory::Pise object: my $factory = new...
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Bio::NEXUS::Block is a Perl module that provides useful functions for blocks in NEXUS file (parent class). SYNOPSIS This module is the super class of all NEXUS block classes. It is not used specifically from a program; in other words, you dont create a new Bio::NEXUS::Block object. Other...
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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. $factory = Bio::Factory::SeqAnalysisParserFactory->new(); # obtain a parser object...
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Bio::Index::Blast is a Perl module with indexes Blast reports and supports retrieval based on query accession(s). SYNOPSIS use strict; use Bio::Index::Blast; my ($indexfile,$file1, $file2); my $index = new Bio::Index::Blast(-filename => $indexfile, -write_flag => 1);...
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Rose::Object::MakeMethods::Generic is a Perl module that can create simple object methods. SYNOPSIS package MyObject; use Rose::Object::MakeMethods::Generic ( scalar => [ power, error, ], scalar --get_set_init => name, boolean --get_set_init => is_tall, boolean => [ is_red,...
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Bio::Phylo::IO Perl module contains input and output of phylogenetic data. SYNOPSIS use Bio::Phylo::IO; # parsing a tree from a newick string my $tree_string = (((A,B),C),D);; my $tree = Bio::Phylo::IO->parse( -string => $tree_string, # old parser, always adds node labels -format =>...
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