= bio.rb - Loading all BioRuby modules
Copyright:: Copyright (C) 2001-2007
Toshiaki Katayama <k@bioruby.org>
License:: The Ruby License
$Id:$
---
(depends on autoload)
require ‘bio/appl/gcg/seq’ +++
--- = bio/appl/blast/format8.rb - BLAST tab-delimited output (-m 8) parser Copyright:: Copyright (C) 2002, 2003, 2007 Toshiaki Katayama <k@bioruby.org> License:: The Ruby License $Id:$ == Note This file is automatically loaded by bio/appl/blast/report.rb --- = bio/appl/emboss.rb - EMBOSS wrapper Copyright:: Copyright (C) 2002, 2005 Toshiaki Katayama<k@bioruby.org> Copyright:: Copyright (C) 2006 Jan Aerts <jan.aerts@bbsrc.ac.uk> License:: The Ruby License $Id: emboss.rb,v 1.9 2008/01/10 03:51:06 ngoto Exp $ ---
(depends on autoload)
require ‘bio/appl/gcg/seq’ +++
---
= bio/appl/gcg/seq.rb - GCG sequence file format class (.seq/.pep file)
Copyright:: Copyright (C) 2003, 2006
Naohisa Goto <ng@bioruby.org>
License:: The Ruby License
$Id: seq.rb,v 1.3 2007/04/05 23:35:39 trevor Exp $
= About Bio::GCG::Seq
Please refer document of Bio::GCG::Seq.
---
= bio/appl/iprscan/report.rb - a class for iprscan output.
Copyright:: Copyright (C) 2006
Mitsuteru C. Nakao <mn@kazusa.or.jp>
License:: The Ruby License
$Id: report.rb,v 1.9 2007/07/18 11:11:57 nakao Exp $
== Report classes for the iprscan program.
---
= bio/appl/meme/motif.rb - Class to represent a sequence motif
Copyright:: Copyright (C) 2008 Adam Kraut <adamnkraut@gmail.com>,
License:: The Ruby License
== Description
This file contains a minimal class to represent meme motifs
== References
* http://meme.sdsc.edu/meme/intro.html
---
= bio/appl/muscle.rb - MUSCLE application wrapper class
Copyright:: Copyright (C) 2006-2007
Jeffrey Blakeslee and John Conery University of Oregon <jeffb@uoregon.edu>
Naohisa Goto <ng@bioruby.org>
License:: The Ruby License
$Id: muscle.rb,v 1.1 2007/07/16 12:25:50 ngoto Exp $
Bio::Muscle is a wrapper class to execute MUSCLE.
== References
* http://www.drive5.com/muscle/
* Edgar R.C.
MUSCLE: multiple sequence alignment with high accuracy and
high throughput. Nucleic Acids Res. 32: 1792-1797, 2004.
* Edgar, R.C.
MUSCLE: a multiple sequence alignment method with reduced time
and space complexity. BMC Bioinformatics 5: 113, 2004.
---
= bio/appl/phylip/alignment.rb - phylip multiple alignment format parser
Copyright:: Copyright (C) 2006
GOTO Naohisa <ng@bioruby.org>
License:: The Ruby License
$Id: alignment.rb,v 1.2 2007/04/05 23:35:40 trevor Exp $
= About Bio::Phylip::PhylipFormat
Please refer document of Bio::Phylip::PhylipFormat class.
---
= bio/appl/probcons.rb - ProbCons application wrapper class
Copyright:: Copyright (C) 2006-2007
Jeffrey Blakeslee and John Conery University of Oregon <jeffb@uoregon.edu>
Naohisa Goto <ng@bioruby.org>
License:: The Ruby License
$Id: probcons.rb,v 1.1 2007/07/16 12:25:50 ngoto Exp $
Bio::Probcons is a wrapper class to execute ProbCons
(Probabilistic Consistency-based Multiple Alignment
of Amino Acid Sequences).
== References
* http://probcons.stanford.edu/
* Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S.
ProbCons: Probabilistic Consistency-based Multiple Sequence Alignment.
Genome Research 15: 330-340, 2005.
---
= bio/appl/sim4/report.rb - sim4 result parser
Copyright:: Copyright (C) 2004 GOTO Naohisa <ng@bioruby.org>
License:: The Ruby License
$Id:$
The sim4 report parser classes.
== References
* Florea, L., et al., A Computer program for aligning a cDNA sequence
with a genomic DNA sequence, Genome Research, 8, 967--974, 1998.
http://www.genome.org/cgi/content/abstract/8/9/967
---
= bio/appl/sosui/report.rb - SOSUI report class
Copyright:: Copyright (C) 2003
Mitsuteru C. Nakao <n@bioruby.org>
License:: The Ruby License
$Id:$
== Example
== References
* http://bp.nuap.nagoya-u.ac.jp/sosui/
* http://bp.nuap.nagoya-u.ac.jp/sosui/sosui_submit.html
---
= bio/appl/targetp/report.rb - TargetP report class
Copyright:: Copyright (C) 2003
Mitsuteru C. Nakao <n@bioruby.org>
License:: The Ruby License
$Id:$
== Description
TargetP class for http://www.cbs.dtu.dk/services/TargetP/
== Example
== References
---
= bio/appl/tcoffee.rb - T-Coffee application wrapper class
Copyright:: Copyright (C) 2006-2007
Jeffrey Blakeslee and John Conery University of Oregon <jeffb@uoregon.edu>
Naohisa Goto <ng@bioruby.org>
License:: The Ruby License
$Id: tcoffee.rb,v 1.1 2007/07/16 12:25:50 ngoto Exp $
Bio::Tcoffee is a wrapper class to execute T-Coffee.
== References
* http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
* Notredame, C., Higgins, D.G. and Heringa, J.
T-Coffee: A novel method for fast and accurate multiple sequence
alignment. J. Mol. Biol. 302: 205-217, 2000.
---
= bio/compat/references.rb - Obsoleted References class
Copyright:: Copyright (C) 2008
Toshiaki Katayama <k@bioruby.org>,
Ryan Raaum <ryan@raaum.org>,
Jan Aerts <jandot@bioruby.org>,
Naohisa Goto <ng@bioruby.org>
License:: The Ruby License
$Id: references.rb,v 1.1.2.1 2008/03/04 10:07:49 ngoto Exp $
== Description
The Bio::References class was obsoleted after BioRuby 1.2.1.
To keep compatibility, some wrapper methods are provided in this file.
As the compatibility methods (and Bio::References) will soon be removed,
Please change your code not to use Bio::References.
Note that Bio::Reference is different from Bio::References.
Bio::Reference still exists for storing a reference information
in sequence entries.
---
= bio/data/aa.rb - Amino Acids
Copyright:: Copyright (C) 2001, 2005
Toshiaki Katayama <k@bioruby.org>
License:: The Ruby License
$Id:$
---
= bio/data/codontable.rb - Codon Table
Copyright:: Copyright (C) 2001, 2004
Toshiaki Katayama <k@bioruby.org>
License:: The Ruby License
$Id:$
== Data source
Data in this class is converted from the NCBI's genetic codes page.
* ((<URL:http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t>))
=== Examples
Obtain a codon table No.1 -- Standard (Eukaryote)
table = Bio::CodonTable[1]
Obtain a copy of the codon table No.1 to modify. In this example,
reassign a seleno cystein ('U') to the 'tga' codon.
table = Bio::CodonTable.copy(1)
table['tga'] = 'U'
Create a new codon table by your own from the Hash which contains
pairs of codon and amino acid. You can also define the table name
in the second argument.
hash = { 'ttt' => 'F', 'ttc' => 'ttc', ... }
table = Bio::CodonTable.new(hash, "my codon table")
Obtain a translated amino acid by codon.
table = Bio::CodonTable[1]
table['ttt'] # => F
Reverse translation of a amino acid into a list of relevant codons.
table = Bio::CodonTable[1]
table.revtrans("A") # => ["gcg", "gct", "gca", "gcc"]
---
= bio/data/na.rb - Nucleic Acids
Copyright:: Copyright (C) 2001, 2005
Toshiaki Katayama <k@bioruby.org>
License:: The Ruby License
$Id:$
== Synopsis
Bio::NucleicAcid class contains data related to nucleic acids.
== Usage
Examples:
require 'bio'
puts "### na = Bio::NucleicAcid.new"
na = Bio::NucleicAcid.new
puts "# na.to_re('yrwskmbdhvnatgc')"
p na.to_re('yrwskmbdhvnatgc')
puts "# Bio::NucleicAcid.to_re('yrwskmbdhvnatgc')"
p Bio::NucleicAcid.to_re('yrwskmbdhvnatgc')
puts "# na.weight('A')"
p na.weight('A')
puts "# Bio::NucleicAcid.weight('A')"
p Bio::NucleicAcid.weight('A')
puts "# na.weight('atgc')"
p na.weight('atgc')
puts "# Bio::NucleicAcid.weight('atgc')"
p Bio::NucleicAcid.weight('atgc')
---
TODO save on db reading from a genbank or embl object
---
require ‘bio/sequence‘
---
= bio/db/fasta/defline.rb - FASTA defline parser class
Copyright:: Copyright (C) 2001, 2002
GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>,
Toshiaki Katayama <k@bioruby.org>
License:: The Ruby License
$Id: defline.rb,v 1.1.2.1 2008/06/20 13:22:32 ngoto Exp $
== Description
Bio::FastaDefline is a parser class for definition line (defline)
of the FASTA format.
== Examples
rub = Bio::FastaDefline.new('>gi|671595|emb|CAA85678.1| rubisco large subunit [Perovskia abrotanoides]')
rub.entry_id ==> 'gi|671595'
rub.get('emb') ==> 'CAA85678.1'
rub.emb ==> 'CAA85678.1'
rub.gi ==> '671595'
rub.accession ==> 'CAA85678'
rub.accessions ==> [ 'CAA85678' ]
rub.acc_version ==> 'CAA85678.1'
rub.locus ==> nil
rub.list_ids ==> [["gi", "671595"],
["emb", "CAA85678.1", nil],
["Perovskia abrotanoides"]]
ckr = Bio::FastaDefline.new(">gi|2495000|sp|Q63931|CCKR_CAVPO CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)\001gi|2147182|pir||I51898 cholecystokinin A receptor - guinea pig\001gi|544724|gb|AAB29504.1| cholecystokinin A receptor; CCK-A receptor [Cavia]")
ckr.entry_id ==> "gi|2495000"
ckr.sp ==> "CCKR_CAVPO"
ckr.pir ==> "I51898"
ckr.gb ==> "AAB29504.1"
ckr.gi ==> "2495000"
ckr.accession ==> "AAB29504"
ckr.accessions ==> ["Q63931", "AAB29504"]
ckr.acc_version ==> "AAB29504.1"
ckr.locus ==> nil
ckr.description ==>
"CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)"
ckr.descriptions ==>
["CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)",
"cholecystokinin A receptor - guinea pig",
"cholecystokinin A receptor; CCK-A receptor [Cavia]"]
ckr.words ==>
["cavia", "cck-a", "cck-ar", "cholecystokinin", "guinea", "pig",
"receptor", "type"]
ckr.id_strings ==>
["2495000", "Q63931", "CCKR_CAVPO", "2147182", "I51898",
"544724", "AAB29504.1", "Cavia"]
ckr.list_ids ==>
[["gi", "2495000"], ["sp", "Q63931", "CCKR_CAVPO"],
["gi", "2147182"], ["pir", nil, "I51898"], ["gi", "544724"],
["gb", "AAB29504.1", nil], ["Cavia"]]
== References
* FASTA format (WikiPedia)
http://en.wikipedia.org/wiki/FASTA_format
* Fasta format description (NCBI)
http://www.ncbi.nlm.nih.gov/BLAST/fasta.shtml
---
= bio/db/kegg/common.rb - Common methods for KEGG database classes
Copyright:: Copyright (C) 2003-2007 Toshiaki Katayama <k@bioruby.org>
Copyright:: Copyright (C) 2003 Masumi Itoh <m@bioruby.org>
Copyright:: Copyright (C) 2009 Kozo Nishida <kozo-ni@is.naist.jp>
License:: The Ruby License
== Description
Note that the modules in this file are intended to be Bio::KEGG::*
internal use only.
This file contains modules that implement methods commonly used from
KEGG database parser classes.
---
= bio/db/kegg/genes.rb - KEGG/GENES database class
Copyright:: Copyright (C) 2001, 2002, 2006
Toshiaki Katayama <k@bioruby.org>
License:: The Ruby License
$Id:$
== KEGG GENES parser
See http://www.genome.jp/kegg/genes.html
=== Examples
require 'bio/io/fetch'
entry_string = Bio::Fetch.query('genes', 'b0002')
entry = Bio::KEGG::GENES.new(entry_string)
# ENTRY
p entry.entry # => Hash
p entry.entry_id # => String
p entry.division # => String
p entry.organism # => String
# NAME
p entry.name # => String
p entry.genes # => Array
p entry.gene # => String
# DEFINITION
p entry.definition # => String
p entry.eclinks # => Array
# PATHWAY
p entry.pathway # => String
p entry.pathways # => Hash
# POSITION
p entry.position # => String
p entry.chromosome # => String
p entry.gbposition # => String
p entry.locations # => Bio::Locations
# MOTIF
p entry.motif # => Hash of Array
# DBLINKS
p entry.dblinks # => Hash of Array
# STRUCTURE
p entry.structure # => Array
# CODON_USAGE
p entry.codon_usage # => Hash
p entry.cu_list # => Array
# AASEQ
p entry.aaseq # => Bio::Sequence::AA
p entry.aalen # => Fixnum
# NTSEQ
p entry.ntseq # => Bio::Sequence::NA
p entry.naseq # => Bio::Sequence::NA
p entry.ntlen # => Fixnum
p entry.nalen # => Fixnum
---
= bio/db/kegg/keggtab.rb - KEGG keggtab class
Copyright:: Copyright (C) 2001 Mitsuteru C. Nakao <n@bioruby.org>
Copyright (C) 2003, 2006 Toshiaki Katayama <k@bioruby.org>
License:: The Ruby License
$Id: keggtab.rb,v 1.10 2007/04/05 23:35:41 trevor Exp $
---
= bio/db/kegg/taxonomy.rb - KEGG taxonomy parser class
Copyright:: Copyright (C) 2007 Toshiaki Katayama <k@bioruby.org>
License:: The Ruby License
$Id:$
---
bio/db/lasergene.rb - Interface for DNAStar Lasergene sequence file format
Author:: Trevor Wennblom <mailto:trevor@corevx.com>
Copyright:: Copyright (c) 2007 Center for Biomedical Research Informatics, University of Minnesota (http://cbri.umn.edu)
License:: The Ruby License
$Id:$
---
definition of the PDB class
---
Autoload definition
---
bio/db/soft.rb - Interface for SOFT formatted files
Author:: Trevor Wennblom <mailto:trevor@corevx.com>
Copyright:: Copyright (c) 2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
License:: The Ruby License
$Id:$
---
= bio/io/flatfile.rb - flatfile access wrapper class
Copyright (C) 2001-2006 Naohisa Goto <ng@bioruby.org>
License:: The Ruby License
$Id:$
Bio::FlatFile is a helper and wrapper class to read a biological data file.
It acts like a IO object.
It can automatically detect data format, and users do not need to tell
the class what the data is.
---
= bio/location.rb - Locations/Location class (GenBank location format)
Copyright:: Copyright (C) 2001, 2005 Toshiaki Katayama <k@bioruby.org>
2006 Jan Aerts <jan.aerts@bbsrc.ac.uk>
2008 Naohisa Goto <ng@bioruby.org>
License:: The Ruby License
$Id:$
---
= bio/sequence/common.rb - common methods for biological sequence
Copyright:: Copyright (C) 2006
Toshiaki Katayama <k@bioruby.org>,
Ryan Raaum <ryan@raaum.org>
License:: The Ruby License
$Id:$
---
= bio/sequence/compat.rb - methods for backward compatibility
Copyright:: Copyright (C) 2006
Toshiaki Katayama <k@bioruby.org>,
Ryan Raaum <ryan@raaum.org>
License:: The Ruby License
$Id:$
---
= bio/sequence/quality_score.rb - Sequence quality score manipulation modules
Copyright:: Copyright (C) 2009
Naohisa Goto <ng@bioruby.org>
License:: The Ruby License
== Description
Sequence quality score manipulation modules, mainly used by Bio::Fastq
and related classes.
== References
* FASTQ format specification
http://maq.sourceforge.net/fastq.shtml
---
= bio/shell/plugin/keggdas.rb - plugin for KEGG DAS
Copyright:: Copyright (C) 2006
Toshiaki Katayama <k@bioruby.org>
License:: The Ruby License
$Id: das.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
---
bio/util/color_scheme.rb - Popular color codings for nucleic and amino acids
Author:: Trevor Wennblom <mailto:trevor@corevx.com>
Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
License:: The Ruby License
$Id:$
---
bio/util/contingency_table.rb - Statistical contingency table analysis for aligned sequences
Author:: Trevor Wennblom <mailto:trevor@corevx.com>
Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
License:: The Ruby License
$Id:$
---
bio/util/restriction_enzyme.rb - Digests DNA based on restriction enzyme cut patterns
Author:: Trevor Wennblom <mailto:trevor@corevx.com>
Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
License:: The Ruby License
$Id:$
---
bio/util/restriction_enzyme/cut_symbol.rb - Defines the symbol used to mark a cut in an enzyme sequence
Author:: Trevor Wennblom <mailto:trevor@corevx.com>
Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
License:: The Ruby License
$Id: cut_symbol.rb,v 1.6 2007/07/16 19:28:48 k Exp $
---
= bio/version.rb - BioRuby version information
Copyright:: Copyright (C) 2001-2009
Toshiaki Katayama <k@bioruby.org>,
Naohisa Goto <ng@bioruby.org>
License:: The Ruby License
| BIORUBY_VERSION | = | [1, 4, 0].extend(Comparable).freeze | BioRuby version (Array containing Integer) | |
| BIORUBY_EXTRA_VERSION | = | nil | Extra version specifier (String or nil). Existance of the value indicates pre-release version or modified version. | |
| BIORUBY_VERSION_ID | = | (BIORUBY_VERSION.join('.') + BIORUBY_EXTRA_VERSION.to_s).freeze | Version identifier, including extra version string (String) Unlike BIORUBY_VERSION, it is not comparable. |
Provide BioRuby shell ‘command’ also as ‘Bio.command’ (like ChemRuby)
# File lib/bio.rb, line 306
306: def self.method_missing(*args)
307: require 'bio/shell'
308: extend Bio::Shell
309: public_class_method(*Bio::Shell.private_instance_methods)
310: if Bio.respond_to?(args.first)
311: Bio.send(*args)
312: else
313: raise NameError
314: end
315: end