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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/sequence.rb - biological sequence class

Copyright

Copyright (C) 2000-2006 Toshiaki Katayama <k@bioruby.org>, Yoshinori K. Okuji <okuji@enbug.org>, Naohisa Goto <ng@bioruby.org>, Ryan Raaum <ryan@raaum.org>, Jan Aerts <jan.aerts@bbsrc.ac.uk>

License

The Ruby License


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/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/db/pdb/chemicalcomponent.rb - PDB Chemical Component Dictionary parser

Copyright

Copyright (C) 2006 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>

License

The Ruby License

About Bio::PDB::ChemicalComponent

Please refer Bio::PDB::ChemicalComponent.

References


bio/db/pdb/model.rb - model class for PDB

Copyright

Copyright (C) 2004, 2006 Alex Gutteridge <alexg@ebi.ac.uk> Naohisa Goto <ng@bioruby.org>

License

The Ruby License

Bio::PDB::Model

Please refer Bio::PDB::Model.


bio/db/pdb/chain.rb - chain class for PDB

Copyright

Copyright (C) 2004, 2006 Alex Gutteridge <alexg@ebi.ac.uk> Naohisa Goto <ng@bioruby.org>

License

The Ruby License

Bio::PDB::Chain

Please refer Bio::PDB::Chain.


bio/db/pdb/residue.rb - residue class for PDB

Copyright

Copyright (C) 2004, 2006 Alex Gutteridge <alexg@ebi.ac.uk> Naohisa Goto <ng@bioruby.org>

License

The Ruby License

Bio::PDB::Residue

Bio::PDB::Heterogen


bio/db/soft.rb - Interface for SOFT formatted files

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

$Id:$

Autoload definition


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


require 'bio/sequence'


definition of the PDB class


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/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/common.rb - Common methods for KEGG database classes

Copyright

Copyright (C) 2001-2007 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, 2010 Toshiaki Katayama <k@bioruby.org>

License

The Ruby License

$Id:$

KEGG GENES parser

See 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.names       # => Array

# 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.motifs      # => 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

TODO save on db reading from a genbank or embl object


bio/db/lasergene.rb - Interface for DNAStar Lasergene sequence file format

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2007 Center for Biomedical Research Informatics, University of Minnesota (cbri.umn.edu)

License

The Ruby License

$Id:$

bio/util/color_scheme.rb - Popular color codings for nucleic and amino acids

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

$Id:$

bio/util/restriction_enzyme.rb - Digests DNA based on restriction enzyme cut patterns

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License


bio/util/contingency_table.rb - Statistical contingency table analysis for aligned sequences

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License

$Id:$

bio/util/restriction_enzyme/string_formatting.rb - Useful functions for string manipulation

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License


bio/util/restriction_enzyme/cut_symbol.rb - Defines the symbol used to mark a cut in an enzyme sequence

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License


bio/util/restriction_enzyme/sorted_num_array.rb - Internal data storage for Bio::RestrictionEnzyme::Range::SequenceRange

Copyright

Copyright (C) 2011 Naohisa Goto <ng@bioruby.org>

License

The Ruby License


bio/util/restriction_enzyme/range/sequence_range.rb - A defined range over a nucleotide sequence

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License


bio/util/restriction_enzyme/range/sequence_range/fragment.rb -

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License


bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb -

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License


bio/util/restriction_enzyme/analysis/fragments.rb -

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License


bio/util/restriction_enzyme/range/vertical_cut_range.rb -

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License


bio/util/restriction_enzyme/range/horizontal_cut_range.rb -

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License


bio/util/restriction_enzyme/range/cut_range.rb - Abstract base class for HorizontalCutRange and VerticalCutRange

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License


bio/util/restriction_enzyme/range/cut_ranges.rb - Container for many CutRange objects or CutRange child objects.

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License


bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb - Stores a cut location pair in 0-based index notation

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License


bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb - Inherits from DoubleStrand::CutLocations

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License


bio/util/restriction_enzyme/double_stranded/aligned_strands.rb - Align two SingleStrand objects

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License


bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb - Inherits from DoubleStranded::CutLocationPair

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License


bio/util/restriction_enzyme/double_stranded/cut_locations.rb - Contains an Array of CutLocationPair objects

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License


bio/util/restriction_enzyme/single_strand_complement.rb - Single strand restriction enzyme sequence in complement orientation

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License


bio/util/restriction_enzyme/double_stranded.rb - DoubleStranded restriction enzyme sequence

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License


bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb - The cut locations, in enzyme notation

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License


bio/util/restriction_enzyme/dense_int_array.rb - Internal data storage for Bio::RestrictionEnzyme::Range::SequenceRange

Copyright

Copyright (C) 2011 Naohisa Goto <ng@bioruby.org> Tomoaki NISHIYAMA

License

The Ruby License


bio/util/restriction_enzyme/analysis.rb - Does the work of fragmenting the DNA from the enzymes

Author

Trevor Wennblom <trevor@corevx.com>

Copyright

Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)

License

The Ruby License


bio/tree/output.rb - Phylogenetic tree formatter

Copyright

Copyright (C) 2004-2006 Naohisa Goto <ng@bioruby.org>

License

The Ruby License

Description

This file contains formatter of Newick, NHX and Phylip distance matrix.

References


bio/version.rb - BioRuby version information

Copyright

Copyright (C) 2001-2012 Toshiaki Katayama <k@bioruby.org>, Naohisa Goto <ng@bioruby.org>

License

The Ruby License


bio/feature.rb - Features/Feature class (GenBank Feature table)

Copyright

Copyright (c) 2002, 2005 Toshiaki Katayama <k@bioruby.org>

2006        Jan Aerts <jan.aerts@bbsrc.ac.uk>

License

The Ruby License


bio/data/aa.rb - Amino Acids

Copyright

Copyright (C) 2001, 2005 Toshiaki Katayama <k@bioruby.org>

License

The Ruby License

$Id:$


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')

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/appl/bl2seq/report.rb - bl2seq (BLAST 2 sequences) parser

Copyright

Copyright (C) 2005 Naohisa Goto <ng@bioruby.org>

License

The Ruby License

Bio::Blast::Bl2seq::Report is a NCBI bl2seq (BLAST 2 sequences) output parser.

Acknowledgements

Thanks to Tomoaki NISHIYAMA <tomoakin __at__ kenroku.kanazawa-u.ac.jp> for providing bl2seq parser patches based on lib/bio/appl/blast/format0.rb.


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


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


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


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


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


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 www.cbs.dtu.dk/services/TargetP/

Example

References


bio/appl/blast/remote.rb - remote BLAST wrapper basic module

Copyright

Copyright (C) 2008 Naohisa Goto <ng@bioruby.org>

License

The Ruby License


bio/appl/blast/wublast.rb - WU-BLAST default output parser

Copyright

Copyright (C) 2003, 2008 Naohisa GOTO <ng@bioruby.org>

License

The Ruby License

Description

WU-BLAST default output parser.

The parser is still incomplete and may contain many bugs, because I didn't have WU-BLAST license. It was tested under web-based WU-BLAST results and obsolete version downloaded from blast.wustl.edu/ .

References


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/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/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 $


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


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/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/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.


Ok Hilmar gives to me some clarification 1) "EMBL/GenBank/SwissProt" name in term table, is only a convention assuming data loaded by genbank embl ans swissprot formats.

If your features come from others ways for example blast or alignment ... whatever.. the user as to take care about the source.

TODO: 1) source_term_id => surce_term and check before if the source term is present or not and the level, the root should always be something "EMBL/GenBank/SwissProt" or contestualized. 2) Into DummyBase class delete connection there and use Bio::ArSQL.establish_connection which reads info from a yml file. 3) Chk Locations in Biofeatures ArSQL


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


bio/sequence/adapter.rb - Bio::Sequence adapter helper module

Copyright

Copyright (C) 2008 Naohisa Goto <ng@bioruby.org>,

License

The Ruby License


bio/sequence/na.rb - nucleic acid sequence class

Copyright

Copyright (C) 2006 Toshiaki Katayama <k@bioruby.org>, Ryan Raaum <ryan@raaum.org>

License

The Ruby License


bio/sequence/generic.rb - generic sequence class to store an intact string

Copyright

Copyright (C) 2006 Toshiaki Katayama <k@bioruby.org>

License

The Ruby License


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


bio/sequence/aa.rb - amino acid sequence class

Copyright

Copyright (C) 2006 Toshiaki Katayama <k@bioruby.org>, Ryan Raaum <ryan@raaum.org>

License

The Ruby License


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


bio/sequence/dblink.rb - sequence ID with database name

Copyright

Copyright (C) 2008 Naohisa Goto <ng@bioruby.org>

License

The Ruby License


bio/sequence/sequence_masker.rb - Sequence masking helper methods

Copyright

Copyright (C) 2010 Naohisa Goto <ng@bioruby.org>

License

The Ruby License

Description

Bio::Sequence::SequenceMasker is a mix-in module to provide helpful methods for masking a sequence.

For details, see documentation of Bio::Sequence::SequenceMasker.


bio.rb - Loading all BioRuby modules

Copyright

Copyright (C) 2001-2007 Toshiaki Katayama <k@bioruby.org>

License

The Ruby License

$Id:$

Constants

BIORUBY_EXTRA_VERSION

Extra version specifier (String or nil). Existance of the value indicates pre-release version or modified version.

nil

Release version.

".0000"..".4999"

Release version with patches.

".5000"

Development unstable version.

".5001"..".8999"

Pre-alpha version.

"-alphaN" (N=0..99)

Alpha version.

"-preN" (N=0..99)

Pre-release test version.

"-rcN" (N=0..99)

Release candidate version.

BIORUBY_VERSION

BioRuby version (Array containing Integer)

BIORUBY_VERSION_ID

Version identifier, including extra version string (String) Unlike BIORUBY_VERSION, it is not comparable.

Public Class Methods

method_missing(*args) click to toggle source

Provide BioRuby shell 'command' also as 'Bio.command' (like ChemRuby)

# File lib/bio.rb, line 309
def self.method_missing(*args)
  require 'bio/shell'
  extend Bio::Shell
  public_class_method(*Bio::Shell.private_instance_methods)
  if Bio.respond_to?(args.first)
    Bio.send(*args)
  else
    raise NameError
  end
end

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