module Bio

bio.rb - Loading all BioRuby modules¶ ↑

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

$Id:$

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/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/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/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/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¶ ↑

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¶ ↑

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¶ ↑

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. 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¶ ↑

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/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¶ ↑

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) en.wikipedia.org/wiki/FASTA_format
Fasta format description (NCBI) www.ncbi.nlm.nih.gov/BLAST/fasta.shtml

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

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 <trevor@corevx.com>
Copyright: Copyright © 2007 Center for Biomedical Research Informatics, University of Minnesota (cbri.umn.edu)
License: The Ruby License

$Id:$

definition of the PDB class

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/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¶ ↑

((<URL:deposit.pdb.org/cc_dict_tut.html>))
deposit.pdb.org/het_dictionary.txt

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/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 © 2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License: The Ruby License

$Id:$

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

Copyright

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

License

The Ruby License

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/location.rb - Locations/Location class (GenBank location format)¶ ↑

Copyright

2006       Jan Aerts <jan.aerts@bbsrc.ac.uk>
2008       Naohisa Goto <ng@bioruby.org>

License

The Ruby License

$Id:$

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/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/adapter.rb - Bio::Sequence adapter helper module¶ ↑

Copyright: Copyright (C) 2008 Naohisa Goto <ng@bioruby.org>,
License: The Ruby License

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

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/quality_score.rb - Sequence quality score manipulation modules¶ ↑

License: The Ruby License

Description¶ ↑

Sequence quality score manipulation modules, mainly used by Bio::Fastq and related classes.

References¶ ↑

FASTQ format specification maq.sourceforge.net/fastq.shtml

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

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/shell/plugin/keggdas.rb - plugin for KEGG DAS¶ ↑

License: The Ruby License

$Id: das.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $

bio/tree/output.rb - Phylogenetic tree formatter¶ ↑

License: The Ruby License

Description¶ ↑

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

References¶ ↑

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

Author: Trevor Wennblom <trevor@corevx.com>
License: The Ruby License

$Id:$

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

Author: Trevor Wennblom <trevor@corevx.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>
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>
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>
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/double_stranded.rb - DoubleStranded restriction enzyme sequence

Author: Trevor Wennblom <trevor@corevx.com>
License: The Ruby License

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

Author: Trevor Wennblom <trevor@corevx.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>
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>
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>
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>
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>
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>
License: The Ruby License

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

Author: Trevor Wennblom <trevor@corevx.com>
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>
License: The Ruby License

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

Author: Trevor Wennblom <trevor@corevx.com>
License: The Ruby License

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

Author: Trevor Wennblom <trevor@corevx.com>
License: The Ruby License

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

Author: Trevor Wennblom <trevor@corevx.com>
License: The Ruby License

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

Author: Trevor Wennblom <trevor@corevx.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>
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>
License: The Ruby License

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

License: The Ruby License

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

Author: Trevor Wennblom <trevor@corevx.com>
License: The Ruby License

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

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