Module: Bio

Defined in:
lib/bio.rb,
lib/bio/db.rb,
lib/bio/map.rb,
lib/bio/tree.rb,
lib/bio/db/go.rb,
lib/bio/io/sql.rb,
lib/bio/db/gff.rb,
lib/bio/db/pdb.rb,
lib/bio/io/das.rb,
lib/bio/data/aa.rb,
lib/bio/io/hinv.rb,
lib/bio/data/na.rb,
lib/bio/feature.rb,
lib/bio/version.rb,
lib/bio/db/soft.rb,
lib/bio/db/nbrf.rb,
lib/bio/command.rb,
lib/bio/pathway.rb,
lib/bio/db/fastq.rb,
lib/bio/location.rb,
lib/bio/db/litdb.rb,
lib/bio/db/nexus.rb,
lib/bio/io/higet.rb,
lib/bio/io/fetch.rb,
lib/bio/sequence.rb,
lib/bio/io/dbget.rb,
lib/bio/db/fasta.rb,
lib/bio/alignment.rb,
lib/bio/appl/pts1.rb,
lib/bio/io/togows.rb,
lib/bio/db/rebase.rb,
lib/bio/reference.rb,
lib/bio/io/pubmed.rb,
lib/bio/db/fantom.rb,
lib/bio/db/newick.rb,
lib/bio/appl/sim4.rb,
lib/bio/db/pdb/pdb.rb,
lib/bio/appl/fasta.rb,
lib/bio/util/sirna.rb,
lib/bio/db/prosite.rb,
lib/bio/db/aaindex.rb,
lib/bio/appl/blast.rb,
lib/bio/db/medline.rb,
lib/bio/appl/psort.rb,
lib/bio/appl/hmmer.rb,
lib/bio/io/ebisoap.rb,
lib/bio/appl/mafft.rb,
lib/bio/io/keggapi.rb,
lib/bio/io/ddbjxml.rb,
lib/bio/io/ensembl.rb,
lib/bio/io/registry.rb,
lib/bio/io/fastacmd.rb,
lib/bio/db/pdb/atom.rb,
lib/bio/io/ncbisoap.rb,
lib/bio/db/transfac.rb,
lib/bio/io/soapwsdl.rb,
lib/bio/io/ncbirest.rb,
lib/bio/io/flatfile.rb,
lib/bio/sequence/na.rb,
lib/bio/appl/emboss.rb,
lib/bio/sequence/aa.rb,
lib/bio/appl/muscle.rb,
lib/bio/db/embl/sptr.rb,
lib/bio/db/embl/embl.rb,
lib/bio/db/kegg/kgml.rb,
lib/bio/db/kegg/drug.rb,
lib/bio/appl/tcoffee.rb,
lib/bio/appl/gcg/msf.rb,
lib/bio/appl/gcg/seq.rb,
lib/bio/db/lasergene.rb,
lib/bio/db/pdb/chain.rb,
lib/bio/db/pdb/model.rb,
lib/bio/db/pdb/utils.rb,
lib/bio/db/fasta/qual.rb,
lib/bio/db/kegg/genes.rb,
lib/bio/appl/clustalw.rb,
lib/bio/appl/probcons.rb,
lib/bio/db/kegg/brite.rb,
lib/bio/db/kegg/module.rb,
lib/bio/db/kegg/genome.rb,
lib/bio/db/kegg/glycan.rb,
lib/bio/db/kegg/common.rb,
lib/bio/db/kegg/enzyme.rb,
lib/bio/appl/meme/mast.rb,
lib/bio/db/pdb/residue.rb,
lib/bio/db/embl/trembl.rb,
lib/bio/db/embl/common.rb,
lib/bio/db/kegg/pathway.rb,
lib/bio/data/codontable.rb,
lib/bio/sequence/compat.rb,
lib/bio/appl/meme/motif.rb,
lib/bio/sequence/format.rb,
lib/bio/compat/features.rb,
lib/bio/sequence/common.rb,
lib/bio/io/flatfile/bdb.rb,
lib/bio/db/embl/uniprot.rb,
lib/bio/db/kegg/keggtab.rb,
lib/bio/db/genbank/ddbj.rb,
lib/bio/appl/blast/rexml.rb,
lib/bio/db/kegg/taxonomy.rb,
lib/bio/sequence/generic.rb,
lib/bio/db/kegg/reaction.rb,
lib/bio/io/biosql/biosql.rb,
lib/bio/db/kegg/compound.rb,
lib/bio/appl/blat/report.rb,
lib/bio/shell/plugin/das.rb,
lib/bio/appl/paml/codeml.rb,
lib/bio/appl/sim4/report.rb,
lib/bio/db/fasta/defline.rb,
lib/bio/appl/paml/common.rb,
lib/bio/db/genbank/refseq.rb,
lib/bio/appl/blast/report.rb,
lib/bio/appl/sosui/report.rb,
lib/bio/db/kegg/orthology.rb,
lib/bio/compat/references.rb,
lib/bio/io/flatfile/index.rb,
lib/bio/db/embl/swissprot.rb,
lib/bio/appl/hmmer/report.rb,
lib/bio/appl/mafft/report.rb,
lib/bio/db/genbank/common.rb,
lib/bio/appl/tmhmm/report.rb,
lib/bio/appl/psort/report.rb,
lib/bio/util/color_scheme.rb,
lib/bio/appl/spidey/report.rb,
lib/bio/appl/bl2seq/report.rb,
lib/bio/db/genbank/genbank.rb,
lib/bio/db/biosql/sequence.rb,
lib/bio/db/genbank/genpept.rb,
lib/bio/appl/blast/format0.rb,
lib/bio/db/kegg/expression.rb,
lib/bio/io/flatfile/buffer.rb,
lib/bio/appl/blast/wublast.rb,
lib/bio/appl/blast/format8.rb,
lib/bio/appl/iprscan/report.rb,
lib/bio/appl/genscan/report.rb,
lib/bio/appl/fasta/format10.rb,
lib/bio/appl/blast/rpsblast.rb,
lib/bio/appl/targetp/report.rb,
lib/bio/io/biosql/ar-biosql.rb,
lib/bio/io/flatfile/indexer.rb,
lib/bio/io/flatfile/splitter.rb,
lib/bio/appl/blast/xmlparser.rb,
lib/bio/appl/clustalw/report.rb,
lib/bio/appl/meme/mast/report.rb,
lib/bio/appl/phylip/alignment.rb,
lib/bio/util/contingency_table.rb,
lib/bio/sequence/quality_score.rb,
lib/bio/util/restriction_enzyme.rb,
lib/bio/sequence/sequence_masker.rb,
lib/bio/db/pdb/chemicalcomponent.rb,
lib/bio/io/flatfile/autodetection.rb,
lib/bio/db/sanger_chromatogram/scf.rb,
lib/bio/db/phyloxml/phyloxml_parser.rb,
lib/bio/db/sanger_chromatogram/abif.rb,
lib/bio/db/phyloxml/phyloxml_writer.rb,
lib/bio/appl/phylip/distance_matrix.rb,
lib/bio/db/phyloxml/phyloxml_elements.rb,
lib/bio/db/phyloxml/phyloxml_elements.rb,
lib/bio/util/restriction_enzyme/analysis.rb,
lib/bio/util/restriction_enzyme/cut_symbol.rb,
lib/bio/db/sanger_chromatogram/chromatogram.rb,
lib/bio/util/restriction_enzyme/single_strand.rb,
lib/bio/util/restriction_enzyme/analysis_basic.rb,
lib/bio/util/restriction_enzyme/range/cut_range.rb,
lib/bio/util/restriction_enzyme/double_stranded.rb,
lib/bio/util/restriction_enzyme/range/cut_ranges.rb,
lib/bio/util/restriction_enzyme/string_formatting.rb,
lib/bio/util/restriction_enzyme/range/sequence_range.rb,
lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb,
lib/bio/util/restriction_enzyme/single_strand_complement.rb,
lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb,
lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb,
lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb,
lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb,
lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb,
lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb,
lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb,
lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb,
lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb,
lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb

Overview

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

License

The Ruby License

$Id: cut_symbol.rb,v 1.6 2007/07/16 19:28:48 k Exp $

Defined Under Namespace

Modules: Alignment, ColorScheme, Command, FANTOM, GCG, Map, Meme, PAML, Phylip, PhyloXML, Shell, TogoWS Classes: AAindex, AAindex1, AAindex2, Abif, AminoAcid, Blast, Blat, ClustalW, CodonTable, ContingencyTable, DAS, DB, DBGET, DDBJ, EBI, EMBL, EMBLDB, EMBOSS, Ensembl, Fasta, FastaDefline, FastaFormat, FastaNumericFormat, Fastq, Feature, Features, Fetch, FlatFile, FlatFileIndex, GFF, GO, GenBank, GenPept, Genscan, HGC, HMMER, Hinv, Iprscan, KEGG, KEGGDB, LITDB, Lasergene, Location, Locations, MAFFT, MEDLINE, Muscle, NBRF, NCBI, NCBIDB, Newick, Nexus, NucleicAcid, PDB, PROSITE, PSORT, PTS1, Pathway, Probcons, PubMed, REBASE, RefSeq, Reference, References, Registry, Relation, RestrictionEnzyme, SOAPWSDL, SOFT, SOSUI, SPTR, SQL, SangerChromatogram, Scf, Sequence, SiRNA, Sim4, Spidey, SwissProt, TMHMM, TRANSFAC, TargetP, Taxonomy, Tcoffee, TrEMBL, Tree, UniProt

Constant Summary

BIORUBY_VERSION =

BioRuby version (Array containing Integer)

[1, 4, 1].extend(Comparable).freeze
BIORUBY_EXTRA_VERSION =

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

".5000"
BIORUBY_VERSION_ID =

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

(BIORUBY_VERSION.join('.') + BIORUBY_EXTRA_VERSION.to_s).freeze

Class Method Summary (collapse)

Class Method Details

+ (Object) method_missing(*args)

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



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# File 'lib/bio.rb', line 308

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