ngoto-bio 1.2.9.9001

data/lib/bio.rb

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+#
+# = bio.rb - Loading all BioRuby modules
+#
+# Copyright::	Copyright (C) 2001-2007
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	The Ruby License
+#
+# $Id:$
+#
+
+module Bio
+
+  BIORUBY_VERSION = [1, 3, 0].extend(Comparable)
+
+  ### Basic data types
+
+  ## Sequence
+
+  autoload :Sequence,       'bio/sequence'
+  ## below are described in bio/sequence.rb
+  #class Sequence
+  #  autoload :Common,  'bio/sequence/common'
+  #  autoload :NA,      'bio/sequence/na'
+  #  autoload :AA,      'bio/sequence/aa'
+  #  autoload :Generic, 'bio/sequence/generic'
+  #  autoload :Format,  'bio/sequence/format'
+  #  autoload :Adapter, 'bio/sequence/adapter'
+  #end
+
+  ## Locations/Location
+
+  autoload :Location,       'bio/location'
+  autoload :Locations,      'bio/location'
+
+  ## Features/Feature
+
+  autoload :Feature,        'bio/feature'
+  autoload :Features,       'bio/compat/features'
+
+  ## References/Reference
+
+  autoload :Reference,      'bio/reference'
+  autoload :References,     'bio/compat/references'
+
+  ## Pathway/Relation
+
+  autoload :Pathway,        'bio/pathway'
+  autoload :Relation,       'bio/pathway'
+
+  ## Alignment
+
+  autoload :Alignment,      'bio/alignment'
+
+  ## Tree
+  autoload :Tree, 'bio/tree'
+
+  ## Map
+  autoload :Map,            'bio/map'
+	
+  ### Constants
+
+  autoload :NucleicAcid,    'bio/data/na'
+  autoload :AminoAcid,      'bio/data/aa'
+  autoload :CodonTable,     'bio/data/codontable'
+
+
+  ### DB parsers
+
+  autoload :DB,             'bio/db'
+  autoload :NCBIDB,         'bio/db'
+  autoload :KEGGDB,         'bio/db'
+  autoload :EMBLDB,         'bio/db'
+
+  ## GenBank/RefSeq/DDBJ
+
+  autoload :GenBank,        'bio/db/genbank/genbank'
+  autoload :GenPept,        'bio/db/genbank/genpept'
+  autoload :RefSeq,         'bio/db/genbank/refseq'
+  autoload :DDBJ,           'bio/db/genbank/ddbj'
+  ## below are described in bio/db/genbank/ddbj.rb
+  #class DDBJ
+  #  autoload :XML,          'bio/io/ddbjxml'
+  #end
+
+  ## EMBL/TrEMBL/Swiss-Prot/SPTR
+
+  autoload :EMBL,           'bio/db/embl/embl'
+  autoload :SPTR,           'bio/db/embl/sptr'
+  autoload :TrEMBL,         'bio/db/embl/trembl'
+  autoload :UniProt,        'bio/db/embl/uniprot'
+  autoload :SwissProt,      'bio/db/embl/swissprot'
+
+  ## KEGG
+
+  class KEGG
+    autoload :GENOME,       'bio/db/kegg/genome'
+    autoload :GENES,        'bio/db/kegg/genes'
+    autoload :ENZYME,       'bio/db/kegg/enzyme'
+    autoload :COMPOUND,     'bio/db/kegg/compound'
+    autoload :DRUG,         'bio/db/kegg/drug'
+    autoload :GLYCAN,       'bio/db/kegg/glycan'
+    autoload :REACTION,     'bio/db/kegg/reaction'
+    autoload :BRITE,        'bio/db/kegg/brite'
+    autoload :CELL,         'bio/db/kegg/cell'
+    autoload :EXPRESSION,   'bio/db/kegg/expression'
+    autoload :ORTHOLOGY,    'bio/db/kegg/orthology'
+    autoload :KGML,         'bio/db/kegg/kgml'
+    autoload :Taxonomy,     'bio/db/kegg/taxonomy'
+  end
+
+  ## other formats
+
+  autoload :FastaFormat,    'bio/db/fasta'
+  autoload :FastaNumericFormat, 'bio/db/fasta' # change to FastaFormat::Numeric ?
+  autoload :FastaDefline,       'bio/db/fasta' # change to FastaFormat::Defline
+  autoload :GFF,            'bio/db/gff'
+  autoload :AAindex,        'bio/db/aaindex'
+  autoload :AAindex1,       'bio/db/aaindex' # change to AAindex::AAindex1 ?
+  autoload :AAindex2,       'bio/db/aaindex' # change to AAindex::AAindex2 ?
+  autoload :TRANSFAC,       'bio/db/transfac'
+  autoload :PROSITE,        'bio/db/prosite'
+  autoload :LITDB,          'bio/db/litdb'
+  autoload :MEDLINE,        'bio/db/medline'
+  autoload :FANTOM,         'bio/db/fantom'
+  autoload :GO,             'bio/db/go'
+  autoload :PDB,            'bio/db/pdb'
+  autoload :NBRF,           'bio/db/nbrf'
+  autoload :REBASE,         'bio/db/rebase'
+  autoload :SOFT,           'bio/db/soft'
+  autoload :Lasergene,      'bio/db/lasergene'
+
+  autoload :Newick,         'bio/db/newick'
+  autoload :Nexus,          'bio/db/nexus'
+
+  ### IO interface modules
+
+  autoload :Registry,       'bio/io/registry'
+  autoload :Fetch,          'bio/io/fetch'
+  autoload :SQL,            'bio/io/sql'
+  autoload :SOAPWSDL,       'bio/io/soapwsdl'
+  autoload :FlatFile,       'bio/io/flatfile'
+  autoload :FlatFileIndex,  'bio/io/flatfile/index' # chage to FlatFile::Index ?
+  ## below are described in bio/io/flatfile/index.rb
+  #class FlatFileIndex
+  #  autoload :Indexer,    'bio/io/flatfile/indexer'
+  #  autoload :BDBdefault, 'bio/io/flatfile/bdb'
+  #  autoload :BDBwrapper, 'bio/io/flatfile/bdb'
+  #  autoload :BDB_1,      'bio/io/flatfile/bdb'
+  #end
+
+  autoload :PubMed,         'bio/io/pubmed'
+  autoload :DAS,            'bio/io/das'
+  autoload :DBGET,          'bio/io/dbget'
+
+  autoload :Ensembl,        'bio/io/ensembl'
+  autoload :Hinv,           'bio/io/hinv'
+
+  ## below are described in bio/appl/blast.rb
+  #class Blast
+  #  autoload :Fastacmd,     'bio/io/fastacmd'
+  #end
+
+  class KEGG
+    autoload :API,          'bio/io/keggapi'
+  end
+
+  ## below are described in bio/db/genbank/ddbj.rb
+  #class DDBJ
+  #  autoload :XML,          'bio/io/ddbjxml'
+  #end
+
+  class HGC
+    autoload :HiGet,        'bio/io/higet'
+  end
+
+  class EBI
+    autoload :SOAP,         'bio/io/ebisoap'
+  end
+
+  class NCBI
+    autoload :SOAP,       'bio/io/ncbisoap'
+    autoload :REST,       'bio/io/ncbirest'
+  end
+
+
+  ### Applications
+
+  autoload :Fasta,          'bio/appl/fasta'
+  ## below are described in bio/appl/fasta.rb
+  #class Fasta
+  #  autoload :Report,       'bio/appl/fasta/format10'
+  #end
+
+  autoload :Blast,          'bio/appl/blast'
+  ## below are described in bio/appl/blast.rb
+  #class Blast
+  #  autoload :Fastacmd,     'bio/io/fastacmd'
+  #  autoload :Report,       'bio/appl/blast/report'
+  #  autoload :Default,      'bio/appl/blast/format0'
+  #  autoload :WU,           'bio/appl/blast/wublast'
+  #  autoload :Bl2seq,       'bio/appl/bl2seq/report'
+  #  autoload :RPSBlast,     'bio/appl/blast/rpsblast'
+  #  autoload :NCBIOptions,  'bio/appl/blast/ncbioptions'
+  #  autoload :Remote,       'bio/appl/blast/remote'
+  #end
+
+  autoload :HMMER,          'bio/appl/hmmer'
+  ## below are described in bio/appl/hmmer.rb
+  #class HMMER
+  #  autoload :Report,       'bio/appl/hmmer/report'
+  #end
+
+  autoload :EMBOSS,         'bio/appl/emboss'    # use bio/command, improve
+
+  autoload :PSORT,          'bio/appl/psort'
+  ## below are described in bio/appl/psort.rb
+  #class PSORT
+  #  class PSORT1
+  #    autoload :Report,       'bio/appl/psort/report'
+  #  end
+  #  class PSORT2
+  #    autoload :Report,       'bio/appl/psort/report'
+  #  end
+  #end
+
+  autoload :TMHMM,          'bio/appl/tmhmm/report'
+  autoload :TargetP,        'bio/appl/targetp/report'
+  autoload :SOSUI,          'bio/appl/sosui/report'
+  autoload :Genscan,        'bio/appl/genscan/report'
+
+  autoload :ClustalW,       'bio/appl/clustalw'
+  ## below are described in bio/appl/clustalw.rb
+  #class ClustalW
+  #  autoload :Report,       'bio/appl/clustalw/report'
+  #end
+
+  autoload :MAFFT,          'bio/appl/mafft'
+  ## below are described in bio/appl/mafft.rb
+  #class MAFFT
+  #  autoload :Report,       'bio/appl/mafft/report'
+  #end
+
+  autoload :Tcoffee,        'bio/appl/tcoffee'
+  autoload :Muscle,         'bio/appl/muscle'
+  autoload :Probcons,       'bio/appl/probcons'
+
+  autoload :Sim4,           'bio/appl/sim4'
+  ## below are described in bio/appl/sim4.rb
+  #class Sim4
+  #  autoload :Report,       'bio/appl/sim4/report'
+  #end
+  
+  autoload :Spidey,         'bio/appl/spidey/report'
+  autoload :Blat,           'bio/appl/blat/report'
+  
+  module GCG
+    autoload :Msf,          'bio/appl/gcg/msf'
+    autoload :Seq,          'bio/appl/gcg/seq'
+  end
+
+  module Phylip
+    autoload :PhylipFormat,   'bio/appl/phylip/alignment'
+    autoload :DistanceMatrix, 'bio/appl/phylip/distance_matrix'
+  end
+
+  autoload :Iprscan,        'bio/appl/iprscan/report'
+
+  autoload :PAML,           'bio/appl/paml/common'
+  ## below are described in bio/appl/paml/common.rb
+  # module PAML
+  #   autoload :Codeml,         'bio/appl/paml/codeml'
+  #   autoload :Baseml,         'bio/appl/paml/baseml'
+  #   autoload :Yn00,           'bio/appl/paml/yn00'
+  # end
+
+  ### Utilities
+
+  autoload :SiRNA,          'bio/util/sirna'
+  autoload :ColorScheme,    'bio/util/color_scheme'
+  autoload :ContingencyTable, 'bio/util/contingency_table'
+  autoload :RestrictionEnzyme, 'bio/util/restriction_enzyme'
+
+  ### Service libraries
+  autoload :Command,        'bio/command'
+
+  ### Provide BioRuby shell 'command' also as 'Bio.command' (like ChemRuby)
+
+  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
+
+end
+

data/rdoc.zsh

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+#!/usr/bin/env zsh
+
+#DIAGRAM='--diagram'
+WEBCVS='http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi'
+
+rdoc ${DIAGRAM} --op rdoc --inline-source \
+  --webcvs "${WEBCVS}/bioruby/\%s?cvsroot=bioruby" \
+  bin/*(.) lib/**/*.rb [A-Z]*(.) doc/*rd etc/bioinformatics/*(.)

data/sample/any2fasta.rb

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+#!/usr/bin/env ruby
+#
+# any2fasta.rb - convert input file into FASTA format using a regex
+#                filter
+#
+#   Copyright (C) 2006 Pjotr Prins <p@bioruby.org>
+#
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  $Id: any2fasta.rb,v 1.1 2006/02/17 14:59:27 pjotr Exp $
+#
+
+require 'bio/io/flatfile'
+
+include Bio
+
+usage = <<USAGE
+
+Usage: any2fasta.rb [regex] infiles
+
+  Examples:
+
+    Output all sequences containing GATC or GATT ignoring case:
+		
+	  any2fasta.rb "/GAT[CT]/i" *.seq > reduced.fasta
+		
+USAGE
+
+if ARGV.size == 0
+  print usage
+	exit 1
+end
+
+# ---- Valid regular expression - if it is not a file
+regex = ARGV[0]
+if regex=~/^\// and !File.exist?(regex)
+  ARGV.shift
+else
+  regex = nil
+end
+
+ARGV.each do | fn |
+  ff = Bio::FlatFile.auto(fn)
+  ff.each_entry do |entry|
+	  if regex != nil
+		  next if eval("entry.seq !~ #{regex}")
+		end
+  	print entry.seq.to_fasta(entry.definition,70)
+	end
+end
+