bio 0.7.0

data/etc/bioinformatics/seqdatabase.ini

@@ -0,0 +1,210 @@
+VERSION=1.00
+
+[embl]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=embl
+
+[embl-upd]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=embl-upd
+
+[embl_biofetch]
+protocol=biofetch
+location=http://www.ebi.ac.uk/cgi-bin/dbfetch
+dbname=embl
+
+[embl_biosql]
+protocol=biosql
+location=localhost
+dbname=biosql
+driver=postgres
+user=hack 
+pass=
+biodbname=embl
+
+[embl_biocorba]
+protocol=bsane-corba
+location=sqldbsrv.ior
+
+[embl_xembl]
+protocol=xembl
+location=http://www.ebi.ac.uk/xembl/XEMBL.wsdl
+format=Bsml
+
+[embl_flat]
+protcol=flat
+location=/export/database/
+dbname=embl
+
+[genbank_bdb]
+protcol=flat
+location=/export/database/
+dbname=genbank
+
+[swissprot]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=swissprot
+
+[swissprot-upd]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=swissprot-upd
+
+[swissprot_biofetch]
+protocol=biofetch
+location=http://www.ebi.ac.uk/cgi-bin/dbfetch
+dbname=swall
+
+[swissprot_biosql]
+protocol=biosql
+location=db.bioruby.org
+dbname=biosql
+driver=mysql
+user=root
+pass= 
+biodbname=sp
+
+
+[genbank]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=genbank
+
+[genbank-upd]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=genbank-upd
+
+[genbank_biosql]
+protocol=biosql
+location=db.bioruby.org
+dbname=biosql
+driver=mysql
+user=root
+pass= 
+biodbname=gb
+
+
+[refseq]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=refseq
+
+[refseq_biosql]
+protocol=biosql
+location=db.bioruby.org
+dbname=biosql
+driver=mysql
+user=
+pass= 
+biodbname=rs
+
+
+[kegg-pathway]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=pathway
+
+[kegg-genome]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=genome
+
+[kegg-genes]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=genes
+
+[kegg-vgenes]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=vgenes
+
+[aaindex]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=aaindex
+
+[blocks]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=blocks
+
+[enzyme]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=enzyme
+
+[epd]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=epd
+
+[litdb]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=litdb
+
+[omim]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=omim
+
+[pdb]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=pdb
+
+[pdbstr]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=pdbstr
+
+[pfam]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=pfam
+
+[pir]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=pir
+
+[pmd]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=pmd
+
+[prf]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=prf
+
+[prints]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=prints
+
+[prodom]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=prodom
+
+[prosdoc]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=prosdoc
+
+[prosite]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=prosite
+
+[transfac]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=transfac
+

data/lib/bio.rb

@@ -0,0 +1,256 @@
+#
+# = bio.rb - Loading all BioRuby modules
+#
+# Copyright::	Copyright (C) 2001-2005
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	LGPL
+#
+# $Id: bio.rb,v 1.58 2005/11/28 04:57:32 k Exp $
+#
+#--
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library 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
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#++
+#
+
+module Bio
+
+  BIORUBY_VERSION = [0, 7, 0].extend(Comparable)
+
+  ### Basic data types
+
+  ## Sequence
+
+  autoload :Seq,            'bio/sequence'
+  autoload :Sequence,       'bio/sequence'
+
+  ## Locations/Location
+
+  autoload :Location,       'bio/location'
+  autoload :Locations,      'bio/location'
+
+  ## Features/Feature
+
+  autoload :Feature,        'bio/feature'
+  autoload :Features,       'bio/feature'
+
+  ## References/Reference
+
+  autoload :Reference,      'bio/reference'
+  autoload :References,     'bio/reference'
+
+  ## Pathway/Relation
+
+  autoload :Pathway,        'bio/pathway'
+  autoload :Relation,       'bio/pathway'
+
+  ## Alignment
+
+  autoload :Alignment,      'bio/alignment'
+
+
+  ### 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
+
+  # module Bio
+  #   autoload :NCBIDB, 'bio/db'
+  #   class GenBank < NCBIDB
+  #     autoload :Common, 'bio/db/genbank/common'
+  #     include Bio::GenBank::Common
+
+  # module Bio
+  #   autoload :NCBIDB, 'bio/db'
+  #  end
+  #  class Bio::GenBank < Bio::NCBIDB
+  #     autoload :Common, 'bio/db/genbank/common'
+  #     include Bio::GenBank::Common
+
+  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 :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 :Keggtab,      'bio/db/kegg/keggtab'
+    autoload :KO,           'bio/db/kegg/ko'
+    autoload :KGML,         'bio/db/kegg/kgml'
+  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 :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'
+
+
+  ### IO interface modules
+
+  autoload :Registry,       'bio/io/registry'
+  autoload :Fetch,          'bio/io/fetch'
+  autoload :SQL,            'bio/io/sql'
+  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'
+
+  ## 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
+
+# autoload :ESOAP,          'bio/io/esoap'      # NCBI::ESOAP ?
+# autoload :BRDB,           'bio/io/brdb'       # remove
+
+
+  ### 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'
+  #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 :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'
+  
+
+  ### Utilities
+
+  autoload :SiRNA,          'bio/util/sirna'
+  autoload :ColorScheme,    'bio/util/color_scheme'
+
+end