bio/compat/references.rb - Obsoleted References class

$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/tree/output.rb - Phylogenetic tree formatter

Description

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

References

• evolution.genetics.washington.edu/phylip/newick_doc.html

• www.phylosoft.org/forester/NHX.html

bio/io/flatfile.rb - flatfile access wrapper class

Copyright (C) 2001-2006 Naohisa Goto <ng@bioruby.org>

$Id:$

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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bio/sequence.rb - biological sequence class

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

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

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

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

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

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

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

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

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

bio/sequence/quality_score.rb - Sequence quality score manipulation modules

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/common.rb - common methods for biological sequence

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

bio/sequence/compat.rb - methods for backward compatibility

bio/version.rb - BioRuby version information

bio/appl/sosui/report.rb - SOSUI report class

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Example

References

• bp.nuap.nagoya-u.ac.jp/sosui/

• bp.nuap.nagoya-u.ac.jp/sosui/sosui_submit.html

bio/appl/blast/format8.rb - BLAST tab-delimited output (-m 8) parser

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Note

This file is automatically loaded by bio/appl/blast/report.rb

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

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

• blast.wustl.edu/

• www.ebi.ac.uk/blast2/

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

bio/appl/sim4/report.rb - sim4 result parser

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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/iprscan/report.rb - a class for iprscan output.

$Id: report.rb,v 1.9 2007/07/18 11:11:57 nakao Exp $

Report classes for the iprscan program.

bio/appl/tcoffee.rb - T-Coffee application wrapper class

$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/appl/meme/motif.rb - Class to represent a sequence motif

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

$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.

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bio/appl/gcg/seq.rb - GCG sequence file format class (.seq/.pep file)

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

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/phylip/alignment.rb - phylip multiple alignment format parser

$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

$Id: emboss.rb,v 1.9 2008/01/10 03:51:06 ngoto Exp $

bio/appl/targetp/report.rb - TargetP report class

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Description

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

Example

References

bio/appl/probcons.rb - ProbCons application wrapper class

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

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Autoload definition

require 'bio/sequence'

bio/db/fasta/defline.rb - FASTA defline parser class

$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/soft.rb - Interface for SOFT formatted files

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bio/db/kegg/keggtab.rb - KEGG keggtab class

$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

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/taxonomy.rb - KEGG taxonomy parser class

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bio/db/kegg/genes.rb - KEGG/GENES database class

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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/pdb/residue.rb - residue class for PDB

Bio::PDB::Residue

Bio::PDB::Heterogen

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

Bio::PDB::Chain

Please refer Bio::PDB::Chain.

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

Bio::PDB::Model

Please refer Bio::PDB::Model.

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

About Bio::PDB::ChemicalComponent

Please refer Bio::PDB::ChemicalComponent.

References

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

• deposit.pdb.org/het_dictionary.txt

TODO save on db reading from a genbank or embl object

definition of the PDB class

bio/data/na.rb - Nucleic Acids

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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

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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/aa.rb - Amino Acids

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bio/shell/plugin/keggdas.rb - plugin for KEGG DAS

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

bio.rb - Loading all BioRuby modules

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