Class: Bio::Blast

Inherits:
Object show all
Defined in:
lib/bio/appl/blast.rb,
lib/bio/io/fastacmd.rb,
lib/bio/appl/blast/rexml.rb,
lib/bio/appl/blast/report.rb,
lib/bio/appl/bl2seq/report.rb,
lib/bio/appl/blast/format0.rb,
lib/bio/appl/blast/format8.rb,
lib/bio/appl/blast/wublast.rb,
lib/bio/appl/blast/xmlparser.rb

Overview

Description

The Bio::Blast class contains methods for running local or remote BLAST searches, as well as for parsing of the output of such BLASTs (i.e. the BLAST reports). For more information on similarity searches and the BLAST program, see www.ncbi.nlm.nih.gov/Education/BLASTinfo/similarity.html.

Usage

require 'bio'

# To run an actual BLAST analysis:
#   1. create a BLAST factory
remote_blast_factory = Bio::Blast.remote('blastp', 'SWISS',
                                         '-e 0.0001', 'genomenet')
#or:
local_blast_factory = Bio::Blast.local('blastn','/path/to/db')

#   2. run the actual BLAST by querying the factory
report = remote_blast_factory.query(sequence_text)

# Then, to parse the report, see Bio::Blast::Report

Available databases for Bio::Blast.remote

----------+-------+---------------------------------------------------
 program  | query | db (supported in GenomeNet)
----------+-------+---------------------------------------------------
 blastp   | AA    | nr-aa, genes, vgenes.pep, swissprot, swissprot-upd,
----------+-------+ pir, prf, pdbstr
 blastx   | NA    | 
----------+-------+---------------------------------------------------
 blastn   | NA    | nr-nt, genbank-nonst, gbnonst-upd, dbest, dbgss,
----------+-------+ htgs, dbsts, embl-nonst, embnonst-upd, epd,
 tblastn  | AA    | genes-nt, genome, vgenes.nuc
----------+-------+---------------------------------------------------

See also

  • Bio::Blast::Report

  • Bio::Blast::Report::Hit

  • Bio::Blast::Report::Hsp

References

Defined Under Namespace

Modules: Default, WU Classes: Bl2seq, Fastacmd, Report

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(program, db, opt = [], server = 'local') ⇒ Blast

Creates a Bio::Blast factory object.

To run any BLAST searches, a factory has to be created that describes a certain BLAST pipeline: the program to use, the database to search, any options and the server to use. E.g.

blast_factory = Bio::Blast.new('blastn','dbsts', '-e 0.0001 -r 4', 'genomenet')

Arguments:

  • program (required): ‘blastn’, ‘blastp’, ‘blastx’, ‘tblastn’ or ‘tblastx’

  • db (required): name of the (local or remote) database

  • options: blastall options \

(see www.genome.jp/dbget-bin/show_man?blast2)

  • server: server to use (e.g. ‘genomenet’; DEFAULT = ‘local’)

Returns

Bio::Blast factory object



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# File 'lib/bio/appl/blast.rb', line 173

def initialize(program, db, opt = [], server = 'local')
  @program  = program
  @db       = db
  @server   = server

  @blastall = 'blastall'
  @matrix   = nil
  @filter   = nil

  @output   = ''
  @parser   = nil

  begin
    a = opt.to_ary
  rescue NameError #NoMethodError
    # backward compatibility
    a = Shellwords.shellwords(opt)
  end
  unless a.find { |x| /\A\-m/ =~ x.to_s } then
    if defined?(XMLParser) or defined?(REXML)
      @format = 7
    else
      @format = 8
    end
  end
  @options = [ *a ]
end

Instance Attribute Details

#blastall ⇒ Object

Full path for blastall. (default: ‘blastall’).



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# File 'lib/bio/appl/blast.rb', line 136

def blastall
  @blastall
end

#db ⇒ Object

Database name (-d option for blastall)



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# File 'lib/bio/appl/blast.rb', line 127

def db
  @db
end

#filter ⇒ Object

Filter option for blastall -F (T or F).



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# File 'lib/bio/appl/blast.rb', line 142

def filter
  @filter
end

#format ⇒ Object (readonly)

Output report format for blastall -m

0, pairwise; 1; 2; 3; 4; 5; 6; 7, XML Blast outpu;, 8, tabular; 9, tabular with comment lines; 10, ASN text; 11, ASN binery [intege].



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# File 'lib/bio/appl/blast.rb', line 151

def format
  @format
end

#matrix ⇒ Object

Substitution matrix for blastall -M



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# File 'lib/bio/appl/blast.rb', line 139

def matrix
  @matrix
end

#options ⇒ Object

Options for blastall



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# File 'lib/bio/appl/blast.rb', line 130

def options
  @options
end

#output ⇒ Object (readonly)

Returns a String containing blast execution output in as is the Bio::Blast#format.



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# File 'lib/bio/appl/blast.rb', line 145

def output
  @output
end

#parser=(value) ⇒ Object (writeonly)

to change :xmlparser, :rexml, :tab



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# File 'lib/bio/appl/blast.rb', line 154

def parser=(value)
  @parser = value
end

#program ⇒ Object

Program name (-p option for blastall): blastp, blastn, blastx, tblastn or tblastx



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# File 'lib/bio/appl/blast.rb', line 124

def program
  @program
end

#server ⇒ Object

Server to submit the BLASTs to



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# File 'lib/bio/appl/blast.rb', line 133

def server
  @server
end

Class Method Details

.local(program, db, option = '') ⇒ Object

This is a shortcut for Bio::Blast.new:

Bio::Blast.local(program, database, options)

is equivalent to

Bio::Blast.new(program, database, options, 'local')

Arguments:

  • program (required): ‘blastn’, ‘blastp’, ‘blastx’, ‘tblastn’ or ‘tblastx’

  • db (required): name of the local database

  • options: blastall options \

(see www.genome.jp/dbget-bin/show_man?blast2)

Returns

Bio::Blast factory object



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# File 'lib/bio/appl/blast.rb', line 87

def self.local(program, db, option = '')
  self.new(program, db, option, 'local')
end

.remote(program, db, option = '', server = 'genomenet') ⇒ Object

Bio::Blast.remote does exactly the same as Bio::Blast.new, but sets the remote server ‘genomenet’ as its default.

Arguments:

  • program (required): ‘blastn’, ‘blastp’, ‘blastx’, ‘tblastn’ or ‘tblastx’

  • db (required): name of the remote database

  • options: blastall options \

(see www.genome.jp/dbget-bin/show_man?blast2)

  • server: server to use (DEFAULT = ‘genomenet’)

Returns

Bio::Blast factory object



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# File 'lib/bio/appl/blast.rb', line 101

def self.remote(program, db, option = '', server = 'genomenet')
  self.new(program, db, option, server)
end

.reports(input, parser = nil) ⇒ Object

the method Bio::Blast.report is moved from bio/appl/blast/report.rb. only for xml format



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# File 'lib/bio/appl/blast.rb', line 107

def self.reports(input, parser = nil)
  ary = []
  input.each("</BlastOutput>\n") do |xml|
    xml.sub!(/[^<]*(<?)/, '\1') # skip before <?xml> tag
    next if xml.empty?          # skip trailing no hits
    if block_given?
      yield Report.new(xml, parser)
    else
      ary << Report.new(xml, parser)
    end
  end
  return ary
end

Instance Method Details

#option ⇒ Object

Returns options of blastall



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# File 'lib/bio/appl/blast.rb', line 216

def option
  # backward compatibility
  Bio::Command.make_command_line(@options)
end

#option=(str) ⇒ Object

Set options for blastall



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# File 'lib/bio/appl/blast.rb', line 222

def option=(str)
  # backward compatibility
  @options = Shellwords.shellwords(str)
end

#query(query) ⇒ Object

This method submits a sequence to a BLAST factory, which performs the actual BLAST.

fasta_sequences = Bio::FlatFile.open(Bio::FastaFormat, 'my_sequences.fa')
report = blast_factory.query(fasta_sequences)

Arguments:

  • query (required): single- or multiple-FASTA formatted sequence(s)

Returns

a Bio::Blast::Report object



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# File 'lib/bio/appl/blast.rb', line 211

def query(query)
  return self.send("exec_#{@server}", query.to_s)
end