class Bio::Fasta

Attributes

db[RW]
format[R]
ktup[RW]
matrix[RW]
options[RW]
output[R]

Returns a String containing fasta execution output in as is format.

program[RW]
server[RW]

Public Class Methods

local(program, db, option = '') click to toggle source

Returns a FASTA factory object (Bio::Fasta) to run FASTA search on local computer.

# File lib/bio/appl/fasta.rb, line 80
def self.local(program, db, option = '')
  self.new(program, db, option, 'local')
end
new(program, db, opt = [], server = 'local') click to toggle source

Returns a FASTA factory object (Bio::Fasta).

# File lib/bio/appl/fasta.rb, line 23
def initialize(program, db, opt = [], server = 'local')
  @format     = 10

  @program    = program
  @db = db
  @server     = server

  @ktup       = nil
  @matrix     = nil

  @output     = ''

  begin
    a = opt.to_ary
  rescue NameError #NoMethodError
    # backward compatibility
    a = Shellwords.shellwords(opt)
  end
  @options    = [ '-Q', '-H', '-m', @format.to_s, *a ] # need -a ?
end
parser(parser) click to toggle source

OBSOLETE. Does nothing and shows warning messages.

Historically, selecting parser to use ('format6' or 'format10' were expected, but only 'format10' was available as a working parser).

# File lib/bio/appl/fasta.rb, line 74
def self.parser(parser)
  warn 'Bio::Fasta.parser is obsoleted and will soon be removed.'
end
remote(program, db, option = '', server = 'genomenet') click to toggle source

Returns a FASTA factory object (Bio::Fasta) to execute FASTA search on remote server.

For the develpper, you can add server 'hoge' by adding exec_hoge(query) method.

# File lib/bio/appl/fasta.rb, line 90
def self.remote(program, db, option = '', server = 'genomenet')
  self.new(program, db, option, server)
end

Public Instance Methods

format=(num) click to toggle source

Accessors for the -m option.

# File lib/bio/appl/fasta.rb, line 59
def format=(num)
  @format = num.to_i
  if i = @options.index('-m') then
    @options[i+1, 1] = @format.to_s
  else
    @options << '-m' << @format.to_s
  end
end
option() click to toggle source
# File lib/bio/appl/fasta.rb, line 48
def option
  # backward compatibility
  Bio::Command.make_command_line(@options)
end
option=(str) click to toggle source
# File lib/bio/appl/fasta.rb, line 53
def option=(str)
  # backward compatibility
  @options = Shellwords.shellwords(str)
end
query(query) click to toggle source

Execute FASTA search and returns Report object (Bio::Fasta::Report).

# File lib/bio/appl/fasta.rb, line 95
def query(query)
  return self.send("exec_#{@server}", query.to_s)
end

Private Instance Methods

exec_genomenet(query) click to toggle source

Available databases for ::remote(@program, @db, option, 'genomenet')

See fasta.genome.jp/ideas/ideas.html#fasta for more details.

----------+-------+---------------------------------------------------
 @program | query | @db (supported in GenomeNet)
----------+-------+---------------------------------------------------
 fasta    | AA    | nr-aa, genes, vgenes.pep, swissprot, swissprot-upd,
          |       | pir, prf, pdbstr
          +-------+---------------------------------------------------
          | NA    | nr-nt, genbank-nonst, gbnonst-upd, dbest, dbgss,
          |       | htgs, dbsts, embl-nonst, embnonst-upd, epd,
          |       | genes-nt, genome, vgenes.nuc
----------+-------+---------------------------------------------------
 tfasta   | AA    | nr-nt, genbank-nonst, gbnonst-upd, dbest, dbgss,
          |       | htgs, dbsts, embl-nonst, embnonst-upd,
          |       | genes-nt, genome, vgenes.nuc
----------+-------+---------------------------------------------------
# File lib/bio/appl/fasta.rb, line 141
def exec_genomenet(query)
  host = "fasta.genome.jp"
  #path = "/sit-bin/nph-fasta"
  path = "/sit-bin/fasta"  # 2005.08.12

  form = {
    'style'        => 'raw',
    'prog'         => @program,
    'dbname'       => @db,
    'sequence'     => query,
    'other_param'  => Bio::Command.make_command_line_unix(@options),
    'ktup_value'   => @ktup,
    'matrix'       => @matrix,
  }

  form.keys.each do |k|
    form.delete(k) unless form[k]
  end

  report = nil

  begin
    http = Bio::Command.new_http(host)
    http.open_timeout = 3000
    http.read_timeout = 6000
    result = Bio::Command.http_post_form(http, path, form)
    # workaround 2006.8.1 - fixed for new batch queuing system
    case result.code
    when "302"
      result_location = result.header['location']
      result_uri = URI.parse(result_location)
      result_path = result_uri.path
      done = false
      until done
        result = http.get(result_path)
        if result.body[/Your job ID is/]
          sleep 15
        else
          done = true
        end
      end
    end
    @output = result.body.to_s
    # workaround 2005.08.12
    re = %r{<A HREF="http://#{host}(/tmp/[^"]+)">Show all result</A>}i # "
    if path = @output[re, 1]
      result = http.get(path)
      @output = result.body
      txt = @output.to_s.split(/\<pre\>/)[1]
      raise 'cannot understand response' unless txt
      txt.sub!(/\<\/pre\>.*\z/m, '')
      txt.sub!(/.*^((T?FASTA|SSEARCH) (searches|compares))/m, '\1')
      txt.sub!(/^\<form method\=\"POST\" name\=\"clust_check\"\>.*\n/, '')
      txt.sub!(/^\<select +name\=\"allch\".+\r?\n/i, '') # 2009.11.26
      txt.gsub!(/\<input[^\>]+value\=\"[^\"]*\"[^\>]*\>/i, '')
      txt.gsub!(/\<(a|form|select|input|option|img)\s+[^\>]+\>/i, '')
      txt.gsub!(/\<\/(a|form|select|input|option|img)\>/i, '')
      txt.gsub!(/\&lt\;/, '<')
      txt.gsub!(/\&gt\;/, '>') # 2009.11.26
      @output = txt
      report = parse_result(@output.dup)
    else
      raise 'cannot understand response'
    end
  end

  return report
end
exec_local(query) click to toggle source
# File lib/bio/appl/fasta.rb, line 108
def exec_local(query)
  cmd = [ @program, *@options ]
  cmd.concat([ '@', @db ])
  cmd.push(@ktup) if @ktup

  report = nil

  @output = Bio::Command.query_command(cmd, query)
  report = parse_result(@output)

  return report
end
parse_result(data) click to toggle source
# File lib/bio/appl/fasta.rb, line 103
def parse_result(data)
  Report.new(data)
end