Class: Bio::GCG::Msf

Inherits:
Object show all
Defined in:
lib/bio/appl/gcg/msf.rb

Overview

The msf is a multiple sequence alignment format developed by Wisconsin. Bio::GCG::Msf is a msf format parser.

Constant Summary collapse

DELIMITER =

delimiter used by Bio::FlatFile

RS = nil

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(str) ⇒ Msf

Creates a new Msf object.



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# File 'lib/bio/appl/gcg/msf.rb', line 31

def initialize(str)
  str = str.sub(/\A[\r\n]+/, '')
  preamble, @data = str.split(/^\/\/$/, 2)
  preamble.sub!(/\A\!\![A-Z]+\_MULTIPLE\_ALIGNMENT.*/, '')
  @heading = $& # '!!NA_MULTIPLE_ALIGNMENT 1.0' or like this
  preamble.sub!(/.*\.\.\s*$/m, '')
  @description = $&.to_s.sub(/^.*\.\.\s*$/, '').to_s
  d = $&.to_s
  if m = /^(?:(.+)\s+)?MSF\:\s+(\d+)\s+Type\:\s+(\w)\s+(.+)\s+(Comp)?Check\:\s+(\d+)/.match(d) then
    @entry_id = m[1].to_s.strip
    @length   = (m[2] ? m[2].to_i : nil)
    @seq_type = m[3]
    @date     = m[4].to_s.strip
    @checksum = (m[6] ? m[6].to_i : nil)
  end

  @seq_info = []
  preamble.each_line do |x|
    if /Name\: / =~ x then
      s = {}
      x.scan(/(\S+)\: +(\S*)/) { |y| s[$1] = $2 }
      @seq_info << s
    end
  end

  @description.sub!(/\A(\r\n|\r|\n)/, '')
  @align = nil
end

Instance Attribute Details

#checksum ⇒ Object (readonly)

checksum



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# File 'lib/bio/appl/gcg/msf.rb', line 76

def checksum
  @checksum
end

#date ⇒ Object (readonly)

date



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# File 'lib/bio/appl/gcg/msf.rb', line 73

def date
  @date
end

#description ⇒ Object (readonly)

description



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# File 'lib/bio/appl/gcg/msf.rb', line 61

def description
  @description
end

#entry_id ⇒ Object (readonly)

ID of the alignment



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# File 'lib/bio/appl/gcg/msf.rb', line 64

def entry_id
  @entry_id
end

#heading ⇒ Object (readonly)

heading (‘!!NA_MULTIPLE_ALIGNMENT 1.0’ or whatever like this)



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# File 'lib/bio/appl/gcg/msf.rb', line 80

def heading
  @heading
end

#length ⇒ Object (readonly)

alignment length



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# File 'lib/bio/appl/gcg/msf.rb', line 67

def length
  @length
end

#seq_type ⇒ Object (readonly)

sequence type (“N” for DNA/RNA or “P” for protein)



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# File 'lib/bio/appl/gcg/msf.rb', line 70

def seq_type
  @seq_type
end

Instance Method Details

#alignment ⇒ Object

returns Bio::Alignment object.



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# File 'lib/bio/appl/gcg/msf.rb', line 176

def alignment
  do_parse
  @align
end

#compcheck ⇒ Object

CompCheck field



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# File 'lib/bio/appl/gcg/msf.rb', line 118

def compcheck
  unless defined?(@compcheck)
    if /CompCheck\: +(\d+)/ =~ @description then
      @compcheck = $1.to_i
    else
      @compcheck = nil
    end
  end
  @compcheck
end

#gap_length_weight ⇒ Object

gap length weight



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# File 'lib/bio/appl/gcg/msf.rb', line 109

def gap_length_weight
  unless defined?(@gap_length_weight)
    /GapLengthWeight\: +(\S+)/ =~ @description
    @gap_length_weight = $1
  end
  @gap_length_weight
end

#gap_weight ⇒ Object

gap weight



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# File 'lib/bio/appl/gcg/msf.rb', line 100

def gap_weight
  unless defined?(@gap_weight)
    /GapWeight\: +(\S+)/ =~ @description
    @gap_weight = $1
  end
  @gap_weight
end

#seq_data ⇒ Object

gets seq data (used internally) (will be obsoleted)



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# File 'lib/bio/appl/gcg/msf.rb', line 182

def seq_data
  do_parse
  @seq_data
end

#symbol_comparison_table ⇒ Object

symbol comparison table



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# File 'lib/bio/appl/gcg/msf.rb', line 91

def symbol_comparison_table
  unless defined?(@symbol_comparison_table)
    /Symbol comparison table\: +(\S+)/ =~ @description
    @symbol_comparison_table = $1
  end
  @symbol_comparison_table
end

#validate_checksum ⇒ Object

validates checksum



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# File 'lib/bio/appl/gcg/msf.rb', line 188

def validate_checksum
  do_parse
  valid = true
  total = 0
  @seq_data.each_with_index do |x, i|
    sum = Bio::GCG::Seq.calc_checksum(x)
    if sum != @seq_info[i]['Check'].to_i
      valid = false
      break
    end
    total += sum
  end
  return false unless valid
  if @checksum != 0 # "Check:" field of BioPerl is always 0
    valid = ((total % 10000) == @checksum)
  end
  valid
end