class Bio::SOSUI::Report

SOSUI output report parsing class

References

Constants

DELIMITER

Delimiter

RS

Attributes

entry_id[R]

Query #entry_id

prediction[R]

Returns the prediction result whether “MEMBRANE PROTEIN” or “SOLUBLE PROTEIN”.

tmhs[R]

Transmembrane helixes ary

Public Class Methods

new(output_report) click to toggle source

Parser for SOSUI output report.

# File lib/bio/appl/sosui/report.rb, line 45
def initialize(output_report)
  entry       = output_report.split(/\n/)

  @entry_id   = entry[0].strip.sub(/^>/,'')
  @prediction = entry[1].strip
  @tms        = 0
  @tmhs       = []
  parse_tmh(entry) if /MEMBRANE/ =~ @prediction
end

Private Instance Methods

parse_tmh(entry) click to toggle source

Parser for TMH lines.

# File lib/bio/appl/sosui/report.rb, line 58
def parse_tmh(entry)
  entry.each do |line|
    if /NUMBER OF TM HELIX = (\d+)/ =~ line
      @tms = $1
    elsif /TM (\d+) +(\d+)- *(\d+) (\w+) +(\w+)/ =~ line
      tmh  = $1.to_i
      range = Range.new($2.to_i, $3.to_i)
      grade = $4
      seq   = $5
      @tmhs.push(TMH.new(range, grade, seq))
    end
  end
end