Class: Bio::Genscan::Report

Inherits:
Object show all
Defined in:
lib/bio/appl/genscan/report.rb

Overview

Bio::Genscan::Report - Class for Genscan report output.

Parser for the Genscan report output.

Defined Under Namespace

Classes: Exon, Gene

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(report) ⇒ Report

Bio::Genscan::Report.new(str)

Parse a Genscan report output string.



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# File 'lib/bio/appl/genscan/report.rb', line 67

def initialize(report)
  @predictions = []
  @genscan_version = nil
  @date_run   = nil
  @time       = nil
  @query_name = nil
  @length     = nil
  @gccontent  = nil
  @isochore   = nil
  @matrix     = nil

  report.each_line("\n") do |line|
    case line
    when /^GENSCAN/
      parse_headline(line)
    when /^Sequence/
      parse_sequence(line)
    when /^Parameter/
      parse_parameter(line)
    when /^Predicted genes/
      break
    end
  end

  # rests
  i = report.index(/^Predicted gene/)
  j = report.index(/^Predicted peptide sequence/)

  # genes/exons
  genes_region = report[i...j]
  genes_region.each_line("\n") do |line|
    if /Init|Intr|Term|PlyA|Prom|Sngl/ =~ line
      gn, en = line.strip.split(" +")[0].split(/\./).map {|i| i.to_i }
      add_exon(gn, en, line)
    end
  end

  # sequences (peptide|CDS)
  sequence_region = report[j...report.size]
  sequence_region.gsub!(/^Predicted .+?:/, '')
  sequence_region.gsub!(/^\s*$/, '')
  sequence_region.split(Bio::FastaFormat::RS).each do |ff|
    add_seq(Bio::FastaFormat.new(ff))
  end
end

Instance Attribute Details

#date_run ⇒ Object (readonly)

Returns



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# File 'lib/bio/appl/genscan/report.rb', line 36

def date_run
  @date_run
end

#gccontent ⇒ Object (readonly)

Returns C+G content of the query sequence.



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# File 'lib/bio/appl/genscan/report.rb', line 50

def gccontent
  @gccontent
end

#genscan_version ⇒ Object (readonly)

Returns Genscan version.



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# File 'lib/bio/appl/genscan/report.rb', line 33

def genscan_version
  @genscan_version
end

#isochore ⇒ Object (readonly)

Returns



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# File 'lib/bio/appl/genscan/report.rb', line 53

def isochore
  @isochore
end

#length ⇒ Object (readonly)

Returns Length of the query sequence.



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# File 'lib/bio/appl/genscan/report.rb', line 47

def length
  @length
end

#matrix ⇒ Object (readonly)

Returns



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# File 'lib/bio/appl/genscan/report.rb', line 56

def matrix
  @matrix
end

#predictions ⇒ Object (readonly) Also known as: prediction, genes

Returns Array of Bio::Genscan::Report::Gene.



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# File 'lib/bio/appl/genscan/report.rb', line 59

def predictions
  @predictions
end

#query_name ⇒ Object (readonly) Also known as: sequence_name, name

Returns Name of query sequence.



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# File 'lib/bio/appl/genscan/report.rb', line 42

def query_name
  @query_name
end

#time ⇒ Object (readonly)

Returns



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# File 'lib/bio/appl/genscan/report.rb', line 39

def time
  @time
end