Class: BioToolsExcelConverter

Inherits:
Object
  • Object
show all
Defined in:
lib/protk/biotools_excel_converter.rb

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(filename) ⇒ BioToolsExcelConverter

Returns a new instance of BioToolsExcelConverter.



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# File 'lib/protk/biotools_excel_converter.rb', line 7

def initialize(filename)
  @inputBook = Spreadsheet.open File.new("#{filename}")
end

Class Method Details

.isBiotools(filename) ⇒ Object 



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# File 'lib/protk/biotools_excel_converter.rb', line 11

def self.isBiotools(filename)
  testBook = Spreadsheet.open File.new("#{filename}")
  testSheet = testBook.worksheet 0
  
  isbiotools=FALSE
  testSheet.each do |row|
    if  (row[0].class==String) && row[0].match(/Digest Matches.*?Score:\s(.*)\)/)   
      isbiotools=TRUE
    end
  end
  
  
  isbiotools
end

Instance Method Details

#get_rows ⇒ Object 



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# File 'lib/protk/biotools_excel_converter.rb', line 26

def get_rows
  
  sheet=@inputBook.worksheet 0
  
  protein_rows=[]

  n_rows=sheet.dimensions[1]

  protein_rows=(0...n_rows).collect do |row_i|      
    new_row=nil
    
    row=sheet.row row_i      
    if ( row[0]!=nil)
      digmatch=row[0].match(/Digest Matches.*?Score:\s(.*)\)/)
      if  ( digmatch!=nil )
        new_row=[]          
        text= sheet.row(row_i-1)[0] 
        m=text.match(/\s(\S*)\s*$/)
        throw "Badly formed protein line in biotools file ... could not parse protein name from #{text}" unless m!=nil
        new_row[0]=m[1]
        new_row[1]=digmatch[1]
      end
    end
    
    new_row
  end
  
  protein_rows.compact!
  protein_rows.insert(0,["Accession","Ion Scores"])
  
  protein_rows
  
end