parse.rb

#!/usr/bin/env ruby

require 'csv'
require 'rubygems'
require 'roo'

PROT_FILE = "/Users/abrader/src/protein/protein.links.detailed.v9.0.txt"
FILENAME = "/Users/abrader/Downloads/silam_symbol_masterlist.csv"
EXCEL_FILE = "SILAM_Symbol_MasterList.xlsx"

class ProteinLinks
  attr_accessor :protein1, :protein2, :neighborhood, :fusion, :cooccurence, :coexpression, :experimental, :database, :textmining, :combined_score
  
  def initialize(p1, p2, n, f, coo, exp, db, tm, cs)
    @protein1 = p1
    @protein2 = p2
    @neighborhood = n
    @fusion = f
    @cooccurence = coo
    @experimental = exp
    @database = db
    @textmining = tm
    @combined_score = cs
  end
  
  def self.get_list
    protein_array = Array.new
    count = 0
    CSV.foreach(PROT_FILE) do |row|
      if count == 0
        # Do nothing
      else
        protein_array << ProteinLinks.new(row[0], row[1], row[2], row[3], row[4], row[5], row[6], row[7], row[8])
      end
      count += 1
    end
    protein_array
  end
  
end

class Silam
  
  attr_accessor :quant_method, :common_name, :gi_number, :approved_symbol, :hgnc_link
  
  def initialize(qm, cm, gi, as, hl)
    @quant_method = qm
    @common_name = cm
    @gi_number = gi
    @approved_symbol = as
    @hgnc_link = hl
  end
  
  # def self.get_list
  #   silam_array = Array.new
  #   count = 0
  #   CSV.foreach(FILENAME) do |row|
  #     if count == 0
  #       #Do Nothing since first row is headers
  #     else
  #       silam_array << Silam.new(row[0], row[1], row[2], row[3])
  #     end
  #     count += 1
  #   end
  #   silam_array
  # end
  # 
  # def self.roo_list
  #   silam_array = Array.new
  #   count = 0
  #   oo = Excelx.new(EXCEL_FILE)
  #   oo.default_sheet = oo.sheets.first
  #   oo.formula(1,'D')
  #   #puts oo.to_yaml
  # end
  
  def self.goog_list
    silam_array = Array.new
    oo = Google.new("0Ao_C0TS02CV1dDYtSWYwM2k3US1POG84S1hrZUpEM2c")
    oo.default_sheet = oo.sheets.first
    count = oo.last_row
    1.upto(count) do |r|
      if oo.formula(r,'D').nil?
        silam_array << Silam.new(oo.cell(r,'A'), oo.cell(r,'B'), oo.cell(r,'C'), oo.cell(r,'D'), nil)
      else
        silam_array << Silam.new(oo.cell(r,'A'), oo.cell(r,'B'), oo.cell(r,'C'), oo.cell(r,'D'), oo.formula(r,'D').split('"')[1])
      end
    end
    silam_array
  end
    
  
end
  

sa = Silam.goog_list

pa = ProteinLinks.get_list

# sa.each do |s|
#   puts "#{s.approved_symbol} = #{s.hgnc_link}"
# end