Class: YouAndMe::RawDataFileLoader

Inherits:
Object
  • Object
show all
Defined in:
lib/youandme/raw_data_file_loader.rb

Overview

Tool for loading raw data files from 23andme into native Ruby structures

Instance Method Summary collapse

Instance Method Details

#check_file(file_name) ⇒ Object

Returns true if and only if the given file exists and is readable.



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# File 'lib/youandme/raw_data_file_loader.rb', line 21

def check_file(file_name)
	valid = false
	if(file_name != nil && File.file?(file_name) && File.readable?(file_name))
		valid = true
	end
	valid
end

#load_file(file_name, max = 0) ⇒ Object

Reads the given raw 23andme data file, parses the data, and shoves it into a native Ruby data structure. The returned data is an Array full of Hashes, where each hash has key/value pairs for the columns in the data file.



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# File 'lib/youandme/raw_data_file_loader.rb', line 31

def load_file(file_name, max = 0)
	snps = []
	# Manually spliting seems to be faster than the built-in CSV parser for
	rows = File.read(file_name).split("\n")
	rows.each do |n|
		row = n.chomp.split("\t")
	# CSV.foreach(file_name, :col_sep => "\t") do |row|
		# Skip if the the line is a comment
		next if row[0][0] == '#'
		break if max > 0 && snps.length >= max
		snp = {
			:rsid => row[0],
			:chromosome => row[1],
			:position => row[2],
			:genotype => row[3]
		} 
		if snp[:genotype].match(/[A-Z]/) == nil
		    snp[:genotype] = '-'
	    end
		# y snp
		snps << snp
	end
	snps
end

#markdown_links(snp) ⇒ Object

Returns Markdown-formatted URLs for the given SNP hash.



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# File 'lib/youandme/raw_data_file_loader.rb', line 9

def markdown_links(snp)
  s = ""
  if(!(snp[:rsid][0] == 'i'))  #how to break a string across rows?
	  s = "[dbSNP](http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=#{snp[:rsid]}) " +
	      " [HapMap](http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/hapmap27_B36/?name=SNP%3A#{snp[:rsid]})" +
	      " [NextBio](http://www.nextbio.com/b/search/details/#{snp[:rsid]}?type=snp&q0=#{snp[:rsid]}&t0=snp#tab=populations)" +
	      " [Ensembl](http://uswest.ensembl.org/Homo_sapiens/Variation/Summary?v=#{snp[:rsid]};vdb=variation)"
  end
  s
end