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.



21
22
23
24
25
26
27
 
# 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 +Hash+es, where each hash has key/value pairs for the columns in the data file.



31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
 
# 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.



9
10
11
12
13
14
15
16
17
18
 
# 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