require 'base64'
require 'erb'
+class Numeric
+ def commify
+ self.to_s.gsub(/(^[-+]?\d+?(?=(?>(?:\d{3})+)(?!\d))|\G\d{3}(?=\d))/, '\1,')
+ end
+end
+
def parse_analysis(file)
data = {}
File.open(file, 'r') do |ios|
ios.each do |line|
- key, val = line.chomp.split(' ')
- data[key] = val.reverse.gsub(/(\d{3})(?=\d)/, '\\1,').reverse
+ key, val = line.chomp.split(': ')
+ begin Integer(val)
+ val = val.to_i.commify
+ rescue
+ begin Float(val)
+ val = val.to_f.commify
+ rescue
+ end
+ end
+
+ data[key] = val
end
end
STDERR.puts "Analyzing sequences ... "
system(
- "read_fastq -e illumina1.8 -i #{seq_file} |
+ "read_fastq -e base_33 -i #{seq_file} |
progress_meter |
analyze_vals -k SEQ -o #{analyze_vals_file} |
trim_seq -l 3 -m 25 |