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 -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 |
- grab -e 'SEQ_LEN > 0' |
+ grab -e 'SEQ_LEN > 20' |
analyze_vals -k SEQ -o #{analyze_vals_trim_file} |
find_adaptor -l 6 -L 6 -f ACACGACGCTCTTCCGATCT -r AGATCGGAAGAGCACACGTC |
clip_adaptor |
analyze_vals -k SEQ -o #{analyze_vals_trim_noadapt_file} |
plot_distribution -k SEQ_LEN -T 'Sequence length distribution' -X 'Sequence length' -t png -o #{lendist_file} |
plot_scores -c -t png -o #{scores_file} |
- plot_nucleotide_distribution -t png -o #{nucdist_file} |
+ plot_nucleotide_distribution -c -t png -o #{nucdist_file} |
bin_vals -k SEQ_LEN -b 25 |
plot_distribution -T '25 bases bin sequence length distribution' -X 'Sequence length' -k SEQ_LEN_BIN -t png -o #{lendist_bin_file} |
mean_scores |
</table>
<p>Sequence trimming was performed by removing from the ends all residues until 3 consecutive</p>
<p>residues with quality score larger than or equal to 25.</p>
- <p>All plots are after sequence trimming.</p>
+ <p>All plots are after sequence trimming and adaptor removal.</p>
<h2>Sequence length distribution</h2>
<p><img src="<%= png2base64(lendist_file) %>" width="600" /></p>
<p><img src="<%= png2base64(lendist_bin_file) %>" width="600" /></p>