File.open(file, 'r') do |ios|
ios.each do |line|
key, val = line.chomp.split(' ')
- data[key] = val.to_i;
+ data[key] = val.reverse.gsub(/(\d{3})(?=\d)/, '\\1,').reverse
end
end
tmpdir = Dir.mktmpdir
seq_file = ARGV.shift
-analyze_vals_file = File.join(tmpdir, 'analyze_vals.txt')
-analyze_vals_trim_file = File.join(tmpdir, 'analyze_vals_trim.txt')
-lendist_file = File.join(tmpdir, 'lendist.png')
-scores_file = File.join(tmpdir, 'scores.png')
-nucdist_file = File.join(tmpdir, 'nucdist.png')
-lendist_bin_file = File.join(tmpdir, 'lendist_bin.png')
-scores_bin_file = File.join(tmpdir, 'scores_bin.png')
+analyze_vals_file = File.join(tmpdir, 'analyze_vals.txt')
+analyze_vals_trim_file = File.join(tmpdir, 'analyze_vals_trim_noadapt.txt')
+analyze_vals_trim_noadapt_file = File.join(tmpdir, 'analyze_vals_trim.txt')
+lendist_file = File.join(tmpdir, 'lendist.png')
+scores_file = File.join(tmpdir, 'scores.png')
+nucdist_file = File.join(tmpdir, 'nucdist.png')
+lendist_bin_file = File.join(tmpdir, 'lendist_bin.png')
+scores_bin_file = File.join(tmpdir, 'scores_bin.png')
STDERR.puts "Analyzing sequences ... "
trim_seq -l 3 -m 25 |
grab -e 'SEQ_LEN > 0' |
analyze_vals -k SEQ -o #{analyze_vals_trim_file} |
+ find_adaptor -l 6 -L 6 -f ACACGACGCTCTTCCGATCT -r AGATCGGAAGAGCACACGTC |
+ clip_adaptor |
+ grab -e 'SEQ_LEN > 0' |
+ 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} |
analysis1 = parse_analysis(analyze_vals_file)
analysis2 = parse_analysis(analyze_vals_trim_file)
+analysis3 = parse_analysis(analyze_vals_trim_noadapt_file)
template = %{
<html>
<p>File: <%= seq_file %></p>
<h2>Sequence composition</h2>
<table>
- <tr><td></td><td>Before trimming</td><td>After trimming</td></tr>
- <tr><td>Number of sequences</td><td align='right'><%= analysis1['COUNT'] %></td><td align='right'><%= analysis2['COUNT'] %></td></tr>
- <tr><td>Number of bases</td><td align='right'><%= analysis1['SUM'] %></td><td align='right'><%= analysis2['SUM'] %></td></tr>
- <tr><td>Min sequence length</td><td align='right'><%= analysis1['MIN'] %></td><td align='right'><%= analysis2['MIN'] %></td></tr>
- <tr><td>Max sequence length</td><td align='right'><%= analysis1['MAX'] %></td><td align='right'><%= analysis2['MAX'] %></td></tr>
- <tr><td>Mean sequence length</td><td align='right'><%= analysis1['MEAN'] %></td><td align='right'><%= analysis2['MEAN'] %></td></tr>
+ <tr><td></td><td>Before trimming</td><td>After trimming</td><td>After adaptor removal</td></tr>
+ <tr><td>Number of sequences</td><td align='right'><%= analysis1['COUNT'] %></td><td align='right'><%= analysis2['COUNT'] %></td><td align='right'><%= analysis3['COUNT'] %></td></tr>
+ <tr><td>Number of bases</td><td align='right'><%= analysis1['SUM'] %></td><td align='right'><%= analysis2['SUM'] %></td><td align='right'><%= analysis3['SUM'] %></td></tr>
+ <tr><td>Min sequence length</td><td align='right'><%= analysis1['MIN'] %></td><td align='right'><%= analysis2['MIN'] %></td><td align='right'><%= analysis3['MIN'] %></td></tr>
+ <tr><td>Max sequence length</td><td align='right'><%= analysis1['MAX'] %></td><td align='right'><%= analysis2['MAX'] %></td><td align='right'><%= analysis3['MAX'] %></td></tr>
+ <tr><td>Mean sequence length</td><td align='right'><%= analysis1['MEAN'] %></td><td align='right'><%= analysis2['MEAN'] %></td><td align='right'><%= analysis3['MEAN'] %></td></tr>
</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>
projects / biopieces.git / commitdiff