adding bzip2 support in ruby

[biopieces.git] / bp_scripts / QA_Illumina_report.rb

diff --git a/bp_scripts/QA_Illumina_report.rb b/bp_scripts/QA_Illumina_report.rb
index d7deb9244d7a3328794bdfcb1c33f310c30be71b..6e0ba0a4c10c9ec695daf0c81dd1fb0c5f591c6c 100755 (executable)
--- a/bp_scripts/QA_Illumina_report.rb
+++ b/bp_scripts/QA_Illumina_report.rb
@@ -66,19 +66,19 @@ scores_bin_file                = File.join(tmpdir, 'scores_bin.png')
 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 -c 12 -l 6 -L 6 -f ACACGACGCTCTTCCGATCT -r AGATCGGAAGAGCACACGTC |
+   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} |
+   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 |
@@ -112,7 +112,7 @@ template = %{
       </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>