Created
December 25, 2013 10:57
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| #!/usr/bin/ruby | |
| $pp = true # pretty print | |
| $head = true # display header | |
| $targetdir = ( ARGV[0] || "fastqc") | |
| files = Dir["#{$targetdir}/*_fastqc/fastqc_data.txt"] | |
| data_read1 = []; data_read2 = []; | |
| data_read1_un = []; data_read2_un = []; | |
| # p files.size | |
| files.each do |f| | |
| # p f | |
| txt = File.open(f).read | |
| m = /^Total Sequences\s+(\d+)/.match(txt) | |
| count = m[1].to_i | |
| name = File.dirname(f).split(%r{/})[-1].sub(/_\d{3}_fastqc$/, '') | |
| if m2 = /^idx(\d+)_[ATGC]+_L(\d+)_R(1|2)$/.match(name) || | |
| m2 = /^idx(\d+)_NoIndex_L(\d+)_R(1|2)$/.match(name) || | |
| m2 = /^(N\d+\-N\d+)_[ATGC]+\-[ATGC]+_L(\d+)_R(1|2)$/.match(name) | |
| lane = m2[2].to_i | |
| read = m2[3].to_i | |
| bc = m2[1] | |
| # p [name, lane, bc, count] | |
| if read == 1 | |
| data_read1 << [name, lane, bc, count] | |
| elsif read == 2 | |
| data_read2 << [name, lane, bc, count] | |
| end | |
| elsif m2 = /^lane(\d+)_Undetermined_L(\d+)_R(1|2)$/.match(name) | |
| lane = m2[1].to_i | |
| read = m2[3].to_i | |
| bc = 0 | |
| if read == 1 | |
| data_read1_un << [name, lane, bc, count] | |
| elsif read == 2 | |
| data_read2_un << [name, lane, bc, count] | |
| end | |
| end | |
| end | |
| ## summary by lane | |
| puts "# " + %w{Lane #idx indexes #reads_total idx:#reads:% }.join("\t") if $head | |
| [data_read1, data_read2, data_read1_un, data_read2_un].each_with_index do |data, i| | |
| case i | |
| when 0 | |
| puts '# Read1' | |
| when 1 | |
| puts "# Read2" | |
| when 2 | |
| puts "# Undetermined (index unknown) Read1" | |
| when 3 | |
| puts "# Undetermined (index unknown) Read2" | |
| end | |
| data.map{|x| x[1]}.sort.uniq.each do |lane| | |
| data2 = [] | |
| data2 << lane | |
| lset = data.select{|y| y[1] == lane} | |
| data2 << lset.length | |
| data2 << lset.map{|y| y[2]}.sort.join(",") | |
| subtotal = lset.map{|y| y[3]}.inject(0){|n, m | n + m} | |
| if $pp | |
| data2 << sprintf("%.1fM", subtotal/1000000.to_f) | |
| else | |
| data2 << subtotal | |
| end | |
| lset.sort{|a, b| a[2] <=> b[2]}.each do |z| | |
| if $pp | |
| data2 << [z[2], | |
| sprintf("%.1fM", z[3]/1000000.to_f), | |
| sprintf("%.1f%%", z[3]/subtotal.to_f*100)].join(":") | |
| else | |
| data2 << [z[2], z[3], sprintf("%.1f%%", z[3]/subtotal.to_f*100)].join(":") | |
| end | |
| end | |
| puts data2.join("\t") | |
| end | |
| puts "//" | |
| end |
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