viral_seq 1.5.0 → 1.6.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 7e42acba2e2ae0e3f17a2786cfa1b5b4a376e0b5723c73ed83d32e9d93509c34
+  metadata.gz: 6bc062e2f207fd9e33d97885125b656c4b24ae8056221020bb611c191104109b
+  data.tar.gz: a0086f02da866821c134a9433317b7016a429e37e775de65d434dbae1b7efd23
 SHA512:
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+  data.tar.gz: f42559bc07b75b2d9a4023af0313cc40e037697970c0ac4a6c34fd04938b5ab879ece19fd95d05237075292c38a93e315018c7e0c03bd0ee9ab8cf1716b894ed

data/README.md

@@ -55,7 +55,7 @@ Example commands:
 ---
 ### `tcs_log`
 
-Use `tcs_log` script to pool run logs and TCS fasta files after one batch of `tcs` jobs.
+Use `tcs_log` script to pool run logs and TCS fasta files after one batch of `tcs` jobs. This command generates log.html to visualize the sequencing runs.
 
 
 Example file structure:  
@@ -179,6 +179,11 @@ qc_seqhash.sdrm_hiv_pr(cut_off)
 
 ## Updates
 
+### Version 1.6.0-01042022
+
+  1. Update the `ViralSeq::TcsCore::detection_limit` with pre-calculated values to save processing time.
+  2. Update `tcs` pipeline to v2.5.0. HTML report will generated after running `tcs_log` script after `tcs` pipeline.
+
 ### Version 1.5.0-01042022
 
   1. Added a function to calcute detection limit/sensitivity for minority variants (R required). `ViralSeq::TcsCore::detection_limit`

data/bin/tcs

@@ -32,9 +32,18 @@ require 'optparse'
 
 options = {}
 
-banner = '-'*50 + "\n" +
-        '| The TCS Pipeline ' + "Version #{ViralSeq::TCS_VERSION}".red.bold + " by " + "Shuntai Zhou".blue.bold + ' |' + "\n" +
-        '-'*50 + "\n"
+# banner = '-'*50 + "\n" +
+#         '| The TCS Pipeline ' + "Version #{ViralSeq::TCS_VERSION}".red.bold + " by " + "Shuntai Zhou".blue.bold + ' |' + "\n" +
+#         '-'*50 + "\n"
+
+banner = "\n" +
+"████████  ██████ ███████     ██████  ██ ██████  ███████ ██      ██ ███    ██ ███████\n".light_red +
+"   ██    ██      ██          ██   ██ ██ ██   ██ ██      ██      ██ ████   ██ ██\n".light_yellow +
+"   ██    ██      ███████     ██████  ██ ██████  █████   ██      ██ ██ ██  ██ █████\n".light_green +
+"   ██    ██           ██     ██      ██ ██      ██      ██      ██ ██  ██ ██ ██\n".light_cyan +
+"   ██     ██████ ███████     ██      ██ ██      ███████ ███████ ██ ██   ████ ███████\n".light_magenta
+
+banner += "\nVersion #{ViralSeq::TCS_VERSION}".red.bold + " by " + "Shuntai Zhou".blue.bold + "\n\n"
 
 OptionParser.new do |opts|
   opts.banner = banner + "Usage: tcs -j"

data/bin/tcs_log

@@ -16,6 +16,7 @@ require 'viral_seq'
 require 'pathname'
 require 'json'
 require 'fileutils'
+require 'csv'
 
 indir = ARGV[0].chomp
 indir_basename = File.basename(indir)
@@ -26,6 +27,7 @@ Dir.mkdir(tcs_dir) unless File.directory?(tcs_dir)
 
 libs = []
 Dir.chdir(indir) {libs = Dir.glob("*")}
+libs.sort_by! {|lib| lib.split("-")[1].to_i}
 
 outdir2 = File.join(tcs_dir, "combined_TCS_per_lib")
 outdir3 = File.join(tcs_dir, "TCS_per_region")
@@ -53,18 +55,26 @@ header = %w{
   Resampling_index
   Combined_TCS
   Combined_TCS_after_QC
+  Detection_Sensitivity
   WARNINGS
 }
 
+pid_dist_data = {}
+
 log.puts header.join(',')
 libs.each do |lib|
   Dir.mkdir(File.join(outdir2, lib)) unless File.directory?(File.join(outdir2, lib))
   fasta_files = []
   json_files = []
+  pid_json_files = []
+  pid_dist_data[lib] = {}
+
   Dir.chdir(File.join(indir, lib)) do
      fasta_files = Dir.glob("**/*.fasta")
      json_files = Dir.glob("**/log.json")
+     pid_json_files = Dir.glob("**/primer_id.json")
   end
+
   fasta_files.each do |f|
     path_array = Pathname(f).each_filename.to_a
     region = path_array[0]
@@ -81,6 +91,14 @@ libs.each do |lib|
 
   json_files.each do |f|
     json_log = JSON.parse(File.read(File.join(indir, lib, f)), symbolize_names: true)
+    tcs_number = json_log[:total_tcs]
+    if json_log[:combined_tcs]
+      tcs_number = json_log[:combined_tcs]
+      if json_log[:combined_tcs_after_qc]
+        tcs_number = json_log[:combined_tcs_after_qc]
+      end
+    end
+
     log.print [lib,
                json_log[:primer_set_name],
                json_log[:total_raw_sequence],
@@ -95,8 +113,604 @@ libs.each do |lib|
                json_log[:resampling_param],
                json_log[:combined_tcs],
                json_log[:combined_tcs_after_qc],
+               ViralSeq::TcsCore::detection_limit(tcs_number.to_i),
                json_log[:warnings],
              ].join(',') + "\n"
   end
+
+  pid_json_files.each do |f|
+    pid_json = JSON.parse(File.read(File.join(indir, lib, f)), symbolize_names: true)
+    region = Pathname(f).each_filename.to_a[-2]
+    pid_dist = {}
+    pid_json[:primer_id_distribution].each {|k,v| pid_dist[k.to_s.to_i] = v}
+    pid_dist_data[lib][region] = pid_dist
+  end
 end
 log.close
+
+# Create HTML page with charts from log.csv above
+
+class String
+    def var_safe
+        gsub '-',''
+    end
+    def shorten_html
+        gsub /\n/, ''
+        gsub /\t/, ''
+    end
+end
+
+colors = ["#332288", "#117733", "#44AA99", "#88CCEE", "#DDCC77", "#CC6677", "#AA4499", "#882255"]
+bool_colors = { true => colors[3], false => colors[5] }
+
+#hold vars for csv input
+raw_sequence_data = ["['Library Name', 'Raw Sequences', { role: 'annotation' }]"]
+lib_names = []
+total_reads = 0
+max_region_char_length = 5
+lib_data = {}
+batch_name = ""
+region_colors = {"Other" => "#808080"}
+
+CSV.foreach(log_file).each_with_index do |row, i|
+    next if i == 0 || row[0] == nil
+
+    lib_name = row[0]
+    region = row[1]
+    raw_sequences_per_barcode = row[2].to_i
+
+    if not region_colors.key?(region)
+        region_colors[region] = colors[region_colors.length % (colors.length - 1)]
+    end
+
+    if region.length > max_region_char_length + 2
+        max_region_char_length = region.length + 2
+    end
+
+    if batch_name == ""
+        batch_name = lib_name.split('-')[0]
+    end
+
+    if not lib_names.include? lib_name
+        lib_names.push(lib_name)
+        total_reads += raw_sequences_per_barcode
+        raw_sequence_data.push("['#{lib_name}', #{raw_sequences_per_barcode}, '#{raw_sequences_per_barcode}']")
+        lib_data[lib_name] = {}
+    end
+
+    lib_data[lib_name][region] = {
+        'lib_name' => lib_name,
+        'region' => region,
+        'raw_sequences_per_barcode' => raw_sequences_per_barcode,
+        'r1_raw' => row[3].to_i,
+        'r2_raw' => row[4].to_i,
+        'paired_raw' => row[5].to_i,
+        'cutoff' => row[6].to_i,
+        'consensus2' => row[9].to_i,
+        'distinct_to_raw' => row[10].to_f,
+        'resampling_index' => row[11].to_f,
+        'combined_TCS' => row[12].to_i,
+        'combined_TCS_after_QC' => row[13].to_i,
+        'detection_sensitivity' => row[14].to_f,
+        'warnings' => row[15].to_s || ""
+    }
+end
+
+#format output
+total_reads = total_reads.to_s.reverse.gsub(/(\d{3})(?=\d)/, '\\1,').reverse
+raw_sequence_data = "[" + raw_sequence_data.join(',') + "]"
+lib_names = lib_names.sort_by { |s| [s.split("-")[0], s.split("-")[1].to_i] }
+
+#calculate 'other'
+lib_data.each do |lib, data|
+    sum = data.values.reduce(0) { |sum, obj| sum + obj['paired_raw'] }
+    raw_sequences_per_barcode = data[data.keys.first]['raw_sequences_per_barcode']
+    other = raw_sequences_per_barcode - sum
+    data['other'] = {
+        "region" => "Other",
+        "paired_raw" => other,
+        "raw_sequences_per_barcode" => raw_sequences_per_barcode
+    }
+end
+
+#process each library's html
+library_links = "
+    <ul>
+        <li id='link_basic-statistics' class='pointer current_page' onclick='showPage(\"basic-statistics\")'>Basic Statistics</li>
+        <li>Libraries
+            <ul style='margin-left: 16px;'>" + lib_names.map { |lib_name| "
+                <li id='link_#{lib_name}' class='pointer' onclick='showPage(\""+lib_name+"\")'>"+lib_name+"</li>"
+                }.join + "
+            </ul>
+        </li>
+    </ul>
+"
+
+library_pages = lib_names.map { |lib_name|
+    "<div id='"+lib_name+"' class='page hidden'>
+        <div class='error-message'></div>
+        <div style='display: flex; gap: 16px; min-height: 45vh;'>
+            <div class='card' style='flex: 1; display: flex; flex-direction: column;'>
+                <h2>Distribution of Raw Sequencing Reads</h2>
+                <div class='pie_chart' style='flex: 1;'></div>
+            </div>
+            <div class='card' style='display: flex; align-items: center; justify-content: center; flex-direction: column; flex: 1;'>
+                " + lib_data[lib_name].map{ |lib, data| data['region'] == "Other" ? "" : "
+                    <div class='#{data['region']}' style='display: flex; align-items: center;'>
+                        <div style='width: #{max_region_char_length.to_s}ch;'>#{data['region']}</div>
+                        <div class='treemap' style='flex: 1; height: #{90 / lib_data[lib_name].length}vh;'></div>
+                    </div>
+                " }.join + "
+            </div>
+        </div>
+        <div class='card'>
+            <h2 style='margin: 32px;'>Number of TCS at Regions</h2>
+            <div class='tcs_bar_chart'></div>
+            <div class='tcs_warnings' style='text-align: center;color: red;font-weight: bold;margin-left: 24px;'><strong></strong></div>
+        </div>
+        <div class='card'>
+            <h2>Detection Sensitivity</h2>
+            <p><i>The lowest abundance of minority mutations that can be detected with 95% confidence</i></p>
+            <div class='detection_sensitivity_chart'></div>
+        </div>
+        <div class='card'>
+            <h2 style='text-align: center;'>Distinct to Raw</h2>
+            <p><i>Distinct to Raw greater than 0.1 suggests more raw sequences are required to fully recover TCS</i></p>
+            <div class='raw_bar_chart'></div>
+        </div>
+        <div class='card'>
+            <h2>Resampling Index</h2>
+            <p><i>Resampling index less than 0.9 suggests Primer ID resampling</i></p>
+            <div class='resampling_bar_chart'></div>
+        </div>
+        <div class='card'>
+            <h2>Primer ID bin size distribution</h2>
+            <p><i>Red vertical line shows the consensus cut-off value</i></p>
+            " + lib_data[lib_name].map{ |lib, data| data['region'] == "Other" ? "" : "
+                <div class='#{data['region']} scatter' style='height: #{90 / 3}vh;'></div>
+            " }.join + "
+        </div>
+    </div>"
+}.join
+
+#format lib_data into charts
+paired_raw = {}
+tree_charts = {}
+tcs_bar_chart = {}
+distinct_bar_chart = {}
+resampling_bar_chart = {}
+detection_sensitivity_chart = {}
+
+lib_data.each do |lib, data|
+    paired_raw[lib] = {}
+
+    paired_raw[lib]['data'] = "
+        [
+            ['Region', 'Paired Raw'], " +
+            data.map { |lib, d| "
+                ['#{d['region']},#{d['paired_raw']}', #{d['paired_raw']}],
+            " }.join + "
+        ]
+    "
+
+    paired_raw[lib]['slices'] = "[#{
+        data.map{ |lib, d| "{color: '#{region_colors[d['region']]}'}" }.join(',')
+    }]"
+
+    paired_raw[lib]['residuel_text'] = data.map { |lib, d|
+        (d['paired_raw'].to_f / d['raw_sequences_per_barcode'].to_f) < (0.5/360) ?
+            "#{d['region']},#{d['paired_raw']}" :
+            nil
+    }.compact.join(" - ")
+
+    tree_charts[lib] = {}
+    data.each do |region, d|
+        if region != "other"
+            tree_charts[lib][region] = "
+                [
+                    ['Location', 'Parent', 'r'],
+                    ['Global', null,0],
+                    ['R1_Raw', 'Global', #{d['r1_raw'].to_s}],
+                    ['R2_Raw', 'Global', #{d['r2_raw'].to_s}],
+                    ['Paired_Raw', 'Global', #{d['paired_raw'].to_s}],
+                ]
+            "
+        end
+    end
+
+    has_c = data.values.inject(0) {|sum, h| sum + (h['combined_TCS'] == nil ? 0 : h['combined_TCS']) } > 0
+    has_qc = data.values.inject(0) {|sum, h| sum + (h['combined_TCS_after_QC'] == nil ? 0 : h['combined_TCS_after_QC']) } > 0
+
+    tcs_bar_chart[lib] = {
+        'data' => "
+            [
+                [
+                    'Region',
+                    'TCS',
+                    #{has_c ? "'Combined TCS'," : ''}
+                    #{has_qc ? "'TCS After QC'," : ''}
+                ],
+                " + data.map{ |region, d| d['region'] === "Other" ? "" : "
+                [
+                    '#{d['region']}#{d['warnings'].length > 0 ? '*' : ''}',
+                    #{d['consensus2']}  ,
+                    #{has_c ? "#{d['combined_TCS']}," : ''}
+                    #{has_qc ? "#{d['combined_TCS_after_QC']}," : ''}
+                ],
+                " }.join + "
+            ]
+        ",
+        'warnings' => data.map{ |region, d|
+            d['region'] != "Other" && d['warnings'].length > 0 ? "#{region} - #{d["warnings"]}<br/>" : ''
+        }.join
+    }
+
+    detection_sensitivity_chart[lib] = "[
+        ['Region', 'Detection Sensitivity'],
+        #{ data.map{ |region, d|
+            d['region'] == 'Other' ? "" : "['#{d['region']}', #{d['detection_sensitivity']}]"
+        }.join(',') }
+    ]"
+
+    distinct_bar_chart[lib] = "
+        [
+            ['Region','Distinct to Raw', {role: 'style'}],
+            "+ data.map{ |region, d| d['region'] == 'Other' ? "" : "
+            [
+                '#{d['region']}', #{d['distinct_to_raw']}, '#{bool_colors[d['distinct_to_raw'].to_f < 0.1]}'
+            ],"}.join + "
+        ]
+    "
+
+    resampling_bar_chart[lib] = "
+        [
+            ['Region','Resampling Index', {role: 'style'}],
+            "+ data.map{ |region, d| d['region'] == 'Other' ? "" : "
+            [
+                '#{d['region']}', #{d['resampling_index']}, '#{bool_colors[d['resampling_index'].to_f > 0.9]}'
+            ]," }.join + "
+        ]
+    "
+end
+
+scatter_charts = {}
+
+pid_dist_data.each do |lib, data|
+    scatter_charts[lib] = {}
+    data.each do |region, d|
+        max_x = d.max_by{|index, distribution| distribution }[1]
+        max_x = "1#{ max_x.to_s.chars.map{ |c| "0"}.join }"
+        scatter_charts[lib][region] = "[
+            ['Index', 'Distribution', 'Cutoff'],
+            [#{lib_data[lib][region]['cutoff'].to_s}, null, 0],
+            [#{lib_data[lib][region]['cutoff'].to_s}, null, #{max_x}],
+            #{d.map{ |index, distribution| "[#{index}, #{distribution}, null]" }.join(',') },
+        ]"
+    end
+end
+
+#create JS that initializes charts
+paired_raw_js = paired_raw.map { |lib, data| '
+    var element_pie_'+lib.var_safe+' = document.querySelector("#'+lib+' .pie_chart")
+    if(isVisible(element_pie_'+lib.var_safe+')){
+        var chart_pie_'+lib.var_safe+' = new google.visualization.PieChart(element_pie_'+lib.var_safe+');
+        chart_pie_'+lib.var_safe+'.draw(
+            google.visualization.arrayToDataTable('+data['data']+'),
+            {
+                title: "Paired Raw",
+                titleTextStyle: {
+                    fontSize: 18
+                },
+                pieSliceText: "label",
+                slices: ' + data['slices'] + ',
+                legend: {
+                    position: "left",
+                    alignment: "center"
+                },
+                chartArea: {
+                    width: "100%",
+                    height: "100%"
+                },
+                ' + (data['residuel_text'].length > 0 ? "pieResidueSliceLabel: '#{data['residuel_text']}'" : "") + '
+            }
+        );
+    }
+' }.join
+
+tree_charts_js = tree_charts.map { |lib, d|
+    d.map { |region, data| '
+        var element_chart_tree_'+lib.var_safe+'_'+region.var_safe+' = document.querySelector("#'+lib+' .'+region+' .treemap")
+        if(isVisible(element_chart_tree_'+lib.var_safe+'_'+region.var_safe+')){
+            var chart_tree_'+lib.var_safe+'_'+region.var_safe+' = new google.visualization.TreeMap(element_chart_tree_'+lib.var_safe+'_'+region.var_safe+');
+            chart_tree_'+lib.var_safe+'_'+region.var_safe+'.draw(
+                google.visualization.arrayToDataTable('+data+'),
+                {
+                    headerHeight: 0,
+                    minColor: "' + colors[1] + '",
+                    maxColor: "' + colors[5] + '",
+                    fontColor: "#fff",
+                }
+            );
+            google.visualization.events.addListener(chart_tree_'+lib.var_safe+'_'+region.var_safe+', "select", function () {
+                chart_tree_'+lib.var_safe+'_'+region.var_safe+'.setSelection([]);
+            });
+        }
+    '}
+}.join
+
+tcs_bar_chart_js = tcs_bar_chart.map { |lib, data| '
+    var element_tcs_bar_chart_'+lib.var_safe+' = document.querySelector("#'+lib+' .tcs_bar_chart")
+    if(isVisible(element_tcs_bar_chart_'+lib.var_safe+')){
+        var tcs_bar_chart_'+lib.var_safe+' = new google.charts.Bar(element_tcs_bar_chart_'+lib.var_safe+');
+        tcs_bar_chart_'+lib.var_safe+'.draw(
+            google.visualization.arrayToDataTable('+data["data"]+'),
+            google.charts.Bar.convertOptions({
+                colors: ["' + colors[0] + '", "' + colors[1] + '", "' + colors[2] + '"],
+                legend: { position: "bottom" },
+                height: Math.round(window.innerHeight * .5),
+                chartArea: {
+                    width: "100%",
+                    height: "100%"
+                }
+            })
+        );
+        document.querySelector("#'+lib+' .tcs_warnings").innerHTML = "'+data['warnings']+'";
+    }
+' }.join
+
+detection_sensitivity_js = detection_sensitivity_chart.map { |lib, data| '
+    var element_detection_'+lib.var_safe+' = document.querySelector("#'+lib+' .detection_sensitivity_chart")
+    if(isVisible(element_detection_'+lib.var_safe+')){
+        var detection_'+lib.var_safe+' = new google.visualization.ColumnChart(element_detection_'+lib.var_safe+');
+        detection_'+lib.var_safe+'.draw(
+            google.visualization.arrayToDataTable('+data+'),
+            {
+                legend: {
+                    position: "none"
+                },
+                height: Math.round(window.innerHeight * .5),
+                colors: ["' + colors[3] + '"],
+                vAxis: {
+                      scaleType: "log",
+                      viewWindow: {
+                        min: 0.00001
+                      },
+                      ticks: [0.00001, 0.0001, 0.001, 0.01, 0.1, 1]
+                }
+            }
+        );
+    }
+'}.join
+
+distinct_bar_chart_js = distinct_bar_chart.map { |lib, data| '
+    var element_distinct_'+lib.var_safe+' = document.querySelector("#'+lib+' .raw_bar_chart")
+    if(isVisible(element_distinct_'+lib.var_safe+')){
+        var distinct_'+lib.var_safe+' = new google.visualization.ColumnChart(element_distinct_'+lib.var_safe+');
+        distinct_'+lib.var_safe+'.draw(
+            google.visualization.arrayToDataTable('+data+'),
+            {
+                legend: {
+                    position: "none"
+                },
+                height: Math.round(window.innerHeight * .5),
+            }
+        );
+    }
+' }.join
+
+resampling_bar_chart_js = resampling_bar_chart.map { |lib, data| '
+    var element_resampling_'+lib.var_safe+' = document.querySelector("#'+lib+' .resampling_bar_chart")
+    if(isVisible(element_resampling_'+lib.var_safe+')){
+        var resampling_'+lib.var_safe+' = new google.visualization.ColumnChart(element_resampling_'+lib.var_safe+');
+        resampling_'+lib.var_safe+'.draw(
+            google.visualization.arrayToDataTable('+data+'),
+            {
+                legend: {
+                    position: "none"
+                },
+                height: Math.round(window.innerHeight * .5),
+            }
+        );
+    }
+' }.join
+
+scatter_charts_js = scatter_charts.map { |lib, d|
+    d.map { |region, data| '
+        var element_chart_scatter_'+lib.var_safe+'_'+region.var_safe+' = document.querySelector("#'+lib+' .'+region+'.scatter")
+        if(isVisible(element_chart_scatter_'+lib.var_safe+'_'+region.var_safe+')){
+            var chart_scatter_'+lib.var_safe+'_'+region.var_safe+' = new google.visualization.ComboChart(element_chart_scatter_'+lib.var_safe+'_'+region.var_safe+');
+
+            var view_'+lib.var_safe+'_'+region.var_safe+' = new google.visualization.DataView(
+                google.visualization.arrayToDataTable(' + data + ')
+            );
+
+            chart_scatter_'+lib.var_safe+'_'+region.var_safe+'.draw(
+                view_'+lib.var_safe+'_'+region.var_safe+',
+                {
+                    pointSize: 5,
+                    title: "' + region + '",
+                    hAxis: {title: "Raw sequencing reads per unique PID"},
+                    vAxis: {
+                        title: "# of PIDs ",
+                        logScale: true
+                    },
+                    colors: ["' + bool_colors[true] + '"],
+                    legend: "none",
+                    seriesType: "scatter",
+                    series: {
+                        1: {
+                            type: "line",
+                            color: "' + bool_colors[false] + '",
+                            pointsVisible: false,
+                        }
+                    }
+                }
+            );
+        }
+    '}
+}.join
+
+html = '
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="UTF-8">
+        <meta http-equiv="X-UA-Compatible" content="IE=edge">
+        <meta name="viewport" content="width=device-width, initial-scale=1.0">
+        <title>TCS Log</title>
+        <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/materialize/1.0.0/css/materialize.min.css">
+        <script src="https://www.gstatic.com/charts/loader.js"></script>
+        <script>
+            google.charts.load("current", {packages: ["corechart", "treemap", "bar"]});
+            google.charts.setOnLoadCallback(drawChart);
+
+            var isInit = false
+
+            function isVisible(el) {
+                return (el.offsetParent !== null)
+            }
+
+            function drawChart() {
+
+                document.querySelectorAll(".error-message").forEach(element => element.innerHTML = "")
+
+                if(! isInit){
+                    isInit = true;
+                    window.onresize = drawChart;
+                }
+
+                try{
+                    var element_home_chart = document.getElementById("raw-sequence-chart")
+                    if(isVisible(element_home_chart)){
+                        var home_chart = new google.visualization.ColumnChart(element_home_chart);
+                        home_chart.draw(
+                            google.visualization.arrayToDataTable('+raw_sequence_data+'),
+                            {
+                                annotations: {alwaysOutside: true},
+                                colors: ["' + bool_colors[true] + '"]
+                            }
+                        );
+                    }'+ paired_raw_js + tree_charts_js + tcs_bar_chart_js + distinct_bar_chart_js + resampling_bar_chart_js + detection_sensitivity_js + scatter_charts_js + '
+                }catch(e){
+                    console.log(e);
+                    document.querySelectorAll(".error-message").forEach(element =>
+                        element.innerHTML = "There was an error displaying your data.<br>To help us improve, please forward this html file to<br>shuntaiz@email.unc.edu"
+                    )
+                }
+            }
+
+            function showPage(pageID){
+                document.querySelectorAll(".page").forEach(element => element.classList.add("hidden"))
+                document.getElementById(pageID).classList.remove("hidden")
+
+                document.querySelectorAll(".current_page").forEach(element => element.classList.remove("current_page"));
+                document.getElementById("link_"+pageID).classList.add("current_page");
+
+                drawChart();
+            }
+        </script>
+    </head>
+    <body>
+        <div style="display: flex; flex-direction: column; height: 100vh; width: 100vw; position: fixed; overflow: hidden;">
+            <div style="display: flex; gap: 4px;">
+                <div id="nav" class="card" style="overflow: auto; min-height: 100vh; text-align: left; margin-top: 0;">
+                    <a href="https://primer-id.org" target="_BLANK">
+                        <h3 style="margin: 24px; font-weight: 600; color: #333 !important">TCS Log</h3>
+                    </a>
+                    '+library_links+'
+                </div>
+                <div id="pages" style="flex: 1; overflow: auto; height: 100vh;">
+                    <div style="display: flex; flex-direction: column; align-items: center; height: 100vh;" id="basic-statistics" class="page">
+                        <div class="error-message"></div>
+                        <div class="card" style="margin-top: 16px; width: 100%;">
+                            <table id="home-table">
+                                <tr>
+                                    <td>Batch Name</td>
+                                    <td>'+batch_name+'</td>
+                                </tr>
+                                <tr>
+                                    <td>Processed Time</td>
+                                    <td>'+Time.now.strftime("%m/%d/%Y")+'</td>
+                                </tr>
+                                <tr>
+                                    <td>TCS Version</td>
+                                    <td>'+ViralSeq::TCS_VERSION+'</td>
+                                </tr>
+                                <tr>
+                                    <td>viral_seq Version</td>
+                                    <td>'+ViralSeq::VERSION+'</td>
+                                </tr>
+                                <tr>
+                                    <td>Number of Libraries</td>
+                                    <td>'+lib_names.length.to_s+'</td>
+                                </tr>
+                                <tr>
+                                    <td>Total Reads</td>
+                                    <td>'+total_reads+'</td>
+                                </tr>
+                            </table>
+                        </div>
+                        <div class="card" style="margin-top: 16px; width: 100%;">
+                            <h2>Raw Sequences Distribution</h2>
+                            <div id="raw-sequence-chart"></div>
+                        </div>
+                    </div>
+                    '+library_pages+'
+                </div>
+            </div>
+        </div>
+    </body>
+    <style>
+        body {
+            font-size: 1.2rem;
+            color: #333;
+        }
+        #nav ul {
+            list-style-type: none;
+        }
+        .page {
+            margin: 16px;
+        }
+        .card {
+            padding: 16px;
+            text-align: center;
+        }
+        .hidden {
+            display: none !important;
+            visibility: hidden !important;
+        }
+        .pointer {
+            cursor: pointer;
+        }
+        #home-table {
+            margin: 0 auto;
+            width: 80%;
+            border-collapse: collapse;
+        }
+        #home-table, #home-table th, #home-table td {
+            border: 1px solid black;
+        }
+        #home-table td {
+            padding: 8px;
+        }
+        .current_page {
+            border-bottom: 1px solid blue;
+        }
+        .error-message {
+            background: red !important;
+            color: white;
+            border-radius: 15px;
+            font-weight: bold;
+            font-size: 1.8rem;
+            text-align: center;
+            padding: 1%;
+            margin: 16px auto;
+        }
+        .error-message:empty {
+            display: none;
+        }
+    </style>
+</html>
+'.shorten_html
+
+File.open(File.join(tcs_dir,"log.html"), 'w') { |file| file.write(html) }

data/lib/viral_seq/constant.rb

@@ -4,7 +4,7 @@ module ViralSeq
   AMINO_ACID_LIST = ["A", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M", "N", "P", "Q", "R", "S", "T", "V", "W", "Y", "*"]
 
   # R script to check if the required libraries are installed, if not, install the missing libraries
-  
+
   R_SCRIPT_CHECK_PACKAGES = 'dir.create(path = Sys.getenv("R_LIBS_USER"), showWarnings = FALSE, recursive = TRUE);' +
                             'packages <- c("ggplot2", "phangorn", "ape", "scales", "ggforce", "cowplot", "magrittr", "gridExtra");' +
                             'install.packages(setdiff(packages, rownames(installed.packages())), lib = Sys.getenv("R_LIBS_USER"), repos = "https://cran.rstudio.com/")'
@@ -44,5 +44,7 @@ module ViralSeq
               }
               dev.off()'
 
+  DETECT_SEN = {0=>1.0, 1=>1.0, 2=>1.0, 3=>0.7076, 4=>0.6024, 5=>0.5218, 6=>0.4593, 7=>0.4096, 8=>0.3694, 9=>0.3363, 10=>0.3085, 11=>0.2849, 12=>0.2646, 13=>0.2471, 14=>0.2316, 15=>0.218, 16=>0.2059, 17=>0.1951, 18=>0.1853, 19=>0.1765, 20=>0.1684, 21=>0.1611, 22=>0.1544, 23=>0.1482, 24=>0.1425, 25=>0.1372, 26=>0.1323, 27=>0.1277, 28=>0.1234, 29=>0.1194, 30=>0.1157, 31=>0.1122, 32=>0.1089, 33=>0.1058, 34=>0.1028, 35=>0.1, 36=>0.0974, 37=>0.0949, 38=>0.0925, 39=>0.0903, 40=>0.0881, 41=>0.086, 42=>0.0841, 43=>0.0822, 44=>0.0804, 45=>0.0787, 46=>0.0771, 47=>0.0755, 48=>0.074, 49=>0.0725, 50=>0.0711, 51=>0.0698, 52=>0.0685, 53=>0.0672, 54=>0.066, 55=>0.0649, 56=>0.0638, 57=>0.0627, 58=>0.0616, 59=>0.0606, 60=>0.0596, 61=>0.0587, 62=>0.0578, 63=>0.0569, 64=>0.056, 65=>0.0552, 66=>0.0544, 67=>0.0536, 68=>0.0528, 69=>0.0521, 70=>0.0513, 71=>0.0506, 72=>0.0499, 73=>0.0493, 74=>0.0486, 75=>0.048, 76=>0.0474, 77=>0.0468, 78=>0.0462, 79=>0.0456, 80=>0.0451, 81=>0.0445, 82=>0.044, 83=>0.0435, 84=>0.043, 85=>0.0425, 86=>0.042, 87=>0.0415, 88=>0.0411, 89=>0.0406, 90=>0.0402, 91=>0.0397, 92=>0.0393, 93=>0.0389, 94=>0.0385, 95=>0.0381, 96=>0.0377, 97=>0.0373, 98=>0.0369, 99=>0.0366, 100=>0.0362, 101=>0.0359, 102=>0.0355, 103=>0.0352, 104=>0.0348, 105=>0.0345, 106=>0.0342, 107=>0.0339, 108=>0.0336, 109=>0.0333, 110=>0.033, 111=>0.0327, 112=>0.0324, 113=>0.0321, 114=>0.0318, 115=>0.0316, 116=>0.0313, 117=>0.031, 118=>0.0308, 119=>0.0305, 120=>0.0303, 121=>0.03, 122=>0.0298, 123=>0.0295, 124=>0.0293, 125=>0.0291, 126=>0.0289, 127=>0.0286, 128=>0.0284, 129=>0.0282, 130=>0.028, 131=>0.0278, 132=>0.0276, 133=>0.0274, 134=>0.0272, 135=>0.027, 136=>0.0268, 137=>0.0266, 138=>0.0264, 139=>0.0262, 140=>0.026, 141=>0.0258, 142=>0.0256, 143=>0.0255, 144=>0.0253, 145=>0.0251, 146=>0.0249, 147=>0.0248, 148=>0.0246, 149=>0.0245, 150=>0.0243, 151=>0.0241, 152=>0.024, 153=>0.0238, 154=>0.0237, 155=>0.0235, 156=>0.0234, 157=>0.0232, 158=>0.0231, 159=>0.0229, 160=>0.0228, 161=>0.0227, 162=>0.0225, 163=>0.0224, 164=>0.0222, 165=>0.0221, 166=>0.022, 167=>0.0218, 168=>0.0217, 169=>0.0216, 170=>0.0215, 171=>0.0213, 172=>0.0212, 173=>0.0211, 174=>0.021, 175=>0.0209, 176=>0.0207, 177=>0.0206, 178=>0.0205, 179=>0.0204, 180=>0.0203, 181=>0.0202, 182=>0.0201, 183=>0.02, 184=>0.0198, 185=>0.0197, 186=>0.0196, 187=>0.0195, 188=>0.0194, 189=>0.0193, 190=>0.0192, 191=>0.0191, 192=>0.019, 193=>0.0189, 194=>0.0188, 195=>0.0187, 196=>0.0186, 197=>0.0186, 198=>0.0185, 199=>0.0184, 200=>0.0183, 201=>0.0182, 202=>0.0181, 203=>0.018, 204=>0.0179, 205=>0.0178, 206=>0.0177, 207=>0.0177, 208=>0.0176, 209=>0.0175, 210=>0.0174, 211=>0.0173, 212=>0.0172, 213=>0.0172, 214=>0.0171, 215=>0.017, 216=>0.0169, 217=>0.0169, 218=>0.0168, 219=>0.0167, 220=>0.0166, 221=>0.0166, 222=>0.0165, 223=>0.0164, 224=>0.0163, 225=>0.0163, 226=>0.0162, 227=>0.0161, 228=>0.016, 229=>0.016, 230=>0.0159, 231=>0.0158, 232=>0.0158, 233=>0.0157, 234=>0.0156, 235=>0.0156, 236=>0.0155, 237=>0.0154, 238=>0.0154, 239=>0.0153, 240=>0.0153, 241=>0.0152, 242=>0.0151, 243=>0.0151, 244=>0.015, 245=>0.0149, 246=>0.0149, 247=>0.0148, 248=>0.0148, 249=>0.0147, 250=>0.0146, 251=>0.0146, 252=>0.0145, 253=>0.0145, 254=>0.0144, 255=>0.0144, 256=>0.0143, 257=>0.0143, 258=>0.0142, 259=>0.0141, 260=>0.0141, 261=>0.014, 262=>0.014, 263=>0.0139, 264=>0.0139, 265=>0.0138, 266=>0.0138, 267=>0.0137, 268=>0.0137, 269=>0.0136, 270=>0.0136, 271=>0.0135, 272=>0.0135, 273=>0.0134, 274=>0.0134, 275=>0.0133, 276=>0.0133, 277=>0.0132, 278=>0.0132, 279=>0.0131, 280=>0.0131, 281=>0.013, 282=>0.013, 283=>0.013, 284=>0.0129, 285=>0.0129, 286=>0.0128, 287=>0.0128, 288=>0.0127, 289=>0.0127, 290=>0.0126, 291=>0.0126, 292=>0.0126, 293=>0.0125, 294=>0.0125, 295=>0.0124, 296=>0.0124, 297=>0.0123, 298=>0.0123, 299=>0.0123, 300=>0.0122, 301=>0.0122, 302=>0.0121, 303=>0.0121, 304=>0.0121, 305=>0.012, 306=>0.012, 307=>0.0119, 308=>0.0119, 309=>0.0119, 310=>0.0118, 311=>0.0118, 312=>0.0118, 313=>0.0117, 314=>0.0117, 315=>0.0116, 316=>0.0116, 317=>0.0116, 318=>0.0115, 319=>0.0115, 320=>0.0115, 321=>0.0114, 322=>0.0114, 323=>0.0114, 324=>0.0113, 325=>0.0113, 326=>0.0113, 327=>0.0112, 328=>0.0112, 329=>0.0111, 330=>0.0111, 331=>0.0111, 332=>0.011, 333=>0.011, 334=>0.011, 335=>0.011, 336=>0.0109, 337=>0.0109, 338=>0.0109, 339=>0.0108, 340=>0.0108, 341=>0.0108, 342=>0.0107, 343=>0.0107, 344=>0.0107, 345=>0.0106, 346=>0.0106, 347=>0.0106, 348=>0.0105, 349=>0.0105, 350=>0.0105, 351=>0.0105, 352=>0.0104, 353=>0.0104, 354=>0.0104, 355=>0.0103, 356=>0.0103, 357=>0.0103, 358=>0.0103, 359=>0.0102, 360=>0.0102, 361=>0.0102, 362=>0.0101, 363=>0.0101, 364=>0.0101, 365=>0.0101, 366=>0.01, 367=>0.01, 368=>0.01, 369=>0.0099, 370=>0.0099, 371=>0.0099, 372=>0.0099, 373=>0.0098, 374=>0.0098, 375=>0.0098, 376=>0.0098, 377=>0.0097, 378=>0.0097, 379=>0.0097, 380=>0.0097, 381=>0.0096, 382=>0.0096, 383=>0.0096, 384=>0.0096, 385=>0.0095, 386=>0.0095, 387=>0.0095, 388=>0.0095, 389=>0.0094, 390=>0.0094, 391=>0.0094, 392=>0.0094, 393=>0.0093, 394=>0.0093, 395=>0.0093, 396=>0.0093, 397=>0.0092, 398=>0.0092, 399=>0.0092, 400=>0.0092, 401=>0.0092, 402=>0.0091, 403=>0.0091, 404=>0.0091, 405=>0.0091, 406=>0.009, 407=>0.009, 408=>0.009, 409=>0.009, 410=>0.009, 411=>0.0089, 412=>0.0089, 413=>0.0089, 414=>0.0089, 415=>0.0088, 416=>0.0088, 417=>0.0088, 418=>0.0088, 419=>0.0088, 420=>0.0087, 421=>0.0087, 422=>0.0087, 423=>0.0087, 424=>0.0087, 425=>0.0086, 426=>0.0086, 427=>0.0086, 428=>0.0086, 429=>0.0086, 430=>0.0085, 431=>0.0085, 432=>0.0085, 433=>0.0085, 434=>0.0085, 435=>0.0084, 436=>0.0084, 437=>0.0084, 438=>0.0084, 439=>0.0084, 440=>0.0083, 441=>0.0083, 442=>0.0083, 443=>0.0083, 444=>0.0083, 445=>0.0083, 446=>0.0082, 447=>0.0082, 448=>0.0082, 449=>0.0082, 450=>0.0082, 451=>0.0081, 452=>0.0081, 453=>0.0081, 454=>0.0081, 455=>0.0081, 456=>0.0081, 457=>0.008, 458=>0.008, 459=>0.008, 460=>0.008, 461=>0.008, 462=>0.008, 463=>0.0079, 464=>0.0079, 465=>0.0079, 466=>0.0079, 467=>0.0079, 468=>0.0079, 469=>0.0078, 470=>0.0078, 471=>0.0078, 472=>0.0078, 473=>0.0078, 474=>0.0078, 475=>0.0077, 476=>0.0077, 477=>0.0077, 478=>0.0077, 479=>0.0077, 480=>0.0077, 481=>0.0076, 482=>0.0076, 483=>0.0076, 484=>0.0076, 485=>0.0076, 486=>0.0076, 487=>0.0075, 488=>0.0075, 489=>0.0075, 490=>0.0075, 491=>0.0075, 492=>0.0075, 493=>0.0075, 494=>0.0074, 495=>0.0074, 496=>0.0074, 497=>0.0074, 498=>0.0074, 499=>0.0074, 500=>0.0074, 501=>0.0073, 502=>0.0073, 503=>0.0073, 504=>0.0073, 505=>0.0073, 506=>0.0073, 507=>0.0072, 508=>0.0072, 509=>0.0072, 510=>0.0072, 511=>0.0072, 512=>0.0072, 513=>0.0072, 514=>0.0072, 515=>0.0071, 516=>0.0071, 517=>0.0071, 518=>0.0071, 519=>0.0071, 520=>0.0071, 521=>0.0071, 522=>0.007, 523=>0.007, 524=>0.007, 525=>0.007, 526=>0.007, 527=>0.007, 528=>0.007, 529=>0.0069, 530=>0.0069, 531=>0.0069, 532=>0.0069, 533=>0.0069, 534=>0.0069, 535=>0.0069, 536=>0.0069, 537=>0.0068, 538=>0.0068, 539=>0.0068, 540=>0.0068, 541=>0.0068, 542=>0.0068, 543=>0.0068, 544=>0.0068, 545=>0.0067, 546=>0.0067, 547=>0.0067, 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9994=>0.0004, 9995=>0.0004, 9996=>0.0004, 9997=>0.0004, 9998=>0.0004, 9999=>0.0004, 10000=>0.0004}
+
 
 end

data/lib/viral_seq/tcs_core.rb

@@ -6,6 +6,10 @@ module ViralSeq
     class << self
 
       # methods to calculate TCS consensus cut-off based on the maximum numbers of PIDs and platform error rate.
+      # @see https://www.ncbi.nlm.nih.gov/pubmed/26041299 reference at Zhou et al. JVI 2016.
+      # @param m [Integer] PID abundance
+      # @param error_rate [Float] estimated platform error rate.
+      # @return [Integer] an abundance cut-off (Integer) for offspring Primer IDs.
 
       def calculate_cut_off(m, error_rate = 0.02)
         n = 0
@@ -289,8 +293,12 @@ module ViralSeq
       #   => 0.0362
 
       def detection_limit(tcs_number)
-        dl =  `Rscript -e "library(dplyr); ifelse(#{tcs_number} > 2, (binom.test(0,#{tcs_number})['conf.int'] %>% unlist %>% unname)[2] %>% round(4) %>% cat, 0)" 2>/dev/null`
-        dl.to_f
+        if ViralSeq::DETECT_SEN[tcs_number]
+          return ViralSeq::DETECT_SEN[tcs_number]
+        else
+          dl =  `Rscript -e "library(dplyr); ifelse(#{tcs_number} > 2, (binom.test(0,#{tcs_number})['conf.int'] %>% unlist %>% unname)[2] %>% round(4) %>% cat, 0)" 2>/dev/null`
+          dl.to_f
+        end
       end
 
       private

data/lib/viral_seq/version.rb

@@ -2,6 +2,6 @@
 # version info and histroy
 
 module ViralSeq
-  VERSION = "1.5.0"
-  TCS_VERSION = "2.4.0"
+  VERSION = "1.6.0"
+  TCS_VERSION = "2.5.0"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: viral_seq
 version: !ruby/object:Gem::Version
-  version: 1.5.0
+  version: 1.6.0
 platform: ruby
 authors:
 - Shuntai Zhou
@@ -9,7 +9,7 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-01-06 00:00:00.000000000 Z
+date: 2022-01-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -172,6 +172,7 @@ files:
 - docs/dr.json
 - docs/sample_miseq_data/hivdr_control/r1.fastq.gz
 - docs/sample_miseq_data/hivdr_control/r2.fastq.gz
+- docs/variants_structure.pdf
 - lib/viral_seq.rb
 - lib/viral_seq/constant.rb
 - lib/viral_seq/enumerable.rb