viral_seq 1.7.1 → 1.8.1.1

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: a69e78c80f22848facb41ad4f9d9fb64e6d4e47ff6e18afa3421d64513ce6558
+  metadata.gz: 11381ab74d67a54b5d922e8f1a7085866fe5349f4124a971b9dc64709fa763f1
+  data.tar.gz: dd578b649b9857cf1c7ff8a23fff62db51f665ef23c74c8000a2b4d7f4500f9e
 SHA512:
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-  data.tar.gz: 254993ea2126ca51d0ad5e2b6be2dca90e1b3ed817266e46b5ca46f91d2a69288c0a87c58906ef3da8ad6465e08788c850d6bc72013e30f1ead13e186ba16dfd
+  metadata.gz: add86e088cd1ef50c0ce546eb4f755b7b5725a072ddf1119982ec0cccd20246bc25aab077c51673032e442f098e15f4c40d9a526ff67af8a5514aab580f255a8
+  data.tar.gz: 4b6cdbe344c2835c3f07c10b86f33613e0d5cdba5a9405da50d9d7f208796da6cdee709993b465f72e2a14a49667ea5ddfed84ddaf8ff21bda4a09448ebdde1b

data/Gemfile.lock

@@ -1,52 +1,57 @@
 PATH
   remote: .
   specs:
-    viral_seq (1.6.5)
+    viral_seq (1.8.0.pre)
       colorize (~> 0.1)
       combine_pdf (~> 1.0, >= 1.0.0)
-      muscle_bio (~> 0.5)
+      muscle_bio (= 0.4)
       prawn (~> 2.3, >= 2.3.0)
       prawn-table (~> 0.2, >= 0.2.0)
 
 GEM
   remote: https://rubygems.org/
   specs:
+    bigdecimal (3.1.7)
     colorize (0.8.1)
-    combine_pdf (1.0.21)
+    combine_pdf (1.0.26)
+      matrix
       ruby-rc4 (>= 0.1.5)
-    diff-lcs (1.3)
-    muscle_bio (0.5.0)
-    pdf-core (0.9.0)
-    prawn (2.4.0)
-      pdf-core (~> 0.9.0)
-      ttfunk (~> 1.7)
+    diff-lcs (1.5.1)
+    matrix (0.4.2)
+    muscle_bio (0.4.0)
+    pdf-core (0.10.0)
+    prawn (2.5.0)
+      matrix (~> 0.4)
+      pdf-core (~> 0.10.0)
+      ttfunk (~> 1.8)
     prawn-table (0.2.2)
       prawn (>= 1.3.0, < 3.0.0)
-    rake (13.0.1)
-    rspec (3.8.0)
-      rspec-core (~> 3.8.0)
-      rspec-expectations (~> 3.8.0)
-      rspec-mocks (~> 3.8.0)
-    rspec-core (3.8.0)
-      rspec-support (~> 3.8.0)
-    rspec-expectations (3.8.3)
+    rake (13.2.1)
+    rspec (3.13.0)
+      rspec-core (~> 3.13.0)
+      rspec-expectations (~> 3.13.0)
+      rspec-mocks (~> 3.13.0)
+    rspec-core (3.13.0)
+      rspec-support (~> 3.13.0)
+    rspec-expectations (3.13.0)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.8.0)
-    rspec-mocks (3.8.0)
+      rspec-support (~> 3.13.0)
+    rspec-mocks (3.13.0)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.8.0)
-    rspec-support (3.8.0)
+      rspec-support (~> 3.13.0)
+    rspec-support (3.13.1)
     ruby-rc4 (0.1.5)
-    ttfunk (1.7.0)
+    ttfunk (1.8.0)
+      bigdecimal (~> 3.1)
 
 PLATFORMS
   ruby
 
 DEPENDENCIES
-  bundler (~> 2.0)
+  bundler (~> 2.5)
   rake (~> 13.0)
   rspec (~> 3.0)
   viral_seq!
 
 BUNDLED WITH
-   2.1.4
+   2.5.7

data/README.md

@@ -10,7 +10,7 @@ A Ruby Gem containing bioinformatics tools for processing viral NGS data.
 
 Specifically for Primer ID sequencing and HIV drug resistance analysis.
 
-CLI tools `tcs`, `tcs_sdrm`, `tcs_log` and `locator` included in the gem. 
+CLI tools `tcs`, `tcs_sdrm`, `tcs_log` and `locator` included in the gem.
 
 #### tcs web app - https://primer-id.org/
 
@@ -20,8 +20,8 @@ CLI tools `tcs`, `tcs_sdrm`, `tcs_log` and `locator` included in the gem.
 ![Primer ID Sequencing](./docs/assets/img/cover.jpg)
 
 ### Reference readings on the Primer ID sequencing
-[Explantion of Primer ID sequencing](https://doi.org/10.21769/BioProtoc.3938)  
-[Primer ID MiSeq protocol](https://doi.org/10.1128/JVI.00522-15)  
+[Explantion of Primer ID sequencing](https://doi.org/10.21769/BioProtoc.3938)
+[Primer ID MiSeq protocol](https://doi.org/10.1128/JVI.00522-15)
 [Application of Primer ID sequencing in COVID-19 research](https://doi.org/10.1126/scitranslmed.abb5883)
 
 ## Requirements
@@ -40,7 +40,7 @@ Required RubyGems version: >= 1.3.6
 
 ### Excutables
 
-### `tcs`  
+### `tcs`
 Use executable `tcs` pipeline to process **Primer ID MiSeq sequencing** data.
 
 Web-based `tcs` analysis can be accessed at https://primer-id.org/
@@ -66,14 +66,14 @@ Example commands:
 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:  
+Example file structure:
 ```
-batch_tcs_jobs/  
-      ├── lib1  
-      ├── lib2  
-      ├── lib3  
-      ├── lib4  
-      ├── ...  
+batch_tcs_jobs/
+      ├── lib1
+      ├── lib2
+      ├── lib3
+      ├── lib4
+      ├── ...
 ```
 
 Example command:
@@ -121,7 +121,7 @@ Output data in a new dir as 'libs_dir_SDRM'
 
 ---
 
-### `locator`  
+### `locator`
 Use executable `locator` to get the coordinates of the sequences on HIV/SIV reference genome from a FASTA file through a terminal
 
 ```bash
@@ -187,21 +187,36 @@ qc_seqhash.sdrm_hiv_pr(cut_off)
 
 ## Updates
 
-### Version-1.7.1-05120203
 
-  1. Add a size check for the raw sequences. If the size smaller than the input params, error messages will be sent to users. IF the actual size is greater than the input params, extra bases will be truncated. 
+### Version-1.8.1-06042024
+
+  1. Fixed a bug that causes `tcs_sdrm` pipeline to crash.
+
+### Version-1.8.0-04052024
+
+  1. Use `muscle-v3.8.1` as default aligner because of the compatibility issues with `muscle-v5` on some platforms.
+  2. Adjust the end-join model for short insert (insert size less than read length substracted by adaptor size)
+  3. Add an option in the DR pipeline for different versions of the pipeline, default version as "v1".
+  4. Add Days Post Infection (DPI) prediction model in the SDRM pipeline.
+  5. Re-organize the R scripts as stand-alone R files.
+  6. Bug fix.
+  7. **NOT SOLVED**: to include versions of DR in reports
+
+### Version-1.7.1-05122023
+
+  1. Add a size check for the raw sequences. If the size smaller than the input params, error messages will be sent to users. IF the actual size is greater than the input params, extra bases will be truncated.
   2. Now allows mismatch for the primer region sequences. Forward primer region allows 2 nt differences and cDNA primer region allows 3 nt differences.
-  3. Bug fix.  
+  3. Bug fix.
   4. TCS version to 2.5.2
 
 ### Version-1.7.0-08242022
 
-  1. Add warnings if `tcs` pipeline is excecuting through source instead of installing from `gem`. 
-  2. Optimized `ViralSeq:SeqHash#a3g` hypermut algorithm. Allowing a external reference other than the sample reference. 
+  1. Add warnings if `tcs` pipeline is excecuting through source instead of installing from `gem`.
+  2. Optimized `ViralSeq:SeqHash#a3g` hypermut algorithm. Allowing a external reference other than the sample reference.
 
 ### Version-1.6.4-07182022
 
-  1. Included region "P17" in the default `tcs -d` pipeline setting. `tcs` pipeline updated to version 2.5.1. 
+  1. Included region "P17" in the default `tcs -d` pipeline setting. `tcs` pipeline updated to version 2.5.1.
   2. Loosen the locator params for the "V1V3" end region for rare alignment issues. Now the default "V1V3" region end with position 7205 to 7210 instead of 7208.
   3. `tcs_sdrm` now analyse "P17" region for pairwise diversity.
 

data/bin/tcs

@@ -31,15 +31,15 @@ def gem_installed?(gem_name)
   begin
     found_gem = Gem::Specification.find_by_name(gem_name)
   rescue Gem::LoadError
-    return false   
+    return false
   else
-    return true 
+    return true
   end
 end
 
 if gem_installed?('viral_seq')
   require 'viral_seq'
-else 
+else
   printf "\n****************************************************\n"
   printf "**** THIS PACKAGE CANNOT BE RUN FROM SOURCE ********\n"
   printf "**** PLEASE INSTALL USING `gem install viral_seq` **\n"
@@ -47,7 +47,6 @@ else
   exit 1
 end
 
-
 require 'json'
 require 'colorize'
 require 'optparse'
@@ -77,8 +76,8 @@ OptionParser.new do |opts|
     options[:input] = p
   end
 
-  opts.on("-dr", "--dr_pipeline", "HIV drug resistance MPID pipeline") do |p|
-    options[:dr] = true
+  opts.on("-d", "--dr_pipeline VERSION", "HIV drug resistance MPID pipeline, choose your version") do |p|
+    options[:dr] = p.downcase
   end
 
   opts.on("-h", "--help", "Prints this help") do
@@ -90,6 +89,14 @@ OptionParser.new do |opts|
     options[:keep] = true
   end
 
+  opts.on("--dr_params VERSION", "show params for a specific VERSION of DR pipeline") do |p|
+    options[:dr_params] = p.downcase
+  end
+
+  opts.on("--dr_list_params", "show params for ALL DR pipeline versions") do |p|
+    options[:dr_list_params] = true
+  end
+
   opts.on("-v", "--version", "Version info") do
     puts "tcs version: " + ViralSeq::TCS_VERSION.red.bold
     puts "viral_seq version: " + ViralSeq::VERSION.red.bold
@@ -101,10 +108,33 @@ OptionParser.new do |opts|
   # end
 end.parse!
 
+def safe_dr_params(version)
+  if version == "r"
+    version = "v1"
+  end # adding this statement to allow the backward compatiblity with previous `tcs -dr` command
+
+  params = ViralSeq::TcsDr::PARAMS[version]
+
+  if params.nil?
+    abort "The input DR version #{version} not exist. \nThe current supported versions for the DR pipeline are: \n#{ViralSeq::TcsDr::PARAMS.keys.join("\n")}\n\nRun `tcs --dr_params [VERSION]` for the detailed params used by each version".red
+  else
+    return params
+  end
+end
+
 if options[:json_generator]
   params = ViralSeq::TcsJson.generate
+elsif options[:dr_params]
+  params = safe_dr_params(options[:dr_params])
+  puts "The DR params for the version you entered is: "
+  puts JSON.pretty_generate params
+  exit
+elsif options[:dr_list_params]
+  params = ViralSeq::TcsDr::PARAMS
+  puts JSON.pretty_generate params
+  exit
 elsif options[:dr]
-  params = ViralSeq::TcsDr::PARAMS  
+  params = safe_dr_params(options[:dr])
 elsif (options[:params_json] && File.exist?(options[:params_json]))
   params = JSON.parse(File.read(options[:params_json]), symbolize_names: true)
 else
@@ -121,6 +151,7 @@ unless indir and File.exist?(indir)
   abort "No input sequence directory found. Script terminated.".red.bold
 end
 
+
 # log file
 
 runtime_log_file = File.join(indir,"runtime.log")
@@ -165,7 +196,7 @@ begin
 
   r1_raw_size = r1_fastq_sh.dna_hash.values[0].size
   r2_raw_size = r2_fastq_sh.dna_hash.values[0].size
- 
+
   if r1_raw_size >= $platform_sequencing_length
     r1_size_diff = r1_raw_size - $platform_sequencing_length
   else

data/bin/tcs_log

@@ -12,6 +12,8 @@
 # command example:
 #   $ tcs_log batch_tcs_jobs
 
+# NOTE some libraries can be named {digit} and these are invalid query selectors, keep prepended with a string
+
 require 'viral_seq'
 require 'pathname'
 require 'json'
@@ -135,8 +137,8 @@ class String
         gsub '-',''
     end
     def shorten_html
-        gsub /\n/, ''
-        gsub /\t/, ''
+        gsub(/\n/, '')
+        gsub(/\t/, '')
     end
 end
 
@@ -216,10 +218,10 @@ 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 id='link_basic-statistics' class='pointer lib_link 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>"
+                <li id='link_#{lib_name}' class='pointer lib_link' onclick='showPage(\""+lib_name+"\")'>"+lib_name+"</li>"
                 }.join + "
             </ul>
         </li>
@@ -227,7 +229,7 @@ library_links = "
 "
 
 library_pages = lib_names.map { |lib_name|
-    "<div id='"+lib_name+"' class='page hidden'>
+    "<div id='page_"+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;'>
@@ -391,7 +393,7 @@ 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")
+    var element_pie_'+lib.var_safe+' = document.querySelector("#page_'+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(
@@ -419,7 +421,7 @@ paired_raw_js = paired_raw.map { |lib, data| '
 
 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")
+        var element_chart_tree_'+lib.var_safe+'_'+region.var_safe+' = document.querySelector("#page_'+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(
@@ -439,7 +441,7 @@ tree_charts_js = tree_charts.map { |lib, d|
 }.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")
+    var element_tcs_bar_chart_'+lib.var_safe+' = document.querySelector("#page_'+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(
@@ -454,12 +456,12 @@ tcs_bar_chart_js = tcs_bar_chart.map { |lib, data| '
                 }
             })
         );
-        document.querySelector("#'+lib+' .tcs_warnings").innerHTML = "'+data['warnings']+'";
+        document.querySelector("#page_'+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")
+    var element_detection_'+lib.var_safe+' = document.querySelector("#page_'+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(
@@ -483,7 +485,7 @@ detection_sensitivity_js = detection_sensitivity_chart.map { |lib, data| '
 '}.join
 
 distinct_bar_chart_js = distinct_bar_chart.map { |lib, data| '
-    var element_distinct_'+lib.var_safe+' = document.querySelector("#'+lib+' .raw_bar_chart")
+    var element_distinct_'+lib.var_safe+' = document.querySelector("#page_'+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(
@@ -499,7 +501,7 @@ distinct_bar_chart_js = distinct_bar_chart.map { |lib, data| '
 ' }.join
 
 resampling_bar_chart_js = resampling_bar_chart.map { |lib, data| '
-    var element_resampling_'+lib.var_safe+' = document.querySelector("#'+lib+' .resampling_bar_chart")
+    var element_resampling_'+lib.var_safe+' = document.querySelector("#page_'+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(
@@ -516,7 +518,7 @@ resampling_bar_chart_js = resampling_bar_chart.map { |lib, data| '
 
 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")
+        var element_chart_scatter_'+lib.var_safe+'_'+region.var_safe+' = document.querySelector("#page_'+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+');
 
@@ -601,7 +603,7 @@ html = '
 
             function showPage(pageID){
                 document.querySelectorAll(".page").forEach(element => element.classList.add("hidden"))
-                document.getElementById(pageID).classList.remove("hidden")
+                document.getElementById("page_"+pageID).classList.remove("hidden")
 
                 document.querySelectorAll(".current_page").forEach(element => element.classList.remove("current_page"));
                 document.getElementById("link_"+pageID).classList.add("current_page");
@@ -620,7 +622,7 @@ html = '
                     '+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 style="display: flex; flex-direction: column; align-items: center; height: 100vh;" id="page_basic-statistics" class="page">
                         <div class="error-message"></div>
                         <div class="card" style="margin-top: 16px; width: 100%;">
                             <table id="home-table">
@@ -694,7 +696,8 @@ html = '
             padding: 8px;
         }
         .current_page {
-            border-bottom: 1px solid blue;
+            color: white;
+            background: #BAA !important;
         }
         .error-message {
             background: red !important;
@@ -709,6 +712,14 @@ html = '
         .error-message:empty {
             display: none;
         }
+
+        .lib_link:nth-child(odd){
+            background: #FFF6FF;
+        }
+
+        .lib_link:hover {
+            background: #EEEFEE;
+        }
     </style>
 </html>
 '.shorten_html

data/bin/tcs_sdrm

@@ -32,13 +32,8 @@ unless ARGV[0] && File.directory?(ARGV[0])
   abort "No sequence data provided. `tcs_sdrm` pipeline aborted. "
 end
 
-begin
-  r_version = `R --version`.split("\n")[0]
-  r_check = `R -e '#{ViralSeq::R_SCRIPT_CHECK_PACKAGES}' > /dev/null 2>&1`
-rescue Errno::ENOENT
-  abort '"R" is not installed. Install R at https://www.r-project.org/' +
-        "\n`tcs_sdrm` pipeline aborted."
-end
+r_version = ViralSeq::R.check_R
+ViralSeq::R.check_R_packages
 
 def abstract_line(data)
   return_data = data[3] + data[2] + data[4] + ":" +
@@ -72,7 +67,7 @@ Dir.mkdir(outdir) unless File.directory?(outdir)
 
 libs.each do |lib|
 
-  r_script = ViralSeq::R_SCRIPT.dup
+  r_script = ViralSeq::R.get_sdrm_rscript
 
   next unless File.directory?(lib)
 
@@ -106,6 +101,8 @@ libs.each do |lib|
   summary_json_file = File.join(out_lib_dir, (lib_name + "_summary.json"))
   summary_json_out = File.open(summary_json_file,"w")
 
+  recency_report_file = File.join(out_lib_dir, (lib_name + "_recency_report.pdf"))
+
   filtered_seq_dir = File.join(out_lib_dir, (lib_name + "_filtered_seq"))
   Dir.mkdir(filtered_seq_dir) unless File.directory?(filtered_seq_dir)
 
@@ -290,12 +287,12 @@ libs.each do |lib|
   tcs_IN = 0
   tcs_V1V3 = 0
   tcs_P17 = 0
-  pi_RT = 0.0
-  pi_V1V3 = 0.0
-  pi_P17 = 0.0
-  dist20_RT = 0.0
-  dist20_V1V3 = 0.0
-  dist20_P17 = 0.0
+  pi_RT = "NA"
+  pi_V1V3 = "NA"
+  pi_P17 = "NA"
+  dist20_RT = "NA"
+  dist20_V1V3 = "NA"
+  dist20_P17 = "NA"
   summary_lines.each do |line|
       data = line.chomp.split(",")
       if data[0] == "PR"
@@ -326,6 +323,12 @@ libs.each do |lib|
                               dist20_V1V3: dist20_V1V3
                               )
 
+  dpi_res = ViralSeq::Recency.dpi(pi_RT, pi_V1V3)
+  dpi = dpi_res[0]
+  dpi_lwr = dpi_res[1]
+  dpi_upr = dpi_res[2]
+  possible_dual_infection = ViralSeq::Recency.possible_dual_infection(recency, dpi_res)
+
   sdrm_lines = File.readlines(point_mutation_file)
   sdrm_lines.shift
   sdrm_PR = ""
@@ -357,6 +360,10 @@ libs.each do |lib|
     dist20_V1V3: dist20_V1V3,
     dist20_P17: dist20_P17,
     recency: recency,
+    dpi: dpi,
+    dpi_lwr: dpi_lwr,
+    dpi_upr: dpi_upr,
+    possible_dual_infection: possible_dual_infection,
     sdrm_PR: sdrm_PR,
     sdrm_RT: sdrm_RT,
     sdrm_IN: sdrm_IN
@@ -365,6 +372,8 @@ libs.each do |lib|
   summary_json_out.puts JSON.pretty_generate(summary_json)
   summary_json_out.close
 
+  ViralSeq::RecencyReport.generate(summary_json[0], recency_report_file)
+
   csvs = [
     {
       name: "summary",

data/lib/viral_seq/R.rb

@@ -0,0 +1,31 @@
+module ViralSeq
+  module R
+
+    # check if R is installed. if R is installed, return the version number of R.
+
+    def self.check_R
+      begin
+        r_version = `R --version`.split("\n")[0]
+      rescue Errno::ENOENT
+        abort '"R" is not installed. Install R at https://www.r-project.org/' +
+              "\n`tcs_sdrm` pipeline aborted."
+      end
+    end # end check_R
+
+    # check if required R packages is installed.
+    def self.check_R_packages
+      if system "Rscript #{File.join( ViralSeq.root, "viral_seq", "util", "check_env.r")}"
+        return 0
+      else
+        raise "Non-zero exit code. Error happens when checking required R packages."
+      end
+    end # end check_R_packages.
+
+    # read sdrm rscript as a string.
+
+    def self.get_sdrm_rscript
+      File.read(File.join(ViralSeq.root, "viral_seq", "util", "sdrm_r.r"))
+    end
+
+  end
+end