viral_seq 1.0.11 → 1.1.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: eb5906a2a3f0c98fa84a15f7fd4b35160f766317a6603b18c62e2e2476af01fd
-  data.tar.gz: 435a32d9ce5078b18b633c14c1585c30835b48d3f013d24bc6b9cc98fef51a55
+  metadata.gz: 7a283f3a09cc5d9807e7622cd1ddf27197919955e85d6472b34fc14b66749c03
+  data.tar.gz: 4f90c5a9c7ea0ec148ba7d45ee88dc441f79da67a97654734194a773499ebb8e
 SHA512:
-  metadata.gz: a65fcfe551b59d2f022f96d009f089941a3bd293545e840ba294ce43b3cb087b2f3a7fef26829fe3b229c9469ca4e5c907362bbf05a5384947af97a12409a5aa
-  data.tar.gz: e4283b03e33aa67feb1dcf623d2613440bcc7299ab33ff77b7dce1ef9617b46e1763d17dda64d54b5fb3c6de37da66880abe43baae932ac36b70d0e2b0cc88d1
+  metadata.gz: 385a94eb93c3d8d9116c16a0d8af56ba714ba6191a454076acf881a036de80d1d598f3fcd1a4de841745ca08a1ad3e8bc028a30db9f96c19f3b217ef4583d652
+  data.tar.gz: 714d035b6f65863746cafb120c9cf6eccb8261f3eac69985bad96e5275351eec71aa3b744ee9b462e2dc3e0e199c2d4112386f6a2d7eef89b5b7824c1ab769be

data/.gitignore

@@ -2,7 +2,6 @@
 /.yardoc
 /_yardoc/
 /coverage/
-/doc/
 /pkg/
 /spec/reports/
 /tmp/

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    viral_seq (1.0.10)
+    viral_seq (1.0.13)
       colorize (~> 0.1)
       muscle_bio (~> 0.4)
 

data/README.md

@@ -1,8 +1,24 @@
 # ViralSeq
 
+[![Gem Version](https://badge.fury.io/rb/viral_seq.svg)](https://rubygems.org/gems/viral_seq)
+![GitHub](https://img.shields.io/github/license/viralseq/viral_seq)
+![Gem](https://img.shields.io/gem/dt/viral_seq?color=%23E9967A)
+![GitHub last commit](https://img.shields.io/github/last-commit/viralseq/viral_seq?color=%2300BFFF)
+[![Join the chat at https://gitter.im/viral_seq/community](https://badges.gitter.im/viral_seq/community.svg)](https://gitter.im/viral_seq/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+
 A Ruby Gem containing bioinformatics tools for processing viral NGS data.
 
-Specifically for Primer-ID sequencing and HIV drug resistance analysis.
+Specifically for Primer ID sequencing and HIV drug resistance analysis.
+
+## Illustration for the Primer ID Sequencing
+
+
+![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)  
+[Application of Primer ID sequencing in COVID-19 research](https://doi.org/10.1126/scitranslmed.abb5883)
 
 ## Install
 
@@ -14,20 +30,55 @@ Specifically for Primer-ID sequencing and HIV drug resistance analysis.
 
 ### Excutables
 
-Use executable `locator` to get the coordinates of the sequences on HIV/SIV reference genome from a FASTA file through a terminal
+### `tcs`  
+Use executable `tcs` pipeline to process **Primer ID MiSeq sequencing** data.
 
+Example commands:
 ```bash
-    $ locator -i sequence.fasta -o sequence.fasta.csv
+    $ tcs -p params.json # run TCS pipeline with params.json
+    $ tcs -p params.json -i DIRECTORY
+    # run TCS pipeline with params.json and DIRECTORY
+    # if DIRECTORY is not defined in params.json
+    $ tcs -dr -i DIRECTORY
+    # run tcs-dr (MPID HIV drug resistance sequencing) pipeline
+    # DIRECTORY needs to be given.
+    $ tcs -j # CLI to generate params.json
+    $ tcs -h # print out the help
 ```
 
-Use executable `tcs` pipeline to process Primer ID MiSeq sequencing data.
+[sample params.json for the tcs-dr pipeline](./docs/dr.json)
+
+---
+### `tcs_log`
+
+Use `tcs_log` script to pool run logs and TCS fasta files after one batch of `tcs` jobs.
 
+
+Example file structure:  
+```
+batch_tcs_jobs/  
+      ├── lib1  
+      ├── lib2  
+      ├── lib3  
+      ├── lib4  
+      ├── ...  
+```
+
+Example command:
 ```bash
-    $ tcs -p params.json # run TCS pipeline with params.json
-    $ tcs -j # CLI to generate params.json
-    $ tcs -h # print out the help
+    $ tcs_log batch_tcs_jobs
 ```
 
+---
+
+### `locator`  
+Use executable `locator` to get the coordinates of the sequences on HIV/SIV reference genome from a FASTA file through a terminal
+
+```bash
+    $ locator -i sequence.fasta -o sequence.fasta.csv
+```
+---
+
 ## Some Examples
 
 Load all ViralSeq classes by requiring 'viral_seq.rb' in your Ruby scripts.
@@ -80,16 +131,47 @@ qc_seqhash.sdrm_hiv_pr(cut_off)
 ```
 ## Known issues
 
-  1. have a conflict with rails.
+  1. ~~have a conflict with rails.~~
+  2. ~~Update on 03032021. Still have conflict. But in rails gem file, can just use `requires: false` globally and only require "viral_seq" when the module is needed in controller.~~
+  3. The conflict seems to be resovled. It was from a combination of using `!` as a function for factorial and the gem name `viral_seq`. @_@
 
 ## Updates
 
-### Version 1.1.1-03022021
+### Version 1.1.1-04012021
+
+  1. Added warning when paired_raw_sequence less than 0.1% of total_raw_sequence.
+  2. Added option `-i WORKING_DIRECTORY` to the `tcs` script.
+  If the `params.json` file does not contain the path to the working directory, it will append path to the run params.
+  3. Added option `-dr` to the `tcs` script.
+
+### Version 1.1.0-03252021
+
+  1. Optimized the algorithm of end-join.
+  2. Fixed a bug in the `tcs` pipeline that sometimes combined tcs files are not saved.
+  3. Added `tcs_log` command to pool run logs and tcs files from one batch of tcs jobs.
+  4. Added the preset of MPID-HIVDR params file [***dr.json***](./docs/dr.json) in /docs.
+  5. Add `platform_format` option in the json generator of the `tcs` Pipeline.
+  Users can choose from 3 MiSeq platforms for processing their sequencing data.
+  MiSeq 300x7x300 is the default option.
+
+### Version 1.0.14-03052021
+
+  1. Add a function `ViralSeq::TcsCore.validate_file_name` to check MiSeq paired-end file names.
+
+### Version 1.0.13-03032021
+
+  1. Fixed the conflict with rails.
+
+### Version 1.0.12-03032021
+
+  1. Fixed an issue that may cause conflicts with ActiveRecord.
+
+### Version 1.0.11-03022021
 
-  1. Fixed a issue when calculating Poisson cutoff for minority mutations `ViralSeq::SeqHash.pm`.
+  1. Fixed an issue when calculating Poisson cutoff for minority mutations `ViralSeq::SeqHash.pm`.
   2. fixed an issue loading class 'OptionParser'in some ruby environments.
 
-### Version 1.1.0-11112020:
+### Version 1.0.10-11112020:
 
   1. Modularize TCS pipeline. Move key functions into /viral_seq/tcs_core.rb
   2. `tcs_json_generator` is removed. This CLI is delivered within the `tcs` pipeline, by running `tcs -j`. The scripts are included in the /viral_seq/tcs_json.rb

data/bin/tcs

@@ -23,7 +23,7 @@
 # THE SOFTWARE.
 
 # Use JSON file as the run param
-# run tcs_json_generator.rb to generate param json file.
+# run `tcs -j` to generate param json file.
 
 require 'viral_seq'
 require 'json'
@@ -46,6 +46,14 @@ OptionParser.new do |opts|
     options[:params_json] = p
   end
 
+  opts.on("-i", "--input PATH_TO_WORKING_DIRECTORY", "Path to the working directory") do |p|
+    options[:input] = p
+  end
+
+  opts.on("-dr", "--dr_pipeline", "HIV drug resistance MPID pipeline") do |p|
+    options[:dr] = true
+  end
+
   opts.on("-h", "--help", "Prints this help") do
     puts opts
     exit
@@ -64,15 +72,21 @@ end.parse!
 
 if options[:json_generator]
   params = ViralSeq::TcsJson.generate
+elsif options[:dr]
+  params = ViralSeq::TcsDr::PARAMS
 elsif (options[:params_json] && File.exist?(options[:params_json]))
   params = JSON.parse(File.read(options[:params_json]), symbolize_names: true)
 else
   abort "No params JSON file found. Script terminated.".red
 end
 
-indir = params[:raw_sequence_dir]
+if options[:input]
+  indir = options[:input]
+else
+  indir = params[:raw_sequence_dir]
+end
 
-unless File.exist?(indir)
+unless indir and File.exist?(indir)
   abort "No input sequence directory found. Script terminated.".red.bold
 end
 
@@ -115,6 +129,12 @@ else
   error_rate = 0.02
 end
 
+if params[:platform_format]
+  $platform_sequencing_length = params[:platform_format]
+else
+  $platform_sequencing_length = 300
+end
+
 primers = params[:primer_pairs]
 if primers.empty?
   ViralSeq::TcsCore.log_and_abort log, "No primer information. Script terminated."
@@ -123,6 +143,7 @@ end
 
 primers.each do |primer|
   summary_json = {}
+  summary_json[:warnings] = []
   summary_json[:tcs_version] = ViralSeq::TCS_VERSION
   summary_json[:viralseq_version] = ViralSeq::VERSION
   summary_json[:runtime] = Time.now.to_s
@@ -175,6 +196,10 @@ primers.each do |primer|
   paired_seq_number = common_keys.size
   log.puts Time.now.to_s + "\t" +  "Paired raw sequences are : #{paired_seq_number.to_s}"
   summary_json[:paired_raw_sequence] = paired_seq_number
+  if paired_seq_number < raw_sequence_number * 0.001
+    summary_json[:warnings] <<
+      "WARNING: Filtered raw sequneces less than 0.1% of the total raw sequences. Possible contamination."
+  end
 
   common_keys.each do |seqtag|
     r1_seq = r1_passed_seq[seqtag]
@@ -273,7 +298,6 @@ primers.each do |primer|
       r1_sub_seq << bio_r1[seq_name]
       r2_sub_seq << bio_r2[seq_name]
     end
-
     #consensus name including the Primer ID and number of raw sequences of that Primer ID, library name and setname.
     consensus_name = ">" + primer_id + "_" + seq_with_same_primer_id.size.to_s + "_" + libname + "_" + region
     r1_consensus = ViralSeq::SeqHash.array(r1_sub_seq).consensus(majority_cut_off)
@@ -364,6 +388,7 @@ primers.each do |primer|
     shp = ViralSeq::SeqHashPair.fa(out_dir_consensus)
     joined_sh = end_join(out_dir_consensus, primer[:end_join_option], primer[:overlap])
     log.puts Time.now.to_s + "\t" + "Paired TCS number: " + joined_sh.size.to_s
+
     summary_json[:combined_tcs] = joined_sh.size
 
     if export_raw
@@ -433,12 +458,15 @@ primers.each do |primer|
       trim_end = primer[:trim_ref_end]
       trim_ref = primer[:trim_ref].to_sym
       joined_sh = joined_sh.trim(trim_start, trim_end, trim_ref)
-      joined_sh.write_nt_fa(File.join(out_dir_consensus, "combined.fasta"))
       if export_raw
         joined_sh_raw = joined_sh_raw.trim(trim_start, trim_end, trim_ref)
-        joined_sh_raw.write_nt_fa(File.join(out_dir_raw, "combined.raw.fasta"))
       end
     end
+
+    joined_sh.write_nt_fa(File.join(out_dir_consensus, "combined.fasta"))
+    if export_raw
+      joined_sh_raw.write_nt_fa(File.join(out_dir_raw, "combined.raw.fasta"))
+    end
   end
 
   File.open(outfile_log, "w") do |f|

data/bin/tcs_log

@@ -0,0 +1,102 @@
+#!/usr/bin/env ruby
+
+# pool run logs from one batch of tcs jobs
+# file structure:
+#   batch_tcs_jobs/
+#   ├── lib1
+#   ├── lib2
+#   ├── lib3
+#   ├── lib4
+#   ├── ...
+#
+# command example:
+#   $ tcs_log batch_tcs_jobs
+
+require 'viral_seq'
+require 'pathname'
+require 'json'
+require 'fileutils'
+
+indir = ARGV[0].chomp
+indir_basename = File.basename(indir)
+indir_dirname = File.dirname(indir)
+
+tcs_dir = File.join(indir_dirname, (indir_basename + "_tcs"))
+Dir.mkdir(tcs_dir) unless File.directory?(tcs_dir)
+
+libs = []
+Dir.chdir(indir) {libs = Dir.glob("*")}
+
+outdir2 = File.join(tcs_dir, "combined_TCS_per_lib")
+outdir3 = File.join(tcs_dir, "TCS_per_region")
+outdir4 = File.join(tcs_dir, "combined_TCS_per_region")
+
+Dir.mkdir(outdir2) unless File.directory?(outdir2)
+Dir.mkdir(outdir3) unless File.directory?(outdir3)
+Dir.mkdir(outdir4) unless File.directory?(outdir4)
+
+log_file = File.join(tcs_dir,"log.csv")
+log = File.open(log_file,'w')
+
+header = %w{
+  lib_name
+  Region
+  Raw_Sequences_per_barcode
+  R1_Raw
+  R2_Raw
+  Paired_Raw
+  Cutoff
+  PID_Length
+  Consensus1
+  Consensus2
+  Distinct_to_Raw
+  Resampling_index
+  Combined_TCS
+  Combined_TCS_after_QC
+  WARNINGS
+}
+
+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 = []
+  Dir.chdir(File.join(indir, lib)) do
+     fasta_files = Dir.glob("**/*.fasta")
+     json_files = Dir.glob("**/log.json")
+  end
+  fasta_files.each do |f|
+    path_array = Pathname(f).each_filename.to_a
+    region = path_array[0]
+    if path_array[-1] == "combined.fasta"
+      FileUtils.cp(File.join(indir, lib, f), File.join(outdir2, lib, (lib + "_" + region)))
+      Dir.mkdir(File.join(outdir4,region)) unless File.directory?(File.join(outdir4,region))
+      FileUtils.cp(File.join(indir, lib, f), File.join(outdir4, region, (lib + "_" + region)))
+    else
+      Dir.mkdir(File.join(outdir3,region)) unless File.directory?(File.join(outdir3,region))
+      Dir.mkdir(File.join(outdir3,region, lib)) unless File.directory?(File.join(outdir3,region, lib))
+      FileUtils.cp(File.join(indir, lib, f), File.join(outdir3, region, lib, (lib + "_" + region + "_" + path_array[-1])))
+    end
+  end
+
+  json_files.each do |f|
+    json_log = JSON.parse(File.read(File.join(indir, lib, f)), symbolize_names: true)
+    log.print [lib,
+               json_log[:primer_set_name],
+               json_log[:total_raw_sequence],
+               json_log[:r1_filtered_raw],
+               json_log[:r2_filtered_raw],
+               json_log[:paired_raw_sequence],
+               json_log[:consensus_cutoff],
+               json_log[:length_of_pid],
+               json_log[:total_tcs_with_ambiguities],
+               json_log[:total_tcs],
+               json_log[:distinct_to_raw],
+               json_log[:resampling_param],
+               json_log[:combined_tcs],
+               json_log[:combined_tcs_after_qc],
+               json_log[:warnings],
+             ].join(',') + "\n"
+  end
+end
+log.close

data/docs/dr.json

@@ -0,0 +1,67 @@
+{
+  "platform_error_rate": 0.02,
+  "primer_pairs": [
+    {
+      "region": "RT",
+      "cdna": "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCACTATAGGCTGTACTGTCCATTTATC",
+      "forward": "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGGCCATTGACAGAAGAAAAAATAAAAGC",
+      "majority": 0.5,
+      "end_join": true,
+      "end_join_option": 1,
+      "overlap": 0,
+      "TCS_QC": true,
+      "ref_genome": "HXB2",
+      "ref_start": 2648,
+      "ref_end": 3257,
+      "indel": true,
+      "trim": false
+    },
+    {
+      "region": "PR",
+      "cdna": "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNCAGTTTAACTTTTGGGCCATCCATTCC",
+      "forward": "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNTCAGAGCAGACCAGAGCCAACAGCCCCA",
+      "majority": 0.5,
+      "end_join": true,
+      "end_join_option": 3,
+      "TCS_QC": true,
+      "ref_genome": "HXB2",
+      "ref_start": 0,
+      "ref_end": 2591,
+      "indel": true,
+      "trim": true,
+      "trim_ref": "HXB2",
+      "trim_ref_start": 2253,
+      "trim_ref_end": 2549
+    },
+    {
+      "region": "IN",
+      "cdna": "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNATCGAATACTGCCATTTGTACTGC",
+      "forward": "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNAAAAGGAGAAGCCATGCATG",
+      "majority": 0.5,
+      "end_join": true,
+      "end_join_option": 3,
+      "overlap": 171,
+      "TCS_QC": true,
+      "ref_genome": "HXB2",
+      "ref_start": 4384,
+      "ref_end": 4751,
+      "indel": false,
+      "trim": false
+    },
+    {
+      "region": "V1V3",
+      "cdna": "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCCATTTTGCTYTAYTRABVTTACAATRTGC",
+      "forward": "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNTTATGGGATCAAAGCCTAAAGCCATGTGTA",
+      "majority": 0.5,
+      "end_join": true,
+      "end_join_option": 1,
+      "overlap": 0,
+      "TCS_QC": true,
+      "ref_genome": "HXB2",
+      "ref_start": 6585,
+      "ref_end": 7208,
+      "indel": true,
+      "trim": false
+    }
+  ]
+}

data/lib/viral_seq.rb

@@ -37,6 +37,6 @@ require_relative "viral_seq/string"
 require_relative "viral_seq/version"
 require_relative "viral_seq/tcs_core"
 require_relative "viral_seq/tcs_json"
-
+require_relative "viral_seq/tcs_dr"
 
 require "muscle_bio"

data/lib/viral_seq/enumerable.rb

@@ -3,10 +3,6 @@
 #   array = [1,2,3,4,5,6,7,8,9,10]
 #   array.median
 #   => 5.5
-# @example sum
-#   array = [1,2,3,4,5,6,7,8,9,10]
-#   array.sum
-#   => 55
 # @example average number (mean)
 #   array = [1,2,3,4,5,6,7,8,9,10]
 #   array.mean
@@ -45,12 +41,6 @@ module Enumerable
     len % 2 == 1 ? sorted[len/2] : (sorted[len/2 - 1] + sorted[len/2]).to_f / 2
   end
 
-  # generate summed value
-  # @return [Numeric] summed value
-  def sum
-     self.inject(0){|accum, i| accum + i }
-  end
-
   # generate mean number
   # @return [Float] mean value
   def mean

data/lib/viral_seq/math.rb

@@ -67,7 +67,7 @@ module ViralSeq
         @k = k
         @poisson_hash = {}
         (0..k).each do |n|
-          p = (rate**n * ::Math::E**(-rate))/!n
+          p = (rate**n * ::Math::E**(-rate))/n.factorial
           @poisson_hash[n] = p
         end
       end
@@ -155,9 +155,9 @@ class Integer
   # factorial method for an Integer
   # @return [Integer] factorial for given Integer
   # @example factorial for 5
-  #   !5
+  #   5.factorial
   #   => 120
-  def !
+  def factorial
     if self == 0
       return 1
     else

data/lib/viral_seq/seq_hash.rb

@@ -394,7 +394,6 @@ module ViralSeq
             end
           end
         end
-
         consensus_seq += call_consensus_base(max_base_list)
       end
       return consensus_seq
@@ -742,6 +741,7 @@ module ViralSeq
       seq_hash_unique_pass = []
 
       seq_hash_unique.each do |seq|
+        next if seq.nil?
         loc = ViralSeq::Sequence.new('', seq).locator(ref_option, path_to_muscle)
         next unless loc # if locator tool fails, skip this seq.
         if start_nt.include?(loc[0]) && end_nt.include?(loc[1])

data/lib/viral_seq/seq_hash_pair.rb

@@ -110,19 +110,21 @@ module ViralSeq
       raise ArgumentError.new(":overlap has to be Integer, input #{overlap} invalid.") unless overlap.is_a? Integer
       raise ArgumentError.new(":diff has to be float or integer, input #{diff} invalid.") unless (diff.is_a? Integer or diff.is_a? Float)
       joined_seq = {}
-      seq_pair_hash.uniq_hash.each do |seq_pair, seq_names|
+      seq_pair_hash.each do |seq_name,seq_pair|
         r1_seq = seq_pair[0]
         r2_seq = seq_pair[1]
         if overlap.zero?
           joined_sequence = r1_seq + r2_seq
+        elsif diff.zero?
+          if r1_seq[-overlap..-1] == r2_seq[0,overlap]
+            joined_sequence= r1_seq + r2_seq[overlap..-1]
+          end
         elsif r1_seq[-overlap..-1].compare_with(r2_seq[0,overlap]) <= (overlap * diff)
           joined_sequence= r1_seq + r2_seq[overlap..-1]
         else
           next
         end
-        seq_names.each do |seq_name|
-          joined_seq[seq_name] = joined_sequence
-        end
+        joined_seq[seq_name] = joined_sequence if joined_sequence
       end
 
       joined_seq_hash = ViralSeq::SeqHash.new

data/lib/viral_seq/tcs_core.rb

@@ -102,9 +102,9 @@ module ViralSeq
       end
 
       # sort array of file names to determine if there is potential errors
-      # input name_array array of file names
-      # output hash { }
-      # need to change for each file name have an error code. and a bool to show if all pass
+      # @param name_array [Array] array of file names
+      # @return [hash] name check results
+
       def validate_file_name(name_array)
         errors = {
                    file_type_error: [] ,
@@ -165,6 +165,13 @@ module ViralSeq
           end
         end
 
+        file_name_with_lib_name = {}
+        passed_libs.each do |lib_name, files|
+          files.each do |f|
+            file_name_with_lib_name[f] = lib_name
+          end
+        end
+
         passed_names = []
 
         passed_libs.values.each { |names| passed_names += names}
@@ -175,7 +182,27 @@ module ViralSeq
           pass = true
         end
 
-        return { errors: errors, all_pass: pass, passed_names: passed_names, passed_libs: passed_libs }
+        file_name_with_error_type = {}
+
+        errors.each do |type, files|
+          files.each do |f|
+            file_name_with_error_type[f] ||= []
+            file_name_with_error_type[f] << type.to_s.tr("_", "\s")
+          end
+        end
+
+        file_check = []
+
+        name_array.each do |name|
+          file_check_hash = {}
+          file_check_hash[:fileName] = name
+          file_check_hash[:errors] = file_name_with_error_type[name]
+          file_check_hash[:libName] = file_name_with_lib_name[name]
+
+          file_check << file_check_hash
+        end
+
+        return { allPass: pass, files: file_check }
       end
 
       # filter r1 raw sequences for non-specific primers.
@@ -278,7 +305,9 @@ module ViralSeq
       end
 
       def general_filter(seq)
-        if seq[1..-2] =~ /N/ # sequences with ambiguities except the 1st and last position removed
+        if seq.size < $platform_sequencing_length
+          return false
+        elsif seq[1..-2] =~ /N/ # sequences with ambiguities except the 1st and last position removed
           return false
         elsif seq =~ /A{11}/ # a string of poly-A indicates adaptor sequence
           return false

data/lib/viral_seq/tcs_dr.rb

@@ -0,0 +1,71 @@
+module ViralSeq
+
+  class TcsDr
+    PARAMS = {:platform_error_rate=>0.02,
+               :primer_pairs=>
+                [{:region=>"RT",
+                  :cdna=>
+                   "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCACTATAGGCTGTACTGTCCATTTATC",
+                  :forward=>
+                   "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGGCCATTGACAGAAGAAAAAATAAAAGC",
+                  :majority=>0.5,
+                  :end_join=>true,
+                  :end_join_option=>1,
+                  :overlap=>0,
+                  :TCS_QC=>true,
+                  :ref_genome=>"HXB2",
+                  :ref_start=>2648,
+                  :ref_end=>3257,
+                  :indel=>true,
+                  :trim=>false},
+                 {:region=>"PR",
+                  :cdna=>
+                   "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNCAGTTTAACTTTTGGGCCATCCATTCC",
+                  :forward=>
+                   "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNTCAGAGCAGACCAGAGCCAACAGCCCCA",
+                  :majority=>0.5,
+                  :end_join=>true,
+                  :end_join_option=>3,
+                  :TCS_QC=>true,
+                  :ref_genome=>"HXB2",
+                  :ref_start=>0,
+                  :ref_end=>2591,
+                  :indel=>true,
+                  :trim=>true,
+                  :trim_ref=>"HXB2",
+                  :trim_ref_start=>2253,
+                  :trim_ref_end=>2549},
+                 {:region=>"IN",
+                  :cdna=>
+                   "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNATCGAATACTGCCATTTGTACTGC",
+                  :forward=>"GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNAAAAGGAGAAGCCATGCATG",
+                  :majority=>0.5,
+                  :end_join=>true,
+                  :end_join_option=>3,
+                  :overlap=>171,
+                  :TCS_QC=>true,
+                  :ref_genome=>"HXB2",
+                  :ref_start=>4384,
+                  :ref_end=>4751,
+                  :indel=>false,
+                  :trim=>false},
+                 {:region=>"V1V3",
+                  :cdna=>
+                   "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCCATTTTGCTYTAYTRABVTTACAATRTGC",
+                  :forward=>
+                   "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNTTATGGGATCAAAGCCTAAAGCCATGTGTA",
+                  :majority=>0.5,
+                  :end_join=>true,
+                  :end_join_option=>1,
+                  :overlap=>0,
+                  :TCS_QC=>true,
+                  :ref_genome=>"HXB2",
+                  :ref_start=>6585,
+                  :ref_end=>7208,
+                  :indel=>true,
+                  :trim=>false}
+                  ]
+                }
+  end
+
+end

data/lib/viral_seq/tcs_json.rb

@@ -13,6 +13,22 @@ module ViralSeq
         print '> '
         param[:raw_sequence_dir] = gets.chomp.rstrip
 
+        puts "Choose MiSeq Platform (1-3):\n1. 150x7x150\n2. 250x7x250\n3. 300x7x300 (default)"
+        print "> "
+        pf_option = gets.chomp.rstrip
+        # while ![1,2,3].include?(pf_option.to_i)
+        #   print "Entered MiSeq Platform #{pf_option.red.bold} not valid (choose 1-3), try again\n> "
+        #   pf_option = gets.chomp.rstrip
+        # end
+        case pf_option.to_i
+        when 1
+          param[:platform_format] = 150
+        when 2
+          param[:platform_format] = 250
+        else
+          param[:platform_format] = 300
+        end
+
         puts 'Enter the estimated platform error rate (for TCS cut-off calculation), default as ' + '0.02'.red.bold
         print '> '
         input_error = gets.chomp.rstrip.to_f
@@ -52,12 +68,12 @@ module ViralSeq
           if ej =~ /y|yes/i
             data[:end_join] = true
 
-            print "End-join option? Choose from (1-4):\n
-            1: simple join, no overlap
-            2: known overlap \n
-            3: unknow overlap, use sample consensus to determine overlap, all sequence pairs have same overlap\n
-            4: unknow overlap, determine overlap by individual sequence pairs, sequence pairs can have different overlap\n
-            > "
+            puts "End-join option? Choose from (1-4):"
+            puts "1: simple join, no overlap"
+            puts "2: known overlap"
+            puts "3: unknow overlap, use sample consensus to determine overlap, all sequence pairs have same overlap"
+            puts "4: unknow overlap, determine overlap by individual sequence pairs, sequence pairs can have different overlap"
+            print "> "
             ej_option = gets.chomp.rstrip
             while ![1,2,3,4].include?(ej_option.to_i)
               puts "Entered end-join option #{ej_option.red.bold} not valid (choose 1-4), try again"
@@ -138,7 +154,12 @@ module ViralSeq
         if save_option =~ /y|yes/i
           print "Path to save JSON file:\n> "
           path = gets.chomp.rstrip
-          File.open(path, 'w') {|f| f.puts JSON.pretty_generate(param)}
+          while !validate_path_name(path)
+            print "Entered path no valid, try again.\n".red.bold
+            print "Path to save JSON file:\n> "
+            path = gets.chomp.rstrip
+          end
+          File.open(validate_path_name(path), 'w') {|f| f.puts JSON.pretty_generate(param)}
         end
 
         print "\nDo you wish to execute tcs pipeline with the input params now? Y/N \n> "
@@ -147,7 +168,7 @@ module ViralSeq
         if rsp =~ /y/i
           return param
         else
-          abort "Params json file generated. You can execute tcs pipeline using `tcs -p [params.json]`"
+          abort "Params json file generated. You can execute tcs pipeline using `tcs -p [params.json]`".blue
         end
 
       end
@@ -172,7 +193,17 @@ module ViralSeq
               when 3
                 :MAC239
               end
-      end
-    end
+      end # end of get_ref
+
+      def validate_path_name(path)
+        if path.empty?
+          return false
+        elsif File.directory? path
+          return File.join(path, 'params.json')
+        elsif File.directory?(File.dirname(path))
+          return path
+        end
+      end # end of validate_path_name
+    end # end of class << self
   end # end TcsJson
 end # end main module

data/lib/viral_seq/version.rb

@@ -2,6 +2,6 @@
 # version info and histroy
 
 module ViralSeq
-  VERSION = "1.0.11"
-  TCS_VERSION = "2.1.1"
+  VERSION = "1.1.1"
+  TCS_VERSION = "2.3.0"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: viral_seq
 version: !ruby/object:Gem::Version
-  version: 1.0.11
+  version: 1.1.1
 platform: ruby
 authors:
 - Shuntai Zhou
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-03-02 00:00:00.000000000 Z
+date: 2021-04-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -90,6 +90,7 @@ email:
 executables:
 - locator
 - tcs
+- tcs_log
 extensions: []
 extra_rdoc_files: []
 files:
@@ -104,6 +105,11 @@ files:
 - Rakefile
 - bin/locator
 - bin/tcs
+- bin/tcs_log
+- docs/assets/img/cover.jpg
+- docs/dr.json
+- docs/sample_miseq_data/hivdr_control/r1.fastq.gz
+- docs/sample_miseq_data/hivdr_control/r2.fastq.gz
 - lib/viral_seq.rb
 - lib/viral_seq/constant.rb
 - lib/viral_seq/enumerable.rb
@@ -120,6 +126,7 @@ files:
 - lib/viral_seq/sequence.rb
 - lib/viral_seq/string.rb
 - lib/viral_seq/tcs_core.rb
+- lib/viral_seq/tcs_dr.rb
 - lib/viral_seq/tcs_json.rb
 - lib/viral_seq/version.rb
 - viral_seq.gemspec