viral_seq 1.1.0 → 1.1.1

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -1,5 +1,11 @@
 # 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.
@@ -7,11 +13,12 @@ Specifically for Primer ID sequencing and HIV drug resistance analysis.
 ## Illustration for the Primer ID Sequencing
 
 
-![Primer ID Sequencing](https://storage.googleapis.com/tcs-dr-public/pid.png)
+![Primer ID Sequencing](./docs/assets/img/cover.jpg)
 
 ### Reference readings on the Primer ID sequencing
-[Primer ID JID paper](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)
 
 ## Install
 
@@ -29,9 +36,18 @@ Use executable `tcs` pipeline to process **Primer ID MiSeq sequencing** data.
 Example commands:
 ```bash
     $ 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
 ```
+
+[sample params.json for the tcs-dr pipeline](./docs/dr.json)
+
 ---
 ### `tcs_log`
 
@@ -121,15 +137,22 @@ qc_seqhash.sdrm_hiv_pr(cut_off)
 
 ## Updates
 
+### 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*** in /doc.
-    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.
+  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
 

data/bin/tcs

@@ -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
 
@@ -129,6 +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
@@ -181,6 +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]

data/bin/tcs_log

@@ -37,8 +37,26 @@ Dir.mkdir(outdir4) unless File.directory?(outdir4)
 
 log_file = File.join(tcs_dir,"log.csv")
 log = File.open(log_file,'w')
-log.puts "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"
 
+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 = []
@@ -77,6 +95,7 @@ libs.each do |lib|
                json_log[:resampling_param],
                json_log[:combined_tcs],
                json_log[:combined_tcs_after_qc],
+               json_log[:warnings],
              ].join(',') + "\n"
   end
 end

data/{doc → docs}/dr.json

@@ -1,5 +1,4 @@
 {
-  "raw_sequence_dir": "MyExampleDir",
   "platform_error_rate": 0.02,
   "primer_pairs": [
     {

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/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/version.rb

@@ -2,6 +2,6 @@
 # version info and histroy
 
 module ViralSeq
-  VERSION = "1.1.0"
-  TCS_VERSION = "2.2.0"
+  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: 1.1.0
+  version: 1.1.1
 platform: ruby
 authors:
 - Shuntai Zhou
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-03-26 00:00:00.000000000 Z
+date: 2021-04-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -106,7 +106,10 @@ files:
 - bin/locator
 - bin/tcs
 - bin/tcs_log
-- doc/dr.json
+- 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
@@ -123,6 +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