viral_seq 1.0.10 → 1.1.0

checksums.yaml

@@ -1,7 +1,7 @@
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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

@@ -2,7 +2,16 @@
 
 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](https://storage.googleapis.com/tcs-dr-public/pid.png)
+
+### 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)
 
 ## Install
 
@@ -14,19 +23,45 @@ 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 -j # CLI to generate params.json
+    $ tcs -h # print out the help
 ```
+---
+### `tcs_log`
 
-Use executable `tcs` pipeline to process Primer ID MiSeq sequencing data.
+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
 
@@ -78,17 +113,49 @@ Examine for drug resistance mutations for HIV PR region
 ```ruby
 qc_seqhash.sdrm_hiv_pr(cut_off)
 ```
+## Known issues
+
+  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 1.1.0-11112020:
+### 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.
+
+### 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 an issue when calculating Poisson cutoff for minority mutations `ViralSeq::SeqHash.pm`.
+  2. fixed an issue loading class 'OptionParser'in some ruby environments.
+
+### Version 1.0.10-11112020:
 
   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
   3. consensus model now includes a true simple majority model, where no nt needs to be over 50% to be called.
   4. a few optimizations.
   5. TCS 2.1.0 delivered.
-  6. Tried parallel processing. Cannot achieve the goal because `parallel` gem by default can't pool data from memory of child processors and `in_threads` does not help with the speed. 
+  6. Tried parallel processing. Cannot achieve the goal because `parallel` gem by default can't pool data from memory of child processors and `in_threads` does not help with the speed.
 
 ### Version 1.0.9-07182020:
 

data/bin/tcs

@@ -23,12 +23,12 @@
 # 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'
 require 'colorize'
-require 'OptionParser'
+require 'optparse'
 
 options = {}
 
@@ -115,6 +115,12 @@ 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."
@@ -273,7 +279,6 @@ 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)
@@ -317,8 +322,12 @@ primers.each do |primer|
   f1 = File.open(outfile_r1, 'w')
   f2 = File.open(outfile_r2, 'w')
   primer_id_in_use = {}
-  r1_seq_length = consensus_filtered.values[0][0].size
-  r2_seq_length = consensus_filtered.values[0][1].size
+  if n_con > 0
+    r1_seq_length = consensus_filtered.values[0][0].size
+    r2_seq_length = consensus_filtered.values[0][1].size
+  else
+    next
+  end
   log.puts Time.now.to_s + "\t" + "R1 sequence #{r1_seq_length} bp"
   log.puts Time.now.to_s + "\t" + "R1 sequence #{r2_seq_length} bp"
   consensus_filtered.each do |seq_name,seq|
@@ -360,6 +369,7 @@ 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
@@ -429,12 +439,15 @@ 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 +1,83 @@
+#!/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')
+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"
+
+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],
+             ].join(',') + "\n"
+  end
+end
+log.close

data/doc/dr.json

@@ -0,0 +1,68 @@
+{
+  "raw_sequence_dir": "MyExampleDir",
+  "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/constant.rb

@@ -1,7 +1,11 @@
 module ViralSeq
-  
+
   # array for all amino acid one letter abbreviations
 
   AMINO_ACID_LIST = ["A", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M", "N", "P", "Q", "R", "S", "T", "V", "W", "Y", "*"]
 
+  SDRM_HIV_PR_LIST = {}
+  SDRM_HIV_RT_LIST = {}
+  SDRM_HIV_IN_LIST = {}
+  
 end

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/hivdr.rb

@@ -1,6 +1,6 @@
 
 module ViralSeq
-  class SeqHash
+  class SDRM
 
     # functions to identify SDRMs from a ViralSeq::SeqHash object at HIV PR region.
     #   works for MPID-DR protocol (dx.doi.org/10.17504/protocols.io.useewbe)

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/sdrm.rb

@@ -0,0 +1,43 @@
+module ViralSeq
+  class DRMs
+    def initialize (mutation_list = {})
+      @mutation_list = mutation_list
+    end
+
+    attr_accessor :mutation_list
+  end
+
+  def self.sdrm_hiv_pr(seq_hash)
+  end
+
+  def self.sdrm_hiv_rt(seq_hash)
+  end
+
+  def self.sdrm_hiv_in(seq_hash)
+  end
+
+  def self.list_from_json(file)
+  end
+
+  def self.list_from_csv(file)
+  end
+
+  def self.export_list_hiv_pr(file, format = :json)
+    if foramt == :json
+
+    end
+  end
+
+  def self.export_list_hiv_rt(file, format = :json)
+
+  end
+
+  def self.export_list_hiv_in(file, format = :json)
+
+  end
+
+  def drm_analysis(seq_hash)
+    mutation_list = self.mutation_list
+
+  end
+end

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
@@ -549,7 +548,7 @@ module ViralSeq
       if sequences.size == 0
         return 0
       else
-        cut_off = 1
+        cut_off = Float::INFINITY
         l = sequences[0].size
         rate = sequences.size * error_rate
         count_mut = variant_for_poisson(sequences)
@@ -558,7 +557,7 @@ module ViralSeq
 
         poisson_hash.each do |k,v|
           cal = l * v
-          obs = count_mut[k] ? count_mut[k] : 0
+          obs = count_mut[k] ? count_mut[k] : 1
           if obs >= fold_cutoff * cal
             cut_off = k
             break
@@ -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

@@ -102,16 +102,18 @@ module ViralSeq
       end
 
       # sort array of file names to determine if there is potential errors
-      # input name_array array of file names
-      # output hash { }
+      # @param name_array [Array] array of file names
+      # @return [hash] name check results
 
       def validate_file_name(name_array)
-        errors = { file_type_error: [] ,
+        errors = {
+                   file_type_error: [] ,
                    missing_r1_file: [] ,
                    missing_r2_file: [] ,
                    extra_r1_r2_file: [],
                    no_region_tag: [] ,
-                   multiple_region_tag: []}
+                   multiple_region_tag: []
+                 }
 
         passed_libs = {}
 
@@ -163,6 +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}
@@ -173,7 +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.
@@ -276,7 +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_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 = "1.0.10"
-  TCS_VERSION = "2.1.0"
+  VERSION = "1.1.0"
+  TCS_VERSION = "2.2.0"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: viral_seq
 version: !ruby/object:Gem::Version
-  version: 1.0.10
+  version: 1.1.0
 platform: ruby
 authors:
 - Shuntai Zhou
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-11-12 00:00:00.000000000 Z
+date: 2021-03-26 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 +105,8 @@ files:
 - Rakefile
 - bin/locator
 - bin/tcs
+- bin/tcs_log
+- doc/dr.json
 - lib/viral_seq.rb
 - lib/viral_seq/constant.rb
 - lib/viral_seq/enumerable.rb
@@ -114,6 +117,7 @@ files:
 - lib/viral_seq/pid.rb
 - lib/viral_seq/ref_seq.rb
 - lib/viral_seq/rubystats.rb
+- lib/viral_seq/sdrm.rb
 - lib/viral_seq/seq_hash.rb
 - lib/viral_seq/seq_hash_pair.rb
 - lib/viral_seq/sequence.rb
@@ -142,7 +146,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements:
 - R required for some functions
-rubygems_version: 3.1.2
+rubygems_version: 3.2.2
 signing_key: 
 specification_version: 4
 summary: A Ruby Gem containing bioinformatics tools for processing viral NGS data.