viral_seq 1.0.10 → 1.0.11

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

@@ -78,9 +78,17 @@ 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.
 
 ## Updates
 
+### Version 1.1.1-03022021
+
+  1. Fixed a 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:
 
   1. Modularize TCS pipeline. Move key functions into /viral_seq/tcs_core.rb
@@ -88,7 +96,7 @@ qc_seqhash.sdrm_hiv_pr(cut_off)
   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

@@ -28,7 +28,7 @@
 require 'viral_seq'
 require 'json'
 require 'colorize'
-require 'OptionParser'
+require 'optparse'
 
 options = {}
 
@@ -317,8 +317,12 @@ 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|

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/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/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

@@ -549,7 +549,7 @@ 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 +558,7 @@ 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

data/lib/viral_seq/tcs_core.rb

@@ -104,14 +104,16 @@ module ViralSeq
       # 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
       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 = {}
 

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 = "1.0.11"
+  TCS_VERSION = "2.1.1"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: viral_seq
 version: !ruby/object:Gem::Version
-  version: 1.0.10
+  version: 1.0.11
 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: 2021-03-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -114,6 +114,7 @@ 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 +143,7 @@ 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.