viral_seq 1.8.0 → 1.8.1.1

checksums.yaml

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

@@ -187,7 +187,12 @@ qc_seqhash.sdrm_hiv_pr(cut_off)
 
 ## Updates
 
-### Version-1.8.0.pre-04052024
+
+### 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)

data/lib/viral_seq/recency.rb

@@ -49,7 +49,10 @@ module ViralSeq
       return recency
     end #end of .define
 
-
+    # function for predict Days Post Infection
+    # @params pi_rt [Float] average pairwise diversity at RT region
+    # @params pi_viv3 [Float] average pairwise diversity at V1V3 region
+    # @return [Array] Array of [DPI, lwr, upr] for DPI prediction as [Numerics]
     def self.dpi(pi_rt, pi_v1v3)
 
       if pi_rt.is_a? Numeric and pi_v1v3.is_a? Numeric
@@ -70,9 +73,9 @@ module ViralSeq
       path = File.join( ViralSeq.root, "viral_seq", "util", "recency_model", model_file)
       data_str = `Rscript -e 'fit = readRDS("#{path}"); test = data.frame(#{var} = #{pi}); pre= predict(fit, test, interval = "prediction", level = 0.9); cat(pre)'`
       dpi_array = data_str.split("\s")
-      dpi = dpi_array[0].to_f
-      lwr = dpi_array[1].to_f
-      upr = dpi_array[2].to_f
+      dpi = dpi_array[0].to_f.round(1)
+      lwr = dpi_array[1].to_f.round(1)
+      upr = dpi_array[2].to_f.round(1)
       if lwr < 0
         return [dpi, 0.0, upr]
       else
@@ -80,6 +83,11 @@ module ViralSeq
       end
     end # end of .dpi
 
+    # given `recency` and `dpi` predict if possible dual infection exists
+    # @params recency [String] Recency from ViralSeq::Recency.define() function
+    # @params dpi [Array] DPI array from ViralSeq::Recency.dpi() function
+    # @return [String] "Yes", "No", or "insufficient data"
+
     def self.possible_dual_infection(recency, dpi)
       if ["recent", "chronic", "indeterminant"].include? recency and dpi[0].is_a? Numeric
         if recency == "indeterminant" and dpi[0] > 730
@@ -92,7 +100,7 @@ module ViralSeq
       end
     end
 
-  end
+  end # end of .possible_dual_infection
 
 
 end

data/lib/viral_seq/recency_report.rb

@@ -141,8 +141,8 @@ module ViralSeq
             },
 
             {
-              text: log[:dpi].round(1).to_s +
-              " (" + log[:dpi_lwr].round(1).to_s + "-" + log[:dpi_upr].round(1).to_s + ") Days",
+              text: log[:dpi].to_s +
+              " (" + log[:dpi_lwr].to_s + "-" + log[:dpi_upr].to_s + ") Days",
               styles: [:bold],
               size: 16,
               color: recency_color[log[:recency]]

data/lib/viral_seq/version.rb

@@ -2,6 +2,6 @@
 # version info and histroy
 
 module ViralSeq
-  VERSION = "1.8.0"
-  TCS_VERSION = "2.6.0"
+  VERSION = "1.8.1.1"
+  TCS_VERSION = "2.6.1"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: viral_seq
 version: !ruby/object:Gem::Version
-  version: 1.8.0
+  version: 1.8.1.1
 platform: ruby
 authors:
 - Shuntai Zhou
@@ -9,7 +9,7 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2024-05-09 00:00:00.000000000 Z
+date: 2024-06-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -222,7 +222,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: 1.3.6
 requirements:
 - R required for some functions
-rubygems_version: 3.5.9
+rubygems_version: 3.5.10
 signing_key:
 specification_version: 4
 summary: A Ruby Gem containing bioinformatics tools for processing viral NGS data.