RubyGems - viral_seq - Versions diffs - 1.7.1 → 1.8.0 - Mend

viral_seq 1.7.1 → 1.8.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (24) hide show

checksums.yaml +4 -4
data/Gemfile.lock +29 -24
data/README.md +28 -18
data/bin/tcs +39 -8
data/bin/tcs_log +27 -16
data/bin/tcs_sdrm +23 -14
data/lib/viral_seq/R.rb +31 -0
data/lib/viral_seq/constant.rb +0 -41
data/lib/viral_seq/muscle.rb +1 -1
data/lib/viral_seq/recency.rb +47 -1
data/lib/viral_seq/recency_report.rb +193 -0
data/lib/viral_seq/root.rb +7 -0
data/lib/viral_seq/seq_hash.rb +4 -4
data/lib/viral_seq/seq_hash_pair.rb +154 -27
data/lib/viral_seq/tcs_dr.rb +168 -81
data/lib/viral_seq/util/check_env.r +9 -0
data/lib/viral_seq/util/recency_model/rt_only_fit.Rdata +0 -0
data/lib/viral_seq/util/recency_model/rt_v1v3_fit.Rdata +0 -0
data/lib/viral_seq/util/recency_model/v1v3_only_fit.Rdata +0 -0
data/lib/viral_seq/util/sdrm_r.r +34 -0
data/lib/viral_seq/version.rb +2 -2
data/lib/viral_seq.rb +6 -0
data/viral_seq.gemspec +2 -2
metadata +17 -9

data/lib/viral_seq/tcs_dr.rb CHANGED Viewed

@@ -1,86 +1,173 @@
 module ViralSeq
-  class TcsDr
-    PARAMS = {:platform_error_rate=>0.02,
-               :primer_pairs=>
-                [{:region=>"RT",
-                  :cdna=>
-                   "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCACTATAGGCTGTACTGTCCATTTATC",
-                  :forward=>
-                   "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGGCCATTGACAGAAGAAAAAATAAAAGC",
-                  :majority=>0,
-                  :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,
-                  :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,
-                  :end_join=>true,
-                  :end_join_option=>2,
-                  :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,
-                  :end_join=>true,
-                  :end_join_option=>1,
-                  :overlap=>0,
-                  :TCS_QC=>true,
-                  :ref_genome=>"HXB2",
-                  :ref_start=>6585,
-                  :ref_end=>7205..7210,
-                  :indel=>true,
-                  :trim=>false},
-                  {:region=>"P17",
-                   :cdna=>
-                    "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCAACAAGGTTTCTGTCATCCAATTTTTTAC",
-                   :forward=>
-                    "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGTCAGCCAAAATTACCCTATAGTGC",
-                   :majority=>0,
-                   :end_join=>true,
-                   :end_join_option=>1,
-                   :overlap=>0,
-                   :TCS_QC=>true,
-                   :ref_genome=>"HXB2",
-                   :ref_start=>1196,
-                   :ref_end=>1725,
-                   :indel=>true,
-                   :trim=>false}
-                  ]
-              }
+  # store preset params for the DR pipeline.
+  # Used in the `tcs` command.
+  # run `tcs --dr_params [VERSION]` to pull the params json string for each version of DR.
+  module TcsDr
+    PARAMS = {
+      "v1" => {:platform_error_rate=>0.02,
+      :primer_pairs=>
+       [{:region=>"RT",
+         :cdna=>
+          "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCACTATAGGCTGTACTGTCCATTTATC",
+         :forward=>
+          "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGGCCATTGACAGAAGAAAAAATAAAAGC",
+         :majority=>0,
+         :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,
+         :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,
+         :end_join=>true,
+         :end_join_option=>2,
+         :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,
+         :end_join=>true,
+         :end_join_option=>1,
+         :overlap=>0,
+         :TCS_QC=>true,
+         :ref_genome=>"HXB2",
+         :ref_start=>6585,
+         :ref_end=>7205..7210,
+         :indel=>true,
+         :trim=>false},
+         {:region=>"P17",
+          :cdna=>
+           "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCAACAAGGTTTCTGTCATCCAATTTTTTAC",
+          :forward=>
+           "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGTCAGCCAAAATTACCCTATAGTGC",
+          :majority=>0,
+          :end_join=>true,
+          :end_join_option=>1,
+          :overlap=>0,
+          :TCS_QC=>true,
+          :ref_genome=>"HXB2",
+          :ref_start=>1196,
+          :ref_end=>1725,
+          :indel=>true,
+          :trim=>false}
+         ]
+      },
+      "v2" => {:platform_error_rate=>0.02,
+      :primer_pairs=>
+      [{:region=>"RT",
+        :cdna=>
+          "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCACTATAGGCTGTACTGTCCATTTATC",
+        :forward=>
+          "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGGCCATTGACAGAAGAAAAAATAAAAGC",
+        :majority=>0,
+        :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=>
+          "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNTTAACCTTTGGGCCATCCATTCC",
+        :forward=>
+          "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNTCAGAGCAGACCAGAGCCAACAGCCCCA",
+        :majority=>0,
+        :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,
+        :end_join=>true,
+        :end_join_option=>2,
+        :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,
+        :end_join=>true,
+        :end_join_option=>1,
+        :overlap=>0,
+        :TCS_QC=>true,
+        :ref_genome=>"HXB2",
+        :ref_start=>6585,
+        :ref_end=>7205..7210,
+        :indel=>true,
+        :trim=>false},
+        {:region=>"P17",
+          :cdna=>
+          "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCAACAAGGTTTCTGTCATCCAATTTTTTAC",
+          :forward=>
+          "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGTCAGCCAAAATTACCCTATAGTGC",
+          :majority=>0,
+          :end_join=>true,
+          :end_join_option=>1,
+          :overlap=>0,
+          :TCS_QC=>true,
+          :ref_genome=>"HXB2",
+          :ref_start=>1196,
+          :ref_end=>1725,
+          :indel=>true,
+          :trim=>false}
+        ]
+      }
+    }
   end
 end

data/lib/viral_seq/util/check_env.r ADDED Viewed

@@ -0,0 +1,9 @@
+dir.create(
+  path = Sys.getenv("R_LIBS_USER"),
+  showWarnings = FALSE,
+  recursive = TRUE
+)
+packages <- c("ggplot2", "phangorn", "ape", "scales", "ggforce", "cowplot", "magrittr", "gridExtra")
+install.packages(setdiff(packages, rownames(installed.packages())), lib = Sys.getenv("R_LIBS_USER"), repos = "https://cran.rstudio.com/")

data/lib/viral_seq/util/recency_model/rt_only_fit.Rdata ADDED Viewed

Binary file

data/lib/viral_seq/util/recency_model/rt_v1v3_fit.Rdata ADDED Viewed

Binary file

data/lib/viral_seq/util/recency_model/v1v3_only_fit.Rdata ADDED Viewed

Binary file

data/lib/viral_seq/util/sdrm_r.r ADDED Viewed

@@ -0,0 +1,34 @@
+setwd("PATH_TO_FASTA")
+library(phangorn)
+library(ape)
+library(ggplot2)
+library(scales)
+library(ggforce)
+library(cowplot)
+library(magrittr)
+library(gridExtra)
+pdf("OUTPUT_PDF", onefile=T, width=11, height=8.5)
+fileNames <- list.files()
+for (fileName in fileNames) {
+    dna <- read.dna(fileName, format="fasta")
+    D<- dist.dna(dna, model="raw")
+    pi <- mean(D)
+    dist20 <- quantile(D, prob=c(0.20))
+    alldist <- data.frame(File=fileName, pi, dist20)
+    write.table(alldist,"OUTPUT_CSV",append=TRUE, sep = ",", row.names = FALSE, col.names=FALSE)
+    D2 <- dist.dna(dna, model="TN93")*100
+    def.par <- par(no.readonly = TRUE)
+    par(mfrow=c(1,2))
+    hist<-hist(D, main=fileName, xlab="% Pairwise Distance", ylab="Frequency", col="gray")
+    abline(v=dist20, col="royalblue",lwd=2)
+    abline(v=pi, col="red", lwd=2)
+    legend(x="topright", c("dist20", "pi"), col = c("royalblue", "red"), lwd = c(2,2), cex=0.5)
+    njtree<-NJ(D2)
+    njtreeplot <- plot(njtree, show.tip.label=F, "unrooted", main=fileName)
+    add.scale.bar(cex=0.7, font=2, col="red")
+}
+dev.off()

data/lib/viral_seq/version.rb CHANGED Viewed

@@ -2,6 +2,6 @@
 # version info and histroy
 module ViralSeq
-  VERSION = "1.7.1"
-  TCS_VERSION = "2.5.2"
+  VERSION = "1.8.0"
+  TCS_VERSION = "2.6.0"
 end

data/lib/viral_seq.rb CHANGED Viewed

@@ -21,6 +21,8 @@
 module ViralSeq; end
 # load all classes
+require_relative "viral_seq/root"
 require_relative "viral_seq/constant"
 require_relative "viral_seq/enumerable"
 require_relative "viral_seq/hash"
@@ -40,7 +42,11 @@ require_relative "viral_seq/tcs_json"
 require_relative "viral_seq/tcs_dr"
 require_relative "viral_seq/sdrm"
 require_relative "viral_seq/recency"
+require_relative "viral_seq/R"
+require_relative "viral_seq/recency_report"
 require "muscle_bio"
 require "json"
 require "securerandom"
+require "prawn"

data/viral_seq.gemspec CHANGED Viewed

@@ -25,7 +25,7 @@ Gem::Specification.new do |spec|
   spec.require_paths = ["lib"]
   spec.post_install_message = "Thanks for installing!"
-  spec.add_development_dependency "bundler", "~> 2.0"
+  spec.add_development_dependency "bundler", "~> 2.5"
   spec.add_development_dependency "rake", "~> 13.0"
   spec.add_development_dependency "rspec", "~> 3.0"
@@ -35,7 +35,7 @@ Gem::Specification.new do |spec|
   spec.required_rubygems_version = '>= 1.3.6'
   # muscle_bio gem required
-  spec.add_runtime_dependency "muscle_bio", "~> 0.5"
+  spec.add_runtime_dependency "muscle_bio", "= 0.4"
   # colorize gem required
   spec.add_runtime_dependency "colorize", "~> 0.1"

metadata CHANGED Viewed

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: viral_seq
 version: !ruby/object:Gem::Version
-  version: 1.7.1
+  version: 1.8.0
 platform: ruby
 authors:
 - Shuntai Zhou
@@ -9,7 +9,7 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2023-05-12 00:00:00.000000000 Z
+date: 2024-05-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -17,14 +17,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.0'
+        version: '2.5'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.0'
+        version: '2.5'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
@@ -57,16 +57,16 @@ dependencies:
   name: muscle_bio
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - '='
       - !ruby/object:Gem::Version
-        version: '0.5'
+        version: '0.4'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - '='
       - !ruby/object:Gem::Version
-        version: '0.5'
+        version: '0.4'
 - !ruby/object:Gem::Dependency
   name: colorize
   requirement: !ruby/object:Gem::Requirement
@@ -174,6 +174,7 @@ files:
 - docs/sample_miseq_data/hivdr_control/r2.fastq.gz
 - docs/variants_structure.pdf
 - lib/viral_seq.rb
+- lib/viral_seq/R.rb
 - lib/viral_seq/constant.rb
 - lib/viral_seq/enumerable.rb
 - lib/viral_seq/hash.rb
@@ -182,7 +183,9 @@ files:
 - lib/viral_seq/muscle.rb
 - lib/viral_seq/pid.rb
 - lib/viral_seq/recency.rb
+- lib/viral_seq/recency_report.rb
 - lib/viral_seq/ref_seq.rb
+- lib/viral_seq/root.rb
 - lib/viral_seq/rubystats.rb
 - lib/viral_seq/sdrm.rb
 - lib/viral_seq/seq_hash.rb
@@ -192,6 +195,11 @@ files:
 - lib/viral_seq/tcs_core.rb
 - lib/viral_seq/tcs_dr.rb
 - lib/viral_seq/tcs_json.rb
+- lib/viral_seq/util/check_env.r
+- lib/viral_seq/util/recency_model/rt_only_fit.Rdata
+- lib/viral_seq/util/recency_model/rt_v1v3_fit.Rdata
+- lib/viral_seq/util/recency_model/v1v3_only_fit.Rdata
+- lib/viral_seq/util/sdrm_r.r
 - lib/viral_seq/version.rb
 - viral_seq.gemspec
 homepage: https://github.com/ViralSeq/viral_seq
@@ -214,7 +222,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: 1.3.6
 requirements:
 - R required for some functions
-rubygems_version: 3.2.2
+rubygems_version: 3.5.9
 signing_key:
 specification_version: 4
 summary: A Ruby Gem containing bioinformatics tools for processing viral NGS data.