viral_seq 1.2.0 → 1.2.1
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- checksums.yaml +4 -4
- data/README.md +43 -1
- data/bin/tcs_sdrm +9 -2
- data/lib/viral_seq/constant.rb +7 -0
- data/lib/viral_seq/version.rb +1 -1
- metadata +2 -2
checksums.yaml
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metadata.gz: f3316ff7e72ca84c6eb2fa861a9fdad14fbcb3ab3c0053ade843ee13cc9ce82e
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metadata.gz: a3ec35b3a40ee9cf66131416a1c20eda38bf8bde818aa41af285c099ddd2b49e4f31fe1d011c95def77fd5c6653d96f4295142fd543444f249242154bb2b671b
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data.tar.gz: daa6e694a841cc615cfde850bf2d98ca7467cb1d27502daf398ab0204e55c4d477f34aafce0149c765a931755fc3a3f7dbdf425964904d0199efb0651b9a09a6
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data/README.md
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# ViralSeq
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[](https://rubygems.org/gems/viral_seq)
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@@ -69,6 +69,44 @@ Example command:
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$ tcs_log batch_tcs_jobs
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```
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---
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### `tcs_sdrm`
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Use `tcs_sdrm` pipeline for HIV-1 drug resistance mutation and recency.
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Example command:
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```bash
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$ tcs_sdrm libs_dir
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```
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lib_dir file structure:
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```
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libs_dir/
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├── lib1
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├── lib1_RT
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├── lib1_PR
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├── lib1_IN
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├── lib1_V1V3
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├── lib2
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├── lib1_RT
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├── lib1_PR
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├── lib1_IN
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├── lib1_V1V3
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├── ...
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```
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Output data in a new dir as 'libs_dir_SDRM'
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**Note: [R](https://www.r-project.org/) and the following R libraries are required:**
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- phangorn
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- ape
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- scales
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- ggforce
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- cowplot
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- magrittr
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- gridExtra
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---
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### `locator`
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@@ -137,6 +175,10 @@ qc_seqhash.sdrm_hiv_pr(cut_off)
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## Updates
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### Version 1.2.1-05172021
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1. Added a function in R to check and install missing R packages for `tcs_sdrm` pipeline.
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### Version 1.2.0-05102021
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1. Added `tcs_sdrm` pipeline as an excutable.
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data/bin/tcs_sdrm
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@@ -32,6 +32,14 @@ unless ARGV[0] && File.directory?(ARGV[0])
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abort "No sequence data provided. `tcs_sdrm` pipeline aborted. "
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end
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begin
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r_version = `R --version`.split("\n")[0]
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r_check = `R -e '#{ViralSeq::R_SCRIPT_CHECK_PACKAGES}' > /dev/null 2>&1`
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rescue Errno::ENOENT
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abort '"R" is not installed. Install R at https://www.r-project.org/' +
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"\n`tcs_sdrm` pipeline aborted."
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end
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def abstract_line(data)
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return_data = data[3] + data[2] + data[4] + ":" +
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(data[6].to_f * 100).round(2).to_s + "(" +
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@@ -45,7 +53,6 @@ log = []
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log << { time: Time.now }
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log << { viral_seq_version: ViralSeq::VERSION }
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log << { tcs_version: ViralSeq::TCS_VERSION }
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r_version = `R --version`.split("\n")[0]
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log << { R_version: r_version}
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sdrm_list = {}
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sdrm_list[:nrti] = ViralSeq::DRMs.sdrm_json(:nrti)
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@@ -395,7 +402,7 @@ libs.each do |lib|
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end
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end
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log_file = indir
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log_file = File.join(File.dirname(indir), "sdrm_log.json")
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File.open(log_file, 'w') { |f| f.puts JSON.pretty_generate(log) }
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data/lib/viral_seq/constant.rb
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@@ -3,6 +3,13 @@ module ViralSeq
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# array for all amino acid one letter abbreviations
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AMINO_ACID_LIST = ["A", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M", "N", "P", "Q", "R", "S", "T", "V", "W", "Y", "*"]
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# R script to check if the required libraries are installed, if not, install the missing libraries
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R_SCRIPT_CHECK_PACKAGES = 'dir.create(path = Sys.getenv("R_LIBS_USER"), showWarnings = FALSE, recursive = TRUE);' +
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'packages <- c("ggplot2", "phangorn", "ape", "scales", "ggforce", "cowplot", "magrittr", "gridExtra");' +
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'install.packages(setdiff(packages, rownames(installed.packages())), lib = Sys.getenv("R_LIBS_USER"), repos = "https://cran.rstudio.com/")'
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# R script for tcs_sdrm script
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R_SCRIPT = 'setwd("PATH_TO_FASTA")
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data/lib/viral_seq/version.rb
CHANGED
metadata
CHANGED
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@@ -1,7 +1,7 @@
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--- !ruby/object:Gem::Specification
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name: viral_seq
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version: !ruby/object:Gem::Version
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version: 1.2.
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version: 1.2.1
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platform: ruby
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authors:
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- Shuntai Zhou
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@@ -9,7 +9,7 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2021-05-
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date: 2021-05-17 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bundler
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