viral_seq 1.8.1.1 → 1.9.0

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Files changed (17) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile.lock +1 -1
  3. data/README.md +6 -0
  4. data/bin/tcs +7 -1
  5. data/bin/tcs_sdrm +87 -131
  6. data/lib/viral_seq/drm_region_config.rb +83 -0
  7. data/lib/viral_seq/drm_version.rb +120 -0
  8. data/lib/viral_seq/hivdr.rb +206 -2
  9. data/lib/viral_seq/sdrm.rb +34 -99
  10. data/lib/viral_seq/sequence.rb +26 -1
  11. data/lib/viral_seq/tcs_core.rb +1 -1
  12. data/lib/viral_seq/tcs_dr.rb +87 -5
  13. data/lib/viral_seq/util/drm_list.json +684 -0
  14. data/lib/viral_seq/util/drm_versions_config.json +114 -0
  15. data/lib/viral_seq/version.rb +2 -2
  16. data/lib/viral_seq.rb +3 -0
  17. metadata +7 -3
data/lib/viral_seq/util/drm_versions_config.json ADDED
@@ -0,0 +1,114 @@
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+ [
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+ {
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+ "version": "v3",
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+ "DRM_range": {
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+ "CAI": [56,57, 66, 67, 70, 74, 105, 107],
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+ "PI": [23, 24, 30, 32, 46, 47, 48, 50, 53, 54, 73, 76, 82, 83, 84, 88, 90],
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+ "NRTI": [41, 65, 67, 69, 70, 74, 75, 77, 115, 116, 151, 184, 210, 215, 219],
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+ "NNRTI": [98, 100, 101, 103, 106, 138, 179, 181, 188, 190],
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+ "INSTI": [95, 97, 121, 140, 143, 147, 148, 155, 263]
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+ },
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+ "seq_coord": {
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+ "CA": {
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+ "minimum": 1196,
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+ "maximum": 1725,
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+ "gap": {
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+ "minimum": 1466,
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+ "maximum": 1471
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+ }
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+ },
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+ "PR": {
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+ "minimum": 2253,
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+ "maximum": 2549
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+ },
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+ "RT": {
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+ "minimum": 2648,
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+ "maximum": 3209,
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+ "gap": {
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+ "minimum": 2915,
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+ "maximum": 2949
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+ }
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+ },
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+ "IN": {
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+ "minimum": 4509,
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+ "maximum": 5048,
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+ "gap": {
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+ "minimum": 4780,
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+ "maximum": 4782
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+ }
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+ }
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+ },
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+ "seq_drm_correlation": {
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+ "CA": ["CAI"],
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+ "RT": ["NRTI", "NNRTI"],
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+ "PR": ["PI"],
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+ "IN": ["INSTI"]
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+ },
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+ "ref_info": {
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+ "ref_type": "HXB2",
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+ "ref_coord": {
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+ "CA": [1186,1878],
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+ "PR": [2253,2549],
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+ "RT": [2550,3869],
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+ "IN": [4230,5096]
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+ }
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+ }
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+
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+ },
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+ {
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+ "version": "v1",
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+ "DRM_range": {
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+ "CAI": [56,57, 66, 67, 70, 74, 105, 107],
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+ "PI": [23, 24, 30, 32, 46, 47, 48, 50, 53, 54, 73, 76, 82, 83, 84, 88, 90],
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+ "NRTI": [41, 65, 67, 69, 70, 74, 75, 77, 115, 116, 151, 184, 210, 215, 219],
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+ "NNRTI": [98, 100, 101, 103, 106, 179, 181, 188, 190, 225, 230],
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+ "INSTI": [66, 74, 92, 95, 97, 121, 140, 143, 147, 148, 155]
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+ },
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+ "seq_coord": {
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+ "CA": {
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+ "minimum": 1196,
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+ "maximum": 1725,
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+ "gap": {
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+ "minimum": 1466,
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+ "maximum": 1471
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+ }
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+ },
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+ "PR": {
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+ "minimum": 2253,
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+ "maximum": 2549
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+ },
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+ "RT": {
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+ "minimum": 2648,
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+ "maximum": 3257,
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+ "gap": {
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+ "minimum": 2915,
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+ "maximum": 3000
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+ }
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+ },
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+ "IN": {
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+ "minimum": 4384,
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+ "maximum": 4751
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+ }
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+ },
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+ "seq_drm_correlation": {
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+ "CA": ["CAI"],
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+ "RT": ["NRTI", "NNRTI"],
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+ "PR": ["PI"],
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+ "IN": ["INSTI"]
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+ },
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+ "ref_info": {
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+ "ref_type": "HXB2",
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+ "ref_coord": {
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+ "CA": [1186,1878],
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+ "PR": [2253,2549],
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+ "RT": [2550,3869],
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+ "IN": [4230,5096]
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+ }
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+ }
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+
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+ }
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+
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+
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+
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+ ]
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+
data/lib/viral_seq/version.rb CHANGED
@@ -2,6 +2,6 @@
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  # version info and histroy
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  module ViralSeq
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- VERSION = "1.8.1.1"
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- TCS_VERSION = "2.6.1"
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+ VERSION = "1.9.0"
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+ TCS_VERSION = "2.7.0"
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  end
data/lib/viral_seq.rb CHANGED
@@ -44,9 +44,12 @@ require_relative "viral_seq/sdrm"
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  require_relative "viral_seq/recency"
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  require_relative "viral_seq/R"
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  require_relative "viral_seq/recency_report"
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+ require_relative "viral_seq/drm_region_config.rb"
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+ require_relative "viral_seq/drm_version.rb"
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  require "muscle_bio"
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  require "json"
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  require "securerandom"
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  require "prawn"
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+ require "colorize"
metadata CHANGED
@@ -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: 1.8.1.1
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+ version: 1.9.0
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  platform: ruby
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  authors:
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  - Shuntai Zhou
@@ -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: 2024-06-04 00:00:00.000000000 Z
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+ date: 2024-11-13 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: bundler
@@ -176,6 +176,8 @@ files:
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  - lib/viral_seq.rb
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  - lib/viral_seq/R.rb
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  - lib/viral_seq/constant.rb
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+ - lib/viral_seq/drm_region_config.rb
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+ - lib/viral_seq/drm_version.rb
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  - lib/viral_seq/enumerable.rb
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  - lib/viral_seq/hash.rb
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  - lib/viral_seq/hivdr.rb
@@ -196,6 +198,8 @@ files:
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  - lib/viral_seq/tcs_dr.rb
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  - lib/viral_seq/tcs_json.rb
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  - lib/viral_seq/util/check_env.r
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+ - lib/viral_seq/util/drm_list.json
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+ - lib/viral_seq/util/drm_versions_config.json
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  - lib/viral_seq/util/recency_model/rt_only_fit.Rdata
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  - lib/viral_seq/util/recency_model/rt_v1v3_fit.Rdata
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  - lib/viral_seq/util/recency_model/v1v3_only_fit.Rdata
@@ -222,7 +226,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  version: 1.3.6
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  requirements:
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  - R required for some functions
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- rubygems_version: 3.5.10
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+ rubygems_version: 3.5.11
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  signing_key:
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  specification_version: 4
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  summary: A Ruby Gem containing bioinformatics tools for processing viral NGS data.