viral_seq 1.6.3 → 1.6.4

checksums.yaml

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

@@ -179,6 +179,12 @@ qc_seqhash.sdrm_hiv_pr(cut_off)
 
 ## Updates
 
+### Version-1.6.4-07182022
+
+  1. Included region "P17" in the default `tcs -d` pipeline setting. `tcs` pipeline updated to version 2.5.1. 
+  2. Loosen the locator params for the "V1V3" end region for rare alignment issues. Now the default "V1V3" region end with position 7205 to 7210 instead of 7208.
+  3. `tcs_sdrm` now analyse "P17" region for pairwise diversity.
+
 ### Version-1.6.3-02052022
 
   1. Updated on `ViralSeq::Muscle` module along with the update of `muscle` from version 3.8.1 to 5.1.

data/bin/tcs_sdrm

@@ -172,6 +172,25 @@ libs.each do |lib|
       linkage_list += sdrm[1]
       aa_report_list += sdrm[2]
 
+    elsif seq_basename =~/P17/i
+      a3g_check = seqs.a3g
+      a3g_seqs = a3g_check[:a3g_seq]
+      a3g_filtered_seqs = a3g_check[:filtered_seq]
+      stop_codon_check = a3g_filtered_seqs.stop_codon(2)
+      stop_codon_seqs = stop_codon_check[:with_stop_codon]
+      filtered_seqs = stop_codon_check[:without_stop_codon]
+      poisson_minority_cutoff = filtered_seqs.pm
+      fdr_hash = filtered_seqs.fdr
+      summary_hash[:P17] = [
+                            seqs.size.to_s,
+                            a3g_seqs.size.to_s,
+                            stop_codon_seqs.size.to_s,
+                            filtered_seqs.size.to_s,
+                            poisson_minority_cutoff.to_s
+                          ].join(',')
+      next if filtered_seqs.size < 3
+      filtered_seqs.write_nt_fa(File.join(filtered_seq_dir,seq_basename))
+
     elsif seq_basename =~/RT/i
       rt_seq1 = {}
       rt_seq2 = {}
@@ -231,7 +250,6 @@ libs.each do |lib|
       next if filtered_sh.size < 3
       aligned_sh = filtered_sh.random_select(1000).align(:Super5)
       aligned_sh.write_nt_fa(File.join(aln_seq_dir, File.basename(seq_file)))
-      puts 'aligned sequence written.'
     end
 
     r_script.gsub!(/PATH_TO_FASTA/,aln_seq_dir)
@@ -250,7 +268,7 @@ libs.each do |lib|
         tag = data[0].split("_")[-1].gsub(/\W/,"").to_sym
         summary_hash[tag] += "," + data[1].to_f.round(4).to_s + "," + data[2].to_f.round(4).to_s
       end
-      [:PR, :RT, :IN, :V1V3].each do |regions|
+      [:PR, :RT, :IN, :V1V3, :P17].each do |regions|
         next unless summary_hash[regions]
         seq_summary_out.puts regions.to_s + "," + summary_hash[regions]
       end
@@ -271,10 +289,13 @@ libs.each do |lib|
   tcs_RT = 0
   tcs_IN = 0
   tcs_V1V3 = 0
+  tcs_P17 = 0
   pi_RT = 0.0
   pi_V1V3 = 0.0
+  pi_P17 = 0.0
   dist20_RT = 0.0
   dist20_V1V3 = 0.0
+  dist20_P17 = 0.0
   summary_lines.each do |line|
       data = line.chomp.split(",")
       if data[0] == "PR"
@@ -289,6 +310,10 @@ libs.each do |lib|
           tcs_V1V3 = data[1].to_i
           pi_V1V3 = data[6].to_f
           dist20_V1V3 = data[7].to_f
+      elsif data[0] == "P17"
+          tcs_P17 = data[4].to_i
+          pi_P17 = data[6].to_f
+          dist20_P17 = data[7].to_f
       end
   end
 
@@ -324,9 +349,13 @@ libs.each do |lib|
     tcs_RT: tcs_RT,
     tcs_IN: tcs_IN,
     tcs_V1V3: tcs_V1V3,
+    tcs_P17: tcs_P17,
     pi_RT: pi_RT,
+    pi_V1V3: pi_V1V3,
+    pi_P17: pi_P17,
     dist20_RT: dist20_RT,
     dist20_V1V3: dist20_V1V3,
+    dist20_P17: dist20_P17,
     recency: recency,
     sdrm_PR: sdrm_PR,
     sdrm_RT: sdrm_RT,

data/docs/dr.json

@@ -62,6 +62,21 @@
       "ref_end": 7208,
       "indel": true,
       "trim": false
+    },
+    {
+      "region": "P17",
+      "cdna": "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCAACAAGGTTTCTGTCATCCAATTTTTTAC",
+      "forward": "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGTCAGCCAAAATTACCCTATAGTGC",
+      "majority": 0.5,
+      "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
     }
   ]
 }

data/lib/viral_seq/hivdr.rb

@@ -5,7 +5,7 @@ module ViralSeq
     # 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)
     #   PR codon 1-99
-    #   RT codon 34-122 (HXB2 2650-2914) and 152-236(3001-3257)
+    #   RT codon 34-122 (HXB2 2649-2914) and 152-236(3001-3257)
     #   IN codon 53-174 (HXB2 4384-4751)
     # @param cutoff [Integer] cut-off for minimal abundance of a mutation to be called as valid mutation,
     #   can be obtained using ViralSeq::SeqHash#poisson_minority_cutoff function

data/lib/viral_seq/tcs_dr.rb

@@ -61,11 +61,26 @@ module ViralSeq
                   :TCS_QC=>true,
                   :ref_genome=>"HXB2",
                   :ref_start=>6585,
-                  :ref_end=>7208,
+                  :ref_end=>7205..7210,
                   :indel=>true,
-                  :trim=>false}
+                  :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/version.rb

@@ -2,6 +2,6 @@
 # version info and histroy
 
 module ViralSeq
-  VERSION = "1.6.3"
-  TCS_VERSION = "2.5.0"
+  VERSION = "1.6.4"
+  TCS_VERSION = "2.5.1"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: viral_seq
 version: !ruby/object:Gem::Version
-  version: 1.6.3
+  version: 1.6.4
 platform: ruby
 authors:
 - Shuntai Zhou
@@ -9,7 +9,7 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-02-05 00:00:00.000000000 Z
+date: 2022-07-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -193,6 +193,7 @@ files:
 - lib/viral_seq/tcs_dr.rb
 - lib/viral_seq/tcs_json.rb
 - lib/viral_seq/version.rb
+- rc_swans.svc@longleaf.unc.edu
 - viral_seq.gemspec
 homepage: https://github.com/ViralSeq/viral_seq
 licenses: