viral_seq 1.3.0 → 1.6.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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+  metadata.gz: 53c276c8975ad7b714e69906210e78950a3a6efa593cc56565fcf1b80d41d5db
+  data.tar.gz: 6171d3fb2594d2c214b6b94420dee99915e59941e4aeb74cd723bbc9a1d42ab8
 SHA512:
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+  data.tar.gz: eb40f1364222f459392edc0dd00eba03b417d2236c4c0d2ea75b88b3153f6bf209aaf9ff0e5b28309de4abc33464cc9e9607d8d4b8bef16a9a1965a850a835ef

data/Gemfile.lock

@@ -1,12 +1,12 @@
 PATH
   remote: .
   specs:
-    viral_seq (1.1.1)
-      colorize (>= 0.1)
-      combine_pdf (>= 1.0.0)
-      muscle_bio (>= 0.4)
-      prawn (>= 2.3.0)
-      prawn-table (>= 0.2.0)
+    viral_seq (1.6.0)
+      colorize (~> 0.1)
+      combine_pdf (~> 1.0, >= 1.0.0)
+      muscle_bio (~> 0.4)
+      prawn (~> 2.3, >= 2.3.0)
+      prawn-table (~> 0.2, >= 0.2.0)
 
 GEM
   remote: https://rubygems.org/

data/README.md

@@ -55,7 +55,7 @@ Example commands:
 ---
 ### `tcs_log`
 
-Use `tcs_log` script to pool run logs and TCS fasta files after one batch of `tcs` jobs.
+Use `tcs_log` script to pool run logs and TCS fasta files after one batch of `tcs` jobs. This command generates log.html to visualize the sequencing runs.
 
 
 Example file structure:  
@@ -179,14 +179,37 @@ qc_seqhash.sdrm_hiv_pr(cut_off)
 
 ## Updates
 
+### Version-1.6.1-02022022
+
+  1. Fixed the `nav bar` in tcs_log html file.
+  2. Fixed a typo in `tcs`. 
+
+### Version 1.6.0-01042022
+
+  1. Update the `ViralSeq::TcsCore::detection_limit` with pre-calculated values to save processing time.
+  2. Update `tcs` pipeline to v2.5.0. HTML report will generated after running `tcs_log` script after `tcs` pipeline.
+
+### Version 1.5.0-01042022
+
+  1. Added a function to calcute detection limit/sensitivity for minority variants (R required). `ViralSeq::TcsCore::detection_limit`
+  2. Added a function to get a sub SeqHash object given a range of nt positions. `ViralSeq::SeqHash#nt_range`
+  3. Added a function to quality check dna sequences comparing with sample consensus for indels. `ViralSeq::SeqHash#qc_indel`
+  4. Added a function for DNA variant analysis. Return a Hash object that can output as a JSON file. `ViralSeq::SeqHash#nt_variants`
+  5. Added a function to check the size of sequences of a SeqHash object. `ViralSeq::SeqHash#check_nt_size`
+
+### Version 1.4.0-10132021
+
+  1. Added a function to calculate false detectionr rate (FDR, aka, Benjamini-Hochberg correction) for minority mutations detected in the sequences. `ViralSeq::SeqHash#fdr`
+  2. Updated `bin\tcs_sdrm` script to add FDR value to each DRMs detected.
+
 ### Version 1.3.0-08302021
 
-  1. Fixed a bug in the `tcs` pipeline. 
+  1. Fixed a bug in the `tcs` pipeline.
 
 ### Version 1.2.9-08022021
 
   1. Fixed a bug when reading the input primer sequences in lowercases.
-  2. Fix a bug in the method ViralSeq::Math::RandomGaussian
+  2. Fixed a bug in the method ViralSeq::Math::RandomGaussian
 
 ### Version 1.2.8-07292021
 

data/bin/tcs

@@ -32,9 +32,18 @@ require 'optparse'
 
 options = {}
 
-banner = '-'*50 + "\n" +
-        '| The TCS Pipeline ' + "Version #{ViralSeq::TCS_VERSION}".red.bold + " by " + "Shuntai Zhou".blue.bold + ' |' + "\n" +
-        '-'*50 + "\n"
+# banner = '-'*50 + "\n" +
+#         '| The TCS Pipeline ' + "Version #{ViralSeq::TCS_VERSION}".red.bold + " by " + "Shuntai Zhou".blue.bold + ' |' + "\n" +
+#         '-'*50 + "\n"
+
+banner = "\n" +
+"████████  ██████ ███████     ██████  ██ ██████  ███████ ██      ██ ███    ██ ███████\n".light_red +
+"   ██    ██      ██          ██   ██ ██ ██   ██ ██      ██      ██ ████   ██ ██\n".light_yellow +
+"   ██    ██      ███████     ██████  ██ ██████  █████   ██      ██ ██ ██  ██ █████\n".light_green +
+"   ██    ██           ██     ██      ██ ██      ██      ██      ██ ██  ██ ██ ██\n".light_cyan +
+"   ██     ██████ ███████     ██      ██ ██      ███████ ███████ ██ ██   ████ ███████\n".light_magenta
+
+banner += "\nVersion #{ViralSeq::TCS_VERSION}".red.bold + " by " + "Shuntai Zhou".blue.bold + "\n\n"
 
 OptionParser.new do |opts|
   opts.banner = banner + "Usage: tcs -j"
@@ -164,7 +173,7 @@ begin
     unless forward_primer
       log.puts Time.now.to_s + "\t" +  region + " does not have forward primer sequence. #{region} skipped."
     end
-    summary_json[:cdan_primer] = cdna_primer
+    summary_json[:cdna_primer] = cdna_primer
     summary_json[:forward_primer] = forward_primer
 
     primer[:majority] ? majority_cut_off = primer[:majority] : majority_cut_off = 0
@@ -200,7 +209,7 @@ begin
     summary_json[:paired_raw_sequence] = paired_seq_number
     if paired_seq_number < raw_sequence_number * 0.001
       summary_json[:warnings] <<
-        "WARNING: Filtered raw sequneces less than 0.1% of the total raw sequences. Possible contamination."
+        "WARNING: Filtered raw sequences less than 0.1% of the total raw sequences. Possible contamination."
     end
 
     common_keys.each do |seqtag|