viral_seq 1.5.0 → 1.6.3
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- checksums.yaml +4 -4
- data/Gemfile.lock +3 -3
- data/README.md +17 -1
- data/bin/tcs +13 -4
- data/bin/tcs_log +614 -0
- data/bin/tcs_sdrm +2 -1
- data/docs/variants_structure.pdf +0 -0
- data/lib/viral_seq/constant.rb +3 -1
- data/lib/viral_seq/muscle.rb +8 -2
- data/lib/viral_seq/seq_hash.rb +8 -3
- data/lib/viral_seq/sequence.rb +12 -13
- data/lib/viral_seq/tcs_core.rb +10 -2
- data/lib/viral_seq/tcs_dr.rb +2 -2
- data/lib/viral_seq/version.rb +2 -2
- data/viral_seq.gemspec +1 -1
- metadata +5 -4
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
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---
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: ed86467ec77cdce9b1175604528937233fb2d3e91081a294b8a9aed2e5ca2b68
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4
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data.tar.gz: 3c9eef94e3252e5f486ee82b69b45e584810281d50c7d7ceaad0d51ec87ba890
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: cf23bedc3bc4be082eeb1e1a512fa5ae4777ca2d7b7d425348e2f95cc934fe6a1aed5875998fd5236f1485ed86797d3b2fed1d416a4cca6442e4dfa35967dd3b
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7
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data.tar.gz: 4958b976b7d97d1c7f052b0341bdbf9eee66db86cabf6aada972afb081a4766d20af3cc0c13e0c14a01b4a1e831c62c49e03ffd6131a21f8215b66fc19cee61b
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data/Gemfile.lock
CHANGED
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@@ -1,10 +1,10 @@
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1
1
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PATH
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remote: .
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specs:
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-
viral_seq (1.
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4
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+
viral_seq (1.6.2)
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5
5
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colorize (~> 0.1)
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6
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combine_pdf (~> 1.0, >= 1.0.0)
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7
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muscle_bio (~> 0.
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+
muscle_bio (~> 0.5)
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8
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prawn (~> 2.3, >= 2.3.0)
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prawn-table (~> 0.2, >= 0.2.0)
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@@ -15,7 +15,7 @@ GEM
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combine_pdf (1.0.21)
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ruby-rc4 (>= 0.1.5)
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diff-lcs (1.3)
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muscle_bio (0.
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+
muscle_bio (0.5.0)
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pdf-core (0.9.0)
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prawn (2.4.0)
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pdf-core (~> 0.9.0)
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data/README.md
CHANGED
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@@ -55,7 +55,7 @@ Example commands:
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---
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### `tcs_log`
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-
Use `tcs_log` script to pool run logs and TCS fasta files after one batch of `tcs` jobs.
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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.
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Example file structure:
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@@ -179,6 +179,22 @@ qc_seqhash.sdrm_hiv_pr(cut_off)
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## Updates
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### Version-1.6.3-02052022
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1. Updated on `ViralSeq::Muscle` module along with the update of `muscle` from version 3.8.1 to 5.1.
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185
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2. Optimized the `locator` algorithm based on `muscle` v5.1.
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3. Optimized the `tcs_sdrm` pipeline based on `muscle` v5.1.
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### Version-1.6.1-02022022
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1. Fixed the `nav bar` in tcs_log html file.
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2. Fixed a typo in `tcs`.
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### Version 1.6.0-01042022
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1. Update the `ViralSeq::TcsCore::detection_limit` with pre-calculated values to save processing time.
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2. Update `tcs` pipeline to v2.5.0. HTML report will generated after running `tcs_log` script after `tcs` pipeline.
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### Version 1.5.0-01042022
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1. Added a function to calcute detection limit/sensitivity for minority variants (R required). `ViralSeq::TcsCore::detection_limit`
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data/bin/tcs
CHANGED
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@@ -32,9 +32,18 @@ require 'optparse'
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options = {}
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-
banner = '-'*50 + "\n" +
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-
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# banner = '-'*50 + "\n" +
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# '| The TCS Pipeline ' + "Version #{ViralSeq::TCS_VERSION}".red.bold + " by " + "Shuntai Zhou".blue.bold + ' |' + "\n" +
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# '-'*50 + "\n"
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banner = "\n" +
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"████████ ██████ ███████ ██████ ██ ██████ ███████ ██ ██ ███ ██ ███████\n".light_red +
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" ██ ██ ██ ██ ██ ██ ██ ██ ██ ██ ██ ████ ██ ██\n".light_yellow +
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" ██ ██ ███████ ██████ ██ ██████ █████ ██ ██ ██ ██ ██ █████\n".light_green +
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" ██ ██ ██ ██ ██ ██ ██ ██ ██ ██ ██ ██ ██\n".light_cyan +
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" ██ ██████ ███████ ██ ██ ██ ███████ ███████ ██ ██ ████ ███████\n".light_magenta
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banner += "\nVersion #{ViralSeq::TCS_VERSION}".red.bold + " by " + "Shuntai Zhou".blue.bold + "\n\n"
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OptionParser.new do |opts|
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opts.banner = banner + "Usage: tcs -j"
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@@ -164,7 +173,7 @@ begin
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164
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unless forward_primer
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log.puts Time.now.to_s + "\t" + region + " does not have forward primer sequence. #{region} skipped."
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166
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end
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167
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-
summary_json[:
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176
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+
summary_json[:cdna_primer] = cdna_primer
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168
177
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summary_json[:forward_primer] = forward_primer
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170
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primer[:majority] ? majority_cut_off = primer[:majority] : majority_cut_off = 0
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