viral_seq 1.2.5 → 1.2.6
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/README.md +7 -1
- data/bin/tcs +56 -60
- data/lib/viral_seq/version.rb +2 -2
- metadata +2 -2
checksums.yaml
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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: aee2536198f5579951f7c5f5f1b97ed27fb0bf5459e6dbfe79137a030951d443
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data.tar.gz: 9ab9b69adf228d3429e02e5d47674ce0a0d137fa6231d940ef8d6cc9abfa1cdf
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: d9b5def3e29f819b6d83902676e80fa2d81531cb44132942244125f6b63110d66389e7f9c61d6e9ea3d80ece57d22d95d5c3948c3f7f71d48835b2714794ffe0
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data.tar.gz: 44b996d9caf9029f2ef522d9058410cdc3b4ec253ccc7bacca5d9ecf66f487624b0b6d18c960b6c7a0af7bfcd2bc72c8c02df59d3c4c7834ab80d4a9eed2a424
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data/README.md
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@@ -179,11 +179,17 @@ qc_seqhash.sdrm_hiv_pr(cut_off)
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## Updates
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### Version 1.2.6-07122021
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1. Optimized the workflow of the `tcs` pipeline in the "end-join/QC/Trimming" section.
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`tcs` version to v2.3.5.
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### Version 1.2.5-06232021
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1. Add error rescue and report in the `tcs` pipeline.
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error messages are stored in the .tcs_error file. `tcs` pipeline updated to v2.3.4.
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2. Use simple majority for the consensus cut-off in the default setting of the `tcs -dr` pipeline.
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2. Use simple majority for the consensus cut-off in the default setting of the `tcs -dr` pipeline.
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### Version 1.2.2-05272021
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data/bin/tcs
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@@ -137,7 +137,7 @@ begin
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end
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primers = params[:primer_pairs]
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if primers.empty?
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if primers.empty? or primers.nil?
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ViralSeq::TcsCore.log_and_abort log, "No primer information. Script terminated."
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end
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@@ -415,71 +415,65 @@ begin
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joined_sh_raw = end_join(out_dir_raw, primer[:end_join_option], primer[:overlap])
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end
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ref_genome = primer[:ref_genome].to_sym
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indel = primer[:indel]
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if ref_start == 0
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ref_start = 0..(ViralSeq::RefSeq.get(ref_genome).size - 1)
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end
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if ref_end == 0
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ref_end = 0..(ViralSeq::RefSeq.get(ref_genome).size - 1)
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end
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if primer[:end_join_option] == 1 and primer[:overlap] == 0
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r1_sh = ViralSeq::SeqHash.fa(outfile_r1)
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r2_sh = ViralSeq::SeqHash.fa(outfile_r2)
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r1_sh = r1_sh.hiv_seq_qc(ref_start, (0..(ViralSeq::RefSeq.get(ref_genome).size - 1)), indel, ref_genome)
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r2_sh = r2_sh.hiv_seq_qc((0..(ViralSeq::RefSeq.get(ref_genome).size - 1)), ref_end, indel, ref_genome)
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new_r1_seq = r1_sh.dna_hash.each_with_object({}) {|(k, v), h| h[k[0..-4]] = v}
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new_r2_seq = r2_sh.dna_hash.each_with_object({}) {|(k, v), h| h[k[0..-4]] = v}
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joined_seq = {}
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new_r1_seq.each do |seq_name, seq|
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next unless seq
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next unless new_r2_seq[seq_name]
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joined_seq[seq_name] = seq + new_r2_seq[seq_name]
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if primer[:TCS_QC]
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ref_start = primer[:ref_start]
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ref_end = primer[:ref_end]
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ref_genome = primer[:ref_genome].to_sym
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indel = primer[:indel]
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if ref_start == 0
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ref_start = 0..(ViralSeq::RefSeq.get(ref_genome).size - 1)
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end
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if ref_end == 0
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ref_end = 0..(ViralSeq::RefSeq.get(ref_genome).size - 1)
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end
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joined_seq_raw = {}
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new_r1_seq_raw.each do |seq_name, seq|
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if primer[:end_join_option] == 1 and primer[:overlap] == 0
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r1_sh = ViralSeq::SeqHash.fa(outfile_r1)
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r2_sh = ViralSeq::SeqHash.fa(outfile_r2)
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r1_sh = r1_sh.hiv_seq_qc(ref_start, (0..(ViralSeq::RefSeq.get(ref_genome).size - 1)), indel, ref_genome)
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r2_sh = r2_sh.hiv_seq_qc((0..(ViralSeq::RefSeq.get(ref_genome).size - 1)), ref_end, indel, ref_genome)
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new_r1_seq = r1_sh.dna_hash.each_with_object({}) {|(k, v), h| h[k[0..-4]] = v}
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new_r2_seq = r2_sh.dna_hash.each_with_object({}) {|(k, v), h| h[k[0..-4]] = v}
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joined_seq = {}
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new_r1_seq.each do |seq_name, seq|
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next unless seq
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next unless
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next unless new_r2_seq[seq_name]
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joined_seq[seq_name] = seq + new_r2_seq[seq_name]
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end
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joined_sh = ViralSeq::SeqHash.new(joined_seq)
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if export_raw
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r1_sh_raw = ViralSeq::SeqHash.fa(outfile_raw_r1)
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r2_sh_raw = ViralSeq::SeqHash.fa(outfile_raw_r2)
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r1_sh_raw = r1_sh_raw.hiv_seq_qc(ref_start, (0..(ViralSeq::RefSeq.get(ref_genome).size - 1)), indel, ref_genome)
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r2_sh_raw = r2_sh_raw.hiv_seq_qc((0..(ViralSeq::RefSeq.get(ref_genome).size - 1)), ref_end, indel, ref_genome)
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new_r1_seq_raw = r1_sh_raw.dna_hash.each_with_object({}) {|(k, v), h| h[k[0..-4]] = v}
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new_r2_seq_raw = r2_sh_raw.dna_hash.each_with_object({}) {|(k, v), h| h[k[0..-4]] = v}
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joined_seq_raw = {}
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new_r1_seq_raw.each do |seq_name, seq|
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next unless seq
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next unless new_r2_seq_raw[seq_name]
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joined_seq_raw[seq_name] = seq + new_r2_seq_raw[seq_name]
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end
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joined_sh_raw = ViralSeq::SeqHash.new(joined_seq_raw)
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end
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else
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joined_sh = joined_sh.hiv_seq_qc(ref_start, ref_end, indel, ref_genome)
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if export_raw
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joined_sh_raw = joined_sh_raw.hiv_seq_qc(ref_start, ref_end, indel, ref_genome)
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end
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end
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end
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log.puts Time.now.to_s + "\t" + "Paired TCS number after QC based on reference genome: " + joined_sh.size.to_s
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summary_json[:combined_tcs_after_qc] = joined_sh.size
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if primer[:trim]
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trim_start = primer[:trim_ref_start]
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trim_end = primer[:trim_ref_end]
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trim_ref = primer[:trim_ref].to_sym
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joined_sh = joined_sh.trim(trim_start, trim_end, trim_ref)
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if export_raw
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joined_sh_raw = joined_sh_raw.trim(trim_start, trim_end, trim_ref)
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end
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end
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end
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if export_raw
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joined_sh_raw.write_nt_fa(File.join(out_dir_raw, "combined.raw.fasta"))
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end
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end
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File.open(outfile_log, "w") do |f|
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f.puts JSON.pretty_generate(summary_json)
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end
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end
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unless options[:keep]
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data/lib/viral_seq/version.rb
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metadata
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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: 1.2.6
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platform: ruby
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authors:
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- Shuntai Zhou
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2021-
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date: 2021-07-12 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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