viral_seq 1.2.6 → 1.2.7
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- checksums.yaml +4 -4
- data/README.md +6 -0
- data/bin/tcs +3 -2
- data/lib/viral_seq/seq_hash.rb +3 -1
- data/lib/viral_seq/tcs_core.rb +1 -1
- data/lib/viral_seq/version.rb +2 -2
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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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: 554845dba339d0e06b84c88bc117258516f391bdf58cce015c2669e7b2c6c0d5
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4
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data.tar.gz: 870280337c90d1f5b9ecbea6e6478d7e2dc22aa70917c6b2ecd94afaa185c1c6
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 54db76e6fd8333ccebb19dee602378ec8dbe5d196ec7bd675e55f65db80cb06ac2ab51ce1f13ab7ea65c0a50ad49978bd3e9581074c497b298f0912858946fa8
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7
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data.tar.gz: 03d02329192465a9f278715c8a85e3a910e5c5c7252026980d29e669df823a5bdb4be323eeb56f7c9804b71fa8f1763c5a526227f3764315d6eb8e208934ce81
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data/README.md
CHANGED
@@ -179,6 +179,12 @@ qc_seqhash.sdrm_hiv_pr(cut_off)
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## Updates
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+
### Version 1.2.7-07152021
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1. Optimzed the workflow of the `tcs` pipeline on raw data with uneven lengths.
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`tcs` version to v2.3.5.
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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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data/bin/tcs
CHANGED
@@ -353,7 +353,8 @@ begin
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353
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r1_seq_length = consensus_filtered.values[0][0].size
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r2_seq_length = consensus_filtered.values[0][1].size
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else
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-
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+
r1_seq_length = "n/a"
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r2_seq_length = "n/a"
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end
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log.puts Time.now.to_s + "\t" + "R1 sequence #{r1_seq_length} bp"
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log.puts Time.now.to_s + "\t" + "R1 sequence #{r2_seq_length} bp"
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@@ -426,7 +427,7 @@ begin
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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
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+
if primer[:end_join_option] == 1
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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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data/lib/viral_seq/seq_hash.rb
CHANGED
@@ -397,7 +397,9 @@ module ViralSeq
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(0..(seq_length - 1)).each do |position|
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all_base = []
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seq_array.each do |seq|
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-
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+
if seq[position]
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all_base << seq[position]
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end
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end
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base_count = all_base.count_freq
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max_base_list = []
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data/lib/viral_seq/tcs_core.rb
CHANGED
@@ -305,7 +305,7 @@ module ViralSeq
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end
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def general_filter(seq)
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-
if seq.size < $platform_sequencing_length
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+
if seq.size < ($platform_sequencing_length - 1)
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return false
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elsif seq[1..-2] =~ /N/ # sequences with ambiguities except the 1st and last position removed
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return false
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data/lib/viral_seq/version.rb
CHANGED
metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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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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4
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+
version: 1.2.7
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platform: ruby
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authors:
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- Shuntai Zhou
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@@ -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: 2021-07-
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+
date: 2021-07-15 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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