viral_seq 1.0.13 → 1.0.14
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 +9 -5
- data/lib/viral_seq/tcs_core.rb +31 -4
- data/lib/viral_seq/version.rb +1 -1
- 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: '048e85ab67fbb667919d02d4509a15111798b116b3f927c921d203dc8565a1a2'
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data.tar.gz: 6951e410bd4f9b727a44fab1aa88f9cc263151cf9aed2a9c25ae9d866ed72450
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 02cc87e245918a5c8f1b16b0db978da66e3bf7e83c6c6140c394c560d31c86ab1845b337a4f53b4b7883ff8e452e8caef0b036ea113c4416d6a29d16f419eb81
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data.tar.gz: 9f53bd6c46f4a49b5c14b8b8019ffa3e1abcf442bf0a6cc09a7dbc768a474f2afd81d5cf168f38eb8ab5abbd601c60f1f824f753bc77dbcc0d3c0d93568b9ae3
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data/README.md
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@@ -86,20 +86,24 @@ qc_seqhash.sdrm_hiv_pr(cut_off)
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## Updates
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### Version 1.
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### Version 1.0.14-03052021
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1.
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1. Add a function `ViralSeq::TcsCore.validate_file_name` to check MiSeq paired-end file names.
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### Version 1.
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### Version 1.0.13-03032021
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1. Fixed the conflict with rails.
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### Version 1.0.12-03032021
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1. Fixed an issue that may cause conflicts with ActiveRecord.
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### Version 1.
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### Version 1.0.11-03022021
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1. Fixed an issue when calculating Poisson cutoff for minority mutations `ViralSeq::SeqHash.pm`.
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2. fixed an issue loading class 'OptionParser'in some ruby environments.
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### Version 1.
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### Version 1.0.10-11112020:
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1. Modularize TCS pipeline. Move key functions into /viral_seq/tcs_core.rb
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2. `tcs_json_generator` is removed. This CLI is delivered within the `tcs` pipeline, by running `tcs -j`. The scripts are included in the /viral_seq/tcs_json.rb
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data/lib/viral_seq/tcs_core.rb
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@@ -102,9 +102,9 @@ module ViralSeq
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end
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# sort array of file names to determine if there is potential errors
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#
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#
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# @param name_array [Array] array of file names
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# @return [hash] name check results
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def validate_file_name(name_array)
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errors = {
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file_type_error: [] ,
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end
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end
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file_name_with_lib_name = {}
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passed_libs.each do |lib_name, files|
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files.each do |f|
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file_name_with_lib_name[f] = lib_name
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end
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end
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passed_names = []
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passed_libs.values.each { |names| passed_names += names}
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@@ -175,7 +182,27 @@ module ViralSeq
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pass = true
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end
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file_name_with_error_type = {}
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errors.each do |type, files|
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files.each do |f|
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file_name_with_error_type[f] ||= []
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file_name_with_error_type[f] << type.to_s.tr("_", "\s")
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end
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end
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file_check = []
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name_array.each do |name|
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file_check_hash = {}
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file_check_hash[:fileName] = name
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file_check_hash[:errors] = file_name_with_error_type[name]
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file_check_hash[:libName] = file_name_with_lib_name[name]
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file_check << file_check_hash
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end
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return { allPass: pass, files: file_check }
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end
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# filter r1 raw sequences for non-specific primers.
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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: 1.0.
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version: 1.0.14
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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: 2021-03-
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date: 2021-03-06 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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