viral_seq 1.0.13 → 1.0.14

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data/README.md CHANGED
@@ -86,20 +86,24 @@ qc_seqhash.sdrm_hiv_pr(cut_off)
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  ## Updates
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- ### Version 1.1.3-03032021
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+ ### Version 1.0.14-03052021
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- 1. Fixed the conflict with rails.
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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 1.1.2-03032021
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+ ### Version 1.0.13-03032021
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+
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+ 1. Fixed the conflict with rails.
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+
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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 1.1.1-03022021
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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 1.1.0-11112020:
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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
@@ -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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- # input name_array array of file names
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- # output hash { }
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- # need to change for each file name have an error code. and a bool to show if all pass
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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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+
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  def validate_file_name(name_array)
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  errors = {
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  file_type_error: [] ,
@@ -165,6 +165,13 @@ module ViralSeq
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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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+
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  passed_names = []
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  passed_libs.values.each { |names| passed_names += names}
@@ -175,7 +182,27 @@ module ViralSeq
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  pass = true
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  end
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- return { errors: errors, all_pass: pass, passed_names: passed_names, passed_libs: passed_libs }
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+ file_name_with_error_type = {}
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+
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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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+
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+ file_check = []
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+
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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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+
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+ file_check << file_check_hash
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+ end
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+
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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.
@@ -2,6 +2,6 @@
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  # version info and histroy
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  module ViralSeq
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- VERSION = "1.0.13"
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+ VERSION = "1.0.14"
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  TCS_VERSION = "2.1.1"
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  end
metadata CHANGED
@@ -1,7 +1,7 @@
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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: 1.0.13
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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
@@ -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: 2021-03-04 00:00:00.000000000 Z
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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