viral_seq 1.0.13 → 1.0.14

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data/README.md

@@ -86,20 +86,24 @@ qc_seqhash.sdrm_hiv_pr(cut_off)
 
 ## Updates
 
-### Version 1.1.3-03032021
+### Version 1.0.14-03052021
 
-  1. Fixed the conflict with rails. 
+  1. Add a function `ViralSeq::TcsCore.validate_file_name` to check MiSeq paired-end file names.
 
-### Version 1.1.2-03032021
+### Version 1.0.13-03032021
+
+  1. Fixed the conflict with rails.
+
+### Version 1.0.12-03032021
 
   1. Fixed an issue that may cause conflicts with ActiveRecord.
 
-### Version 1.1.1-03022021
+### Version 1.0.11-03022021
 
   1. Fixed an issue when calculating Poisson cutoff for minority mutations `ViralSeq::SeqHash.pm`.
   2. fixed an issue loading class 'OptionParser'in some ruby environments.
 
-### Version 1.1.0-11112020:
+### Version 1.0.10-11112020:
 
   1. Modularize TCS pipeline. Move key functions into /viral_seq/tcs_core.rb
   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

data/lib/viral_seq/tcs_core.rb

@@ -102,9 +102,9 @@ module ViralSeq
       end
 
       # sort array of file names to determine if there is potential errors
-      # input name_array array of file names
-      # output hash { }
-      # need to change for each file name have an error code. and a bool to show if all pass
+      # @param name_array [Array] array of file names
+      # @return [hash] name check results
+
       def validate_file_name(name_array)
         errors = {
                    file_type_error: [] ,
@@ -165,6 +165,13 @@ module ViralSeq
           end
         end
 
+        file_name_with_lib_name = {}
+        passed_libs.each do |lib_name, files|
+          files.each do |f|
+            file_name_with_lib_name[f] = lib_name
+          end
+        end
+
         passed_names = []
 
         passed_libs.values.each { |names| passed_names += names}
@@ -175,7 +182,27 @@ module ViralSeq
           pass = true
         end
 
-        return { errors: errors, all_pass: pass, passed_names: passed_names, passed_libs: passed_libs }
+        file_name_with_error_type = {}
+
+        errors.each do |type, files|
+          files.each do |f|
+            file_name_with_error_type[f] ||= []
+            file_name_with_error_type[f] << type.to_s.tr("_", "\s")
+          end
+        end
+
+        file_check = []
+
+        name_array.each do |name|
+          file_check_hash = {}
+          file_check_hash[:fileName] = name
+          file_check_hash[:errors] = file_name_with_error_type[name]
+          file_check_hash[:libName] = file_name_with_lib_name[name]
+
+          file_check << file_check_hash
+        end
+
+        return { allPass: pass, files: file_check }
       end
 
       # filter r1 raw sequences for non-specific primers.

data/lib/viral_seq/version.rb

@@ -2,6 +2,6 @@
 # version info and histroy
 
 module ViralSeq
-  VERSION = "1.0.13"
+  VERSION = "1.0.14"
   TCS_VERSION = "2.1.1"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: viral_seq
 version: !ruby/object:Gem::Version
-  version: 1.0.13
+  version: 1.0.14
 platform: ruby
 authors:
 - Shuntai Zhou
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-03-04 00:00:00.000000000 Z
+date: 2021-03-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler