From 365fed5d9ff37e4280e365d3a9ec23ea49de300e Mon Sep 17 00:00:00 2001
From: rhliang <rliang@cfenet.ubc.ca>
Date: Wed, 20 Nov 2024 15:13:30 -0800
Subject: [PATCH] Added more tests for remove_inserts.

These tests were not run on my workstation; they're also an experiment
to see whether CI is working.
---
 ruby/lib/cfe_gotoh.rb       |   4 +-
 ruby/test/cfe_gotoh_test.rb | 112 ++++++++++++++++++++++++++++++++++++
 2 files changed, 114 insertions(+), 2 deletions(-)

diff --git a/ruby/lib/cfe_gotoh.rb b/ruby/lib/cfe_gotoh.rb
index 349e0ba..5229e7e 100644
--- a/ruby/lib/cfe_gotoh.rb
+++ b/ruby/lib/cfe_gotoh.rb
@@ -365,10 +365,10 @@ def self.frame_align(
 
   #Returns a [seq_sans_inserts, [list of inserts]]
   def self.remove_inserts(elem)
-    return remove_insertions_from_query(elem[1])
+    return remove_insertions_from_query(elem[0], elem[1])
   end
 
-  def self.remove_insertions_from_query(query)
+  def self.remove_insertions_from_query(standard, query)
     seq = '' + query
     inserts = []
     
diff --git a/ruby/test/cfe_gotoh_test.rb b/ruby/test/cfe_gotoh_test.rb
index 0667c08..c661522 100644
--- a/ruby/test/cfe_gotoh_test.rb
+++ b/ruby/test/cfe_gotoh_test.rb
@@ -1081,3 +1081,115 @@ def test_unmerged_deletions_raise_error
     end
   end
 end
+
+
+class RemoveInsertsTest < CfeGotohTest
+  REMOVE_INSERTS_TEST_CASES = [
+    {
+      name: 'no_insertions',
+      std: 'AAACCCGGGTTT',
+      query: 'AAACCCGGGTTT',
+      expected_seq: 'AAACCCGGGTTT',
+      expected_inserts: []
+    },
+    {
+      name: 'no_insertions_deletions_ignored',
+      std: 'AAACCCGGGTTT',
+      query: 'AAACCC---TTT',
+      expected_seq: 'AAACCC---TTT',
+      expected_inserts: []
+    },
+    {
+      name: 'single_base_insertion_in_middle',
+      std: 'AAACCC-GGGTTT',
+      query: 'AAACCCTGGGTTT',
+      expected_seq: 'AAACCCGGGTTT',
+      expected_inserts: [[2, 'T']]
+    },
+    {
+      name: 'single_base_insertion_in_middle_mid_codon',
+      std: 'AAACCCGG-GTTT',
+      query: 'AAACCCGGTGTTT',
+      expected_seq: 'AAACCCGGGTTT',
+      expected_inserts: [[2, 'T']]
+    },
+    {
+      name: 'single_base_insertion_at_beginning',
+      std: '-AAACCCGGGTTT',
+      query: 'TAAACCCGGGTTT',
+      expected_seq: 'AAACCCGGGTTT',
+      expected_inserts: [[0, 'T']]
+    },
+    {
+      name: 'single_base_insertion_at_end',
+      std: 'AAACCCGGGTTT-',
+      query: 'AAACCCGGGTTTA',
+      expected_seq: 'AAACCCGGGTTT',
+      expected_inserts: [[4, 'A']]
+    },
+    {
+      name: 'several_single_base_insertions',
+      std: '-AAACCC-GGGT-TT-',
+      query: 'TAAACCCAG-GTCTTA',
+      expected_seq: 'AAACCCG-GTTT',
+      expected_inserts: [[0, 'T'], [2, 'A'], [3, 'C'], [4, A]]
+    },
+    {
+      name: 'multiple_base_insertion_in_middle',
+      std: 'AAACCC--GGGTTT',
+      query: 'AAACCCCAGGGTTT',
+      expected_seq: 'AAACCCGGGTTT',
+      expected_inserts: [[2, 'CA']]
+    },
+    {
+      name: 'multiple_base_insertion_in_middle_mid_codon',
+      std: 'AAACC---CGGGTTT',
+      query: 'AAACCAGTCGGGTTT',
+      expected_seq: 'AAACCCGGGTTT',
+      expected_inserts: [[1, 'AGT']]
+    },
+    {
+      name: 'multiple_base_insertion_at_beginning',
+      std: '---AAACCCGGGTTT',
+      query: 'CGTAAACCCGGGTTT',
+      expected_seq: 'AAACCCGGGTTT',
+      expected_inserts: [[0, 'CGT']]
+    },
+    {
+      name: 'multiple_base_insertion_at_end',
+      std: 'AAACCCGGGTTT----',
+      query: 'AAACCCGGGTTTACGT',
+      expected_seq: 'AAACCCGGGTTT',
+      expected_inserts: [[4, 'ACGT']]
+    },
+    {
+      name: 'distinct_insertions_at_same_codon',
+      std: 'AAA---C-CCGGGTTT',
+      query: 'AAAGTGCTCCGGGTTT',
+      expected_seq: 'AAACCCGGGTTT',
+      expected_inserts: [[1, 'GTG'], [1, 'T']]
+    },
+    {
+      name: 'typical_case',
+      std: '---AAACC-CGGG---TT-T----',
+      query: 'CGTAAACGGCG-GACGTTATACGT',
+      expected_seq: 'AAACGCG-GTTT',
+      expected_inserts: [[0, 'CGT'], [1, 'C'], [3, 'ACG'], [3, 'A'], [4, 'ACGT']]
+    }
+  ]
+
+  REMOVE_INSERTS_TEST_CASES.each do |test_entry|
+    define_method("test_#{test_entry[:name]}") do
+      result = CfeGotoh.remove_insertions_from_query(
+        test_entry[:std],
+        test_entry[:query]
+      )
+      assert_equal(test_entry[:expected_seq], result[0])
+      assert_equal(test_entry[:expected_inserts], result[1])
+
+      wrapper_result = CfeGotoh.remove_inserts([test_entry[:std], test_entry[:query]])
+      assert_equal(test_entry[:expected_seq], wrapper_result[0])
+      assert_equal(test_entry[:expected_inserts], wrapper_result[1])
+    end
+  end
+end