Merge pull request #14 from phac-nml/dev

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phac-nml · Dec 20, 2024 · 58efd38 · 58efd38
2 parents 5368769 + beab20e
commit 58efd38
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Showing 8 changed files with 59 additions and 2 deletions.
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
@@ -12,7 +12,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'phac-nml/profile_dists'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == phac-nml/profile_dists]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == phac-nml/profile_dists ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets

diff --git a/tests.py b/tests.py
diff --git a/tests/data/data_empty_row.tsv b/tests/data/data_empty_row.tsv
@@ -0,0 +1,7 @@
+Sample	A1	A2	A3	A4
+r1	1	1	1	0
+r2	1	1	1	0
+r3	1	1	1	0
+r4	1	1	1	0
+r5	2	2	2	0
+r6	1	0	0	0
diff --git a/tests/data/data_empty_row_q.tsv b/tests/data/data_empty_row_q.tsv
@@ -0,0 +1,7 @@
+Sample	A1	A2	A3	A4
+r1	1	1	1	0
+r2	1	1	1	0
+r3	1	1	1	0
+r4	1	1	1	0
+r5	2	2	2	0
+r6	1	?	?	?
diff --git a/tests/data/data_empty_row_space.tsv b/tests/data/data_empty_row_space.tsv
@@ -0,0 +1,7 @@
+Sample	A1	A2	A3	A4
+r1	1	1	1	0
+r2	1	1	1	0
+r3	1	1	1	0
+r4	1	1	1	0
+r5	2	2	2	0
+r6	1	 	 	 
diff --git a/tests/data/data_empty_row_us.tsv b/tests/data/data_empty_row_us.tsv
@@ -0,0 +1,7 @@
+Sample	A1	A2	A3	A4
+r1	1	1	1	0
+r2	1	1	1	0
+r3	1	1	1	0
+r4	1	1	1	0
+r5	2	2	2	0
+r6	1	_	_	_
diff --git a/tests/test_utils.py b/tests/test_utils.py
@@ -17,11 +17,11 @@
     (["14", "1000", "12"], 'int'),
     ([14, 1000, 12], 'int'),
     ([""], ''),
+    ([14, 20, "AA"], 'hash'),
     #! These tests are commented out for the sake of having some 
     #! set of tests be present and readily testable but if 
     #! further development is to be performed on Profile Dists
     #! these tests should be addressed.
-    #! ([14, 20, "AA"], 'mix'),
     #! (["0.00", "1.0", "3.0"], 'mix'),
     #! (["0.3", 1.0, "4.2"], 'mix'),
     #! ([0.00, 1.0, 3.0], 'mix'),

diff --git a/tests/test_workflows.yml b/tests/test_workflows.yml
@@ -25,3 +25,32 @@
   - path: scaled/results.text
     md5sum: 6eb56fbf3a925fa7b50f65b78febdad4
 
+- name: Hamming Distance and drop empty columns
+  command: profile_dists -q tests/data/data.tsv -r tests/data/data.tsv -d hamming -o hamming_count_missing --missing_thresh 0.0
+  files:
+  - path: hamming_count_missing/results.text
+    md5sum: ab0b4f36fcb14e1f50722c52fee9f327
+
+- name: Hamming Distance and drop row 0
+  command: profile_dists -q tests/data/data_empty_row.tsv -r tests/data/data_empty_row.tsv -d hamming -o hamming --sample_qual_thresh 0.70
+  files:
+  - path: hamming/results.text
+    md5sum: ab0b4f36fcb14e1f50722c52fee9f327
+
+- name: Hamming Distance and drop row question mark
+  command: profile_dists -q tests/data/data_empty_row_q.tsv -r tests/data/data_empty_row_q.tsv -d hamming -o hamming --sample_qual_thresh 0.70
+  files:
+  - path: hamming/results.text
+    md5sum: ab0b4f36fcb14e1f50722c52fee9f327
+
+- name: Hamming Distance and drop row underscore
+  command: profile_dists -q tests/data/data_empty_row_us.tsv -r tests/data/data_empty_row_us.tsv -d hamming -o hamming --sample_qual_thresh 0.70
+  files:
+  - path: hamming/results.text
+    md5sum: ab0b4f36fcb14e1f50722c52fee9f327
+
+- name: Hamming Distance and drop space
+  command: profile_dists -q tests/data/data_empty_row_space.tsv -r tests/data/data_empty_row_space.tsv -d hamming -o hamming --sample_qual_thresh 0.70
+  files:
+  - path: hamming/results.text
+    md5sum: ab0b4f36fcb14e1f50722c52fee9f327