Merge pull request #13 from phac-nml/tests

Tests

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

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	?	?	?

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	 	 	 

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	_	_	_

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'),

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