Basic filtering system and tests completed

tests/modvcfsamples/test_sample.py

@@ -0,0 +1,38 @@
+from modvcfsamples.sample import filter_sample_datatype, filter_all_sample_datatypes, get_records_from_vcf
+import os
+
+def test_get_records_from_vcf_not_none():
+    records = get_records_from_vcf(os.path.abspath("tests/resources/test_files_shortened.vcf"))
+    assert len(records) > 0
+
+def test_filter_sample_datatype_not_none():
+    records = get_records_from_vcf(os.path.abspath("tests/resources/test_files_shortened.vcf"))
+    filter_for = ["GT"]
+    modified_record = filter_sample_datatype(records[0], *filter_for)
+    assert modified_record is not None
+
+def test_filter_sample_datatype_only_filtered():
+    records = get_records_from_vcf(os.path.abspath("tests/resources/test_files_shortened.vcf"))
+    filter_for = ["GT"]
+    modified_record = filter_sample_datatype(records[0], *filter_for)
+    for sample in modified_record.samples:
+        assert len(sample) <= len(filter_for)
+        for key, _ in sample._asdict().items():
+            assert key in filter_for
+
+def test_filter_all_sample_datatypes_not_empty():
+    records = get_records_from_vcf(os.path.abspath("tests/resources/test_files_shortened.vcf"))
+    filter_for = ["GT"]
+    modified_records = list(filter_all_sample_datatypes(records, *filter_for))
+    assert len(modified_records) == 11
+
+def test_filter_all_sample_datatypes_filtered():
+    records = get_records_from_vcf(os.path.abspath("tests/resources/test_files_shortened.vcf"))
+    filter_for = ["GT"]
+    modified_records = list(filter_all_sample_datatypes(records, *filter_for))
+    for modified_record in modified_records:
+        for sample in modified_record.samples:
+            assert len(sample) <= len(filter_for)
+            for key, _ in sample._asdict().items():
+                assert key in filter_for
+

tests/program/test_program.py

@@ -1,2 +0,0 @@
-# TODO Test program!
-

tests/resources/test_files_shortened.vcf

@@ -0,0 +1,17 @@
+##fileformat=VCFv4.1
+##fileDate=10122015_22h01m13s
+##source=SHAPEIT2.v837
+##log_file=shapeit_10122015_22h01m13s_3f764d75-2fbb-42df-ab75-8c2dfd5731ce.log
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Phased Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Gambian	Chinese	French	Brazilian	Nigerian	Pakistani	English	Colombian	Indian	Japanese
+1	846808	rs4475691	C	T	100	.	AC=1276;AN=5008;DP=20368	GT:GQ:DP	1|1:70:60	0|0:30:10	0|0:20:40	./.:0:0	0|0:70:60	0|0:90:30	0|0:80:70	0|0:50:80	./.:0:0	0|0:100:80	
+1	846854	rs111957712	G	A	100	.	AC=114;AN=5008;DP=20538	GT:GQ:DP	./.:0:0	0|0:40:30	0|0:80:30	0|0:0:20	0|0:40:80	0|0:10:30	./.:0:0	./.:0:0	0|0:70:0	0|0:90:30	
+1	846864	rs950122	G	C	100	.	AC=1116;AN=5008;DP=20582	GT:GQ:DP	1|1:60:0	0|0:20:0	0|0:90:70	0|0:80:50	0|0:80:30	0|0:10:80	0|0:100:20	0|0:30:40	./.:0:0	0|0:30:90	
+1	847228	rs3905286	C	T	100	.	AC=1215;AN=5008;DP=20731	GT:GQ:DP	1|1:70:80	0|0:90:80	0|0:60:50	0|0:60:90	0|0:30:40	0|0:70:10	0|0:100:80	0|0:100:50	0|1:70:100	0|0:40:40	
+1	847297	rs11507768	G	A	100	.	AC=359;AN=5008;DP=20809	GT:GQ:DP	1|0:0:60	0|0:10:30	0|0:80:60	./.:0:0	0|0:10:100	0|0:10:100	./.:0:0	0|0:100:40	0|0:20:20	0|0:10:0	
+1	847491	rs28407778	G	A	100	.	AC=1262;AN=5008;DP=16939	GT:GQ:DP	1|1:0:100	0|0:70:40	0|0:0:60	0|0:90:90	0|0:90:90	./.:0:0	0|0:70:60	0|0:70:0	0|1:90:100	0|0:60:60	
+1	848023	rs144407116	C	A	100	.	AC=52;AN=5008;DP=22562	GT:GQ:DP	0|1:10:60	0|0:20:80	0|0:20:50	0|0:20:90	0|0:90:10	0|0:70:60	0|0:40:30	0|0:60:0	0|0:40:40	0|0:10:10	
+1	848090	rs4246505	G	A	100	.	AC=857;AN=5008;DP=19301	GT:GQ:DP	0|0:70:70	0|0:90:30	0|0:40:10	0|0:80:20	0|0:50:50	0|0:10:30	./.:0:0	0|0:20:60	./.:0:0	0|0:90:0	
+1	848445	rs4626817	G	A	100	.	AC=1255;AN=5008;DP=18444	GT:GQ:DP	1|1:100:40	0|0:80:90	0|0:30:100	0|0:100:60	0|0:40:90	0|0:20:30	0|0:70:100	./.:0:0	./.:0:0	0|0:80:30	
+1	848456	rs11507767	A	G	100	.	AC=1266;AN=5008;DP=18137	GT:GQ:DP	1|1:40:30	./.:0:0	0|0:60:90	0|0:60:40	0|0:100:80	0|0:50:50	0|0:0:10	0|0:60:0	0|1:100:100	./.:0:0 
+1	848738	rs3829741	C	T	100	.	AC=855;AN=5008;DP=16663	GT:GQ:DP	0|0:50:90	0|0:50:50	0|0:50:30	0|0:60:60	0|0:80:40	0|0:50:80	0|0:0:80	0|0:0:30	0|1:10:0	0|0:70:30