Tested and completed adding call sample filtering

tests/modvcfsamples/test_sample.py

@@ -1,38 +1,18 @@
-from modvcfsamples.sample import filter_sample_datatype, filter_all_sample_datatypes, get_records_from_vcf
+from modvcfsamples.sample import keep_specific_call_data, 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"))
+    records, header = 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))
+    modified_records, header = keep_specific_call_data(records, header, *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"))
+    records, header = 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))
+    modified_records, header = keep_specific_call_data(records, header, *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():
+        for call in modified_record.calls:
+            assert len(call.data.keys()) <= len(filter_for)
+            for key, _ in call.data.items():
                 assert key in filter_for
-

tests/resources/expected_out/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	1|1	0|0	0|0	./.	0|0	0|0	0|0	0|0	./.	0|0
+1	846854	rs111957712	G	A	100	.	AC=114;AN=5008;DP=20538	GT	./.	0|0	0|0	0|0	0|0	0|0	./.	./.	0|0	0|0
+1	846864	rs950122	G	C	100	.	AC=1116;AN=5008;DP=20582	GT	1|1	0|0	0|0	0|0	0|0	0|0	0|0	0|0	./.	0|0
+1	847228	rs3905286	C	T	100	.	AC=1215;AN=5008;DP=20731	GT	1|1	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|1	0|0
+1	847297	rs11507768	G	A	100	.	AC=359;AN=5008;DP=20809	GT	1|0	0|0	0|0	./.	0|0	0|0	./.	0|0	0|0	0|0
+1	847491	rs28407778	G	A	100	.	AC=1262;AN=5008;DP=16939	GT	1|1	0|0	0|0	0|0	0|0	./.	0|0	0|0	0|1	0|0
+1	848023	rs144407116	C	A	100	.	AC=52;AN=5008;DP=22562	GT	0|1	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+1	848090	rs4246505	G	A	100	.	AC=857;AN=5008;DP=19301	GT	0|0	0|0	0|0	0|0	0|0	0|0	./.	0|0	./.	0|0
+1	848445	rs4626817	G	A	100	.	AC=1255;AN=5008;DP=18444	GT	1|1	0|0	0|0	0|0	0|0	0|0	0|0	./.	./.	0|0
+1	848456	rs11507767	A	G	100	.	AC=1266;AN=5008;DP=18137	GT	1|1	./.	0|0	0|0	0|0	0|0	0|0	0|0	0|1	./.
+1	848738	rs3829741	C	T	100	.	AC=855;AN=5008;DP=16663	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|1	0|0