diff options
| -rw-r--r-- | gn3/db/genotypes.py | 32 | ||||
| -rw-r--r-- | tests/unit/db/test_genotypes.py | 10 |
2 files changed, 21 insertions, 21 deletions
diff --git a/gn3/db/genotypes.py b/gn3/db/genotypes.py index b5d14a5..b03d55c 100644 --- a/gn3/db/genotypes.py +++ b/gn3/db/genotypes.py @@ -88,7 +88,7 @@ def parse_genotype_labels(lines: list): item for item in (__parse_label(line) for line in lines) if item is not None) -def parse_genotype_header(line: str, parlist = tuple()): +def parse_genotype_header(line: str, parlist: tuple = tuple()): """ Parse the genotype file header line @@ -97,13 +97,13 @@ def parse_genotype_header(line: str, parlist = tuple()): https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/utility/gen_geno_ob.py#L94-L114 """ items = [item.strip() for item in line.split("\t")] - Mbmap = "Mb" in items - prgy = ((parlist + tuple(items[4:])) if Mbmap + mbmap = "Mb" in items + prgy = ((parlist + tuple(items[4:])) if mbmap else (parlist + tuple(items[3:]))) return ( - ("Mbmap", Mbmap), + ("Mbmap", mbmap), ("cm_column", items.index("cM")), - ("mb_column", None if not Mbmap else items.index("Mb")), + ("mb_column", None if not mbmap else items.index("Mb")), ("prgy", prgy), ("nprgy", len(prgy))) @@ -131,16 +131,16 @@ def parse_genotype_marker(line: str, geno_obj: dict, parlist: list): if len(parlist) > 0: genotype = (-1, 1) + genotype try: - cM = float(geno_obj["cm_column"]) + cm_val = float(geno_obj["cm_column"]) except: if geno_obj["Mbmap"]: - cM = float(geno_obj["mb_column"]) + cm_val = float(geno_obj["mb_column"]) else: - cM = 0 + cm_val = 0 return ( ("chr", marker_row[0]), ("name", marker_row[1]), - ("cM", cM), + ("cM", cm_val), ("Mb", float(geno_obj["mb_column"]) if geno_obj["Mbmap"] else None), ("genotype", genotype)) @@ -155,9 +155,9 @@ def build_genotype_chromosomes(geno_obj, markers): ("name", chr_name), ("mb_exists", geno_obj["Mbmap"]), ("cm_column", 2), ("mb_column", geno_obj["mb_column"]), ("loci", tuple(marker for marker in mrks if marker["chr"] == chr_name))) - for chr_name in sorted(chr_names)) + for chr_name in sorted(chr_names)) -def parse_genotype_file(filename: str, parlist = tuple()): +def parse_genotype_file(filename: str, parlist: tuple = tuple()): """ Parse the provided genotype file into a usable pytho3 data structure. """ @@ -165,16 +165,16 @@ def parse_genotype_file(filename: str, parlist = tuple()): contents = infile.readlines() lines = tuple(line for line in contents if - ((not line.strip().startswith("#")) and - (not line.strip() == ""))) + ((not line.strip().startswith("#")) and + (not line.strip() == ""))) labels = parse_genotype_labels( - line for line in lines if line.startswith("@")) + [line for line in lines if line.startswith("@")]) data_lines = tuple(line for line in lines if not line.startswith("@")) header = parse_genotype_header(data_lines[0], parlist) geno_obj = dict(labels + header) markers = tuple( - parse_genotype_marker(line, geno_obj, parlist) - for line in data_lines[1:]) + [parse_genotype_marker(line, geno_obj, parlist) + for line in data_lines[1:]]) chromosomes = tuple( dict(chromosome) for chromosome in build_genotype_chromosomes(geno_obj, markers)) diff --git a/tests/unit/db/test_genotypes.py b/tests/unit/db/test_genotypes.py index a05ce48..c125224 100644 --- a/tests/unit/db/test_genotypes.py +++ b/tests/unit/db/test_genotypes.py @@ -18,9 +18,9 @@ class TestGenotypes(TestCase): "@type:test_type", "@mat:test_mat \t", "@pat:test_pat ", "@het: test_het ", "@unk: test_unk", "@other: test_other", "@brrr: test_brrr "]), - (("group", "test_group"), ("filler", "test_filler"), - ("type", "test_type"), ("mat", "test_mat"), ("pat", "test_pat"), - ("het", "test_het"), ("unk", "test_unk"))) + (("group", "test_group"), ("filler", "test_filler"), + ("type", "test_type"), ("mat", "test_mat"), ("pat", "test_pat"), + ("het", "test_het"), ("unk", "test_unk"))) def test_parse_genotype_header(self): """Test that the genotype header is parsed correctly.""" @@ -71,7 +71,7 @@ class TestGenotypes(TestCase): (("chr", "1"), ("name", "rs31443144"), ("cM", 2.0), ("Mb", 3.0), ("genotype", (-1, -1, 1, 0, 1, -1, "U", 1, -1, -1)))]]: - with self.subTest(line = line): + with self.subTest(line=line): self.assertEqual( parse_genotype_marker(line, geno_obj, parlist), expected) @@ -110,7 +110,7 @@ class TestGenotypes(TestCase): ("loci", ({"chr": "1", "name": "rs31443144", "cM": 2.0, "Mb": None, "genotype": (-1, 1, 1, 0, 1, -1, "U", 1, -1, -1)},))),)]]: - with self.subTest(markers = markers): + with self.subTest(markers=markers): self.assertEqual( build_genotype_chromosomes(geno_obj, markers), expected) |