diff options
| -rw-r--r-- | gn3/db/genotypes.py | 37 | ||||
| -rw-r--r-- | tests/unit/db/test_genotypes.py | 38 |
2 files changed, 74 insertions, 1 deletions
diff --git a/gn3/db/genotypes.py b/gn3/db/genotypes.py index be0dfc2..8710d2e 100644 --- a/gn3/db/genotypes.py +++ b/gn3/db/genotypes.py @@ -106,3 +106,40 @@ def parse_genotype_header(line: str, parlist = tuple()): ("mb_column", None if not Mbmap else items.index("Mb")), ("prgy", prgy), ("nprgy", len(prgy))) + +def parse_genotype_data_line(line: str, geno_obj: dict, parlist: list): + """ + Parse a data line in a genotype file + + DESCRIPTION: + Reworks + https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/utility/gen_geno_ob.py#L143-L190 + """ + marker_row = [item.strip() for item in line.split("\t")] + geno_table = { + geno_obj["mat"]: -1, geno_obj["pat"]: 1, geno_obj["het"]: 0, + geno_obj["unk"]: "U" + } + start_pos = 4 if geno_obj["Mbmap"] else 3 + if len(parlist) > 0: + start_pos = start_pos + 2 + + alleles = marker_row[start_pos:] + genotype = tuple( + (geno_table[allele] if allele in geno_table.keys() else "U") + for allele in alleles) + if len(parlist) > 0: + genotype = (-1, 1) + genotype + try: + cM = float(geno_obj["cm_column"]) + except: + if geno_obj["Mbmap"]: + cM = float(geno_obj["mb_column"]) + else: + cM = 0 + return ( + ("chr", marker_row[0]), + ("name", marker_row[1]), + ("cM", cM), + ("Mb", float(geno_obj["mb_column"]) if geno_obj["Mbmap"] else None), + ("genotype", genotype)) diff --git a/tests/unit/db/test_genotypes.py b/tests/unit/db/test_genotypes.py index 4fa8a53..ba90191 100644 --- a/tests/unit/db/test_genotypes.py +++ b/tests/unit/db/test_genotypes.py @@ -1,11 +1,13 @@ """Tests gn3.db.genotypes""" from unittest import TestCase -from gn3.db.genotypes import parse_genotype_labels, parse_genotype_header +from gn3.db.genotypes import ( + parse_genotype_labels, parse_genotype_header, parse_genotype_data_line) class TestGenotypes(TestCase): """Tests for functions in `gn3.db.genotypes`.""" def test_parse_genotype_labels(self): + """Test that the genotype labels are parsed correctly.""" self.assertEqual( parse_genotype_labels([ "@name: test_group\t", "@filler: test_filler ", @@ -17,6 +19,7 @@ class TestGenotypes(TestCase): ("het", "test_het"), ("unk", "test_unk"))) def test_parse_genotype_header(self): + """Test that the genotype header is parsed correctly.""" for header, expected in [ [("Chr\tLocus\tcM\tMb\tBXD1\tBXD2\tBXD5\tBXD6\tBXD8\tBXD9\t" "BXD11\tBXD12\tBXD13\tBXD14\tBXD15\tBXD16\tBXD18\tBXD19"), @@ -35,3 +38,36 @@ class TestGenotypes(TestCase): ("nprgy", 13))]]: with self.subTest(header=header): self.assertEqual(parse_genotype_header(header), expected) + + def test_parse_genotype_data_line(self): + """Test parsing of data lines.""" + for line, geno_obj, parlist, expected in [ + ["1\trs31443144\t1.50\t3.010274\tB\tB\tD\tD\tD\tB\tB\tD\tB\tB", + {"mat": "test_mat", "pat": "test_pat", "het": "test_het", + "unk": "test_unk", "cm_column": 2, "Mbmap": True, + "mb_column": 3}, + tuple(), + (("chr", "1"), ("name", "rs31443144"), ("cM", 2.0), + ("Mb", 3.0), + ("genotype", + ("U", "U", "U", "U", "U", "U", "U", "U", "U", "U")))], + ["1\trs31443144\t1.50\t3.010274\tB\tB\tD\tD\tD\tB\tB\tD\tB\tB", + {"mat": "test_mat", "pat": "test_pat", "het": "test_het", + "unk": "test_unk", "cm_column": 2, "Mbmap": True, + "mb_column": 3}, + ("some", "parlist", "content"), + (("chr", "1"), ("name", "rs31443144"), ("cM", 2.0), + ("Mb", 3.0), + ("genotype", + (-1, 1, "U", "U", "U", "U", "U", "U", "U", "U")))], + ["1\trs31443144\t1.50\t3.010274\tB\tB\tD\tH\tD\tB\tU\tD\tB\tB", + {"mat": "B", "pat": "D", "het": "H", "unk": "U", + "cm_column": 2, "Mbmap": True, "mb_column": 3}, + tuple(), + (("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): + self.assertEqual( + parse_genotype_data_line(line, geno_obj, parlist), + expected) |