diff options
| -rw-r--r-- | r_qtl/r_qtl2.py | 72 | ||||
| -rw-r--r-- | tests/r_qtl/test_r_qtl2_geno.py | 8 | ||||
| -rw-r--r-- | tests/r_qtl/test_r_qtl2_gmap.py | 12 | ||||
| -rw-r--r-- | tests/r_qtl/test_r_qtl2_pheno.py | 4 |
4 files changed, 14 insertions, 82 deletions
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py index 4dac24b..da7db22 100644 --- a/r_qtl/r_qtl2.py +++ b/r_qtl/r_qtl2.py @@ -134,78 +134,6 @@ def make_process_data_geno(cdata) -> tuple[ for items in zip(ids, vals[1:])) return (__non_transposed__, __transposed__) -def genotype_data(zfile: ZipFile, cdata: dict) -> Iterator[dict]: - """Load the genotype file, making use of the control data.""" - def replace_genotype_codes(val): - return cdata["genotypes"].get(val, val) - - def replace_na_strings(val): - nastrings = cdata.get("na.strings") - if bool(nastrings): - return (None if val in nastrings else val) - return val - - if not cdata.get("geno_transposed", False): - for line in with_non_transposed( - zfile, - "geno", - cdata, - lambda row: { - key: thread_op(value, replace_genotype_codes, replace_na_strings) - for key,value in row.items() - }): - yield line - return None - - def __merge__(key, samples, line): - marker = line[0] - return tuple( - dict(zip( - [key, marker], - (thread_op(item, replace_genotype_codes, replace_na_strings) - for item in items))) - for items in zip(samples, line[1:])) - - for row in with_transposed(zfile, "geno", cdata, __merge__): - yield row - -def map_data(zfile: ZipFile, map_type: str, cdata: dict) -> Iterator[dict]: - """Read gmap files to get the genome mapping data""" - assert map_type in ("genetic-map", "physical-map"), "Invalid map type" - map_file_key = { - "genetic-map": "gmap", - "physical-map": "pmap" - }[map_type] - transposed_dict = { - "genetic-map": "gmap_transposed", - "physical-map": "pmap_transposed" - } - if not cdata.get(transposed_dict[map_type], False): - for row in with_non_transposed(zfile, map_file_key, cdata): - yield row - return None - - def __merge__(key, samples, line): - marker = line[0] - return tuple(dict(zip([key, marker], items)) - for items in zip(samples, line[1:])) - - for row in with_transposed(zfile, map_file_key, cdata, __merge__): - yield row - -def phenotype_data(zfile: ZipFile, cdata: dict) -> Iterator[dict]: - """Load phenotype file data.""" - if not cdata.get("pheno_transposed", False): - for row in with_non_transposed(zfile, "pheno", cdata, lambda val: val): - yield row - return - - def __merge__(id_key, ids, vals): - return tuple(dict(zip([id_key, vals[0]], items)) - for items in zip(ids, vals[1:])) - for row in with_transposed(zfile, "pheno", cdata, __merge__): - yield row - def __default_process_value_transposed__( id_key: str, ids: tuple[str, ...], diff --git a/tests/r_qtl/test_r_qtl2_geno.py b/tests/r_qtl/test_r_qtl2_geno.py index 787d13a..c33984e 100644 --- a/tests/r_qtl/test_r_qtl2_geno.py +++ b/tests/r_qtl/test_r_qtl2_geno.py @@ -171,8 +171,12 @@ def test_parse_geno_files(relpath, expected): THEN: ensure that the data we get is as expected """ with ZipFile(Path(relpath).absolute(), "r") as zfile: - assert tuple( - rqtl2.genotype_data(zfile, rqtl2.control_data(zfile))) == expected + cdata = rqtl2.control_data(zfile) + assert tuple(rqtl2.file_data( + zfile, + "geno", + cdata, + *rqtl2.make_process_data_geno(cdata))) == expected @pytest.mark.unit_test @pytest.mark.parametrize( diff --git a/tests/r_qtl/test_r_qtl2_gmap.py b/tests/r_qtl/test_r_qtl2_gmap.py index ba46c42..5c8ca6a 100644 --- a/tests/r_qtl/test_r_qtl2_gmap.py +++ b/tests/r_qtl/test_r_qtl2_gmap.py @@ -10,28 +10,28 @@ from r_qtl import r_qtl2 as rqtl2 @pytest.mark.parametrize( "relpath,mapfiletype,expected", (("tests/r_qtl/test_files/test_gmap.zip", - "genetic-map", + "gmap", ({"marker": "PVV4", "chr": "1", "pos": "0.000000"}, {"marker": "AXR-1", "chr": "1", "pos": "6.250674"}, {"marker": "HH.335C-Col/PhyA", "chr": "1", "pos": "9.303868"}, {"marker": "EC.480C", "chr": "1", "pos": "12.577629"}, {"marker": "EC.66C", "chr": "1", "pos": "18.392830"})), ("tests/r_qtl/test_files/test_gmap_transposed.zip", - "genetic-map", + "gmap", ({"marker": "PVV4", "chr": "1", "pos": "0.000000"}, {"marker": "AXR-1", "chr": "1", "pos": "6.250674"}, {"marker": "HH.335C-Col/PhyA", "chr": "1", "pos": "9.303868"}, {"marker": "EC.480C", "chr": "1", "pos": "12.577629"}, {"marker": "EC.66C", "chr": "1", "pos": "18.392830"})), ("tests/r_qtl/test_files/test_pmap.zip", - "physical-map", + "pmap", ({"marker": "D1Mit18", "chr": "1", "pos": "52.418656"}, {"marker": "D1Mit80", "chr": "1", "pos": "86.377953"}, {"marker": "D1Mit17", "chr": "1", "pos": "189.571337"}, {"marker": "D2Mit379", "chr": "2", "pos": "37.451062"}, {"marker": "D2Mit75", "chr": "2", "pos": "80.584782"})), ("tests/r_qtl/test_files/test_pmap_transposed.zip", - "physical-map", + "pmap", ({"marker": "D1Mit18", "chr": "1", "pos": "52.418656"}, {"marker": "D1Mit80", "chr": "1", "pos": "86.377953"}, {"marker": "D1Mit17", "chr": "1", "pos": "189.571337"}, @@ -44,5 +44,5 @@ def test_parse_map_files(relpath, mapfiletype, expected): THEN: ensure the parsed data is as expected. """ with ZipFile(Path(relpath).absolute(), "r") as zfile: - assert tuple(rqtl2.map_data( - zfile, mapfiletype, rqtl2.control_data(zfile))) == expected + cdata = rqtl2.control_data(zfile) + assert tuple(rqtl2.file_data(zfile, mapfiletype, cdata)) == expected diff --git a/tests/r_qtl/test_r_qtl2_pheno.py b/tests/r_qtl/test_r_qtl2_pheno.py index 554d9c8..46be469 100644 --- a/tests/r_qtl/test_r_qtl2_pheno.py +++ b/tests/r_qtl/test_r_qtl2_pheno.py @@ -29,5 +29,5 @@ def test_parse_pheno_files(filepath, expected): THEN: verify the parsed data is as expected """ with ZipFile(Path(filepath).absolute(), "r") as zfile: - assert tuple( - rqtl2.phenotype_data(zfile, rqtl2.control_data(zfile))) == expected + cdata = rqtl2.control_data(zfile) + assert tuple(rqtl2.file_data(zfile, "pheno", cdata)) == expected |