diff options
Diffstat (limited to 'r_qtl')
| -rw-r--r-- | r_qtl/r_qtl2.py | 31 |
1 files changed, 18 insertions, 13 deletions
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py index 26d6dd4..a221f26 100644 --- a/r_qtl/r_qtl2.py +++ b/r_qtl/r_qtl2.py @@ -65,20 +65,27 @@ def genotype_data(zfile: ZipFile, cdata: dict) -> Iterator[dict]: def map_data(zfile: ZipFile, map_type: str, cdata: dict) -> dict: """Read gmap files to get the genome mapping data""" assert map_type in ("genetic-map", "physical-map"), "Invalid map type" - map_key = {"genetic-map": "gmap", "physical-map": "pmap"}[map_type] - if not cdata.get("geno_transposed", False): - with zfile.open(cdata[map_key]) as gmapfile: + map_file = cdata[{ + "genetic-map": "gmap", + "physical-map": "pmap" + }[map_type]] + # TODO: Might need to check `gmap_transposed` and `pmap_transposed` instead + # of `geno_transposed` -- see + # https://github.com/rqtl/qtl2data/blob/main/ArabMAGIC/arabmagic_tair8.json + # for the *_transposed values + transposed_dict = { + "genetic-map": "gmap_transposed", + "physical-map": "pmap_transposed" + } + if not cdata.get(transposed_dict[map_type], False): + with zfile.open(map_file) as gmapfile: reader = csv.DictReader( filter(lambda line: not line.startswith("#"), io.TextIOWrapper(gmapfile)), delimiter=cdata.get("sep", ",")) - return { - line["marker"]: { - key: value for key,value in line.items() if key != "marker" - } for line in reader - } + return tuple(row for row in reader) - with zfile.open(cdata["gmap"]) as gmapfile: + with zfile.open(map_file) as gmapfile: lines = [[field.strip() for field in line.strip().split(cdata.get("sep", ","))] for line in @@ -87,11 +94,9 @@ def map_data(zfile: ZipFile, map_type: str, cdata: dict) -> dict: headers = tuple(line[0] for line in lines) return reduce( - lambda gmap, row: { - **gmap, - row[0]: dict(zip(headers[1:], row[1:]))}, + lambda gmap, row: gmap + (dict(zip(headers, row)),), zip(*(line[1:] for line in lines)), - {}) + tuple()) def read_r_qtl2_files(filepath: Path): """Read R/qtl2 format zip files.""" |