diff options
Diffstat (limited to 'r_qtl/r_qtl2.py')
| -rw-r--r-- | r_qtl/r_qtl2.py | 50 |
1 files changed, 34 insertions, 16 deletions
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py index e019d99..47f101e 100644 --- a/r_qtl/r_qtl2.py +++ b/r_qtl/r_qtl2.py @@ -32,7 +32,6 @@ def control_data(zfile: ZipFile) -> dict: def genotype_metadata(zfile: ZipFile, cdata: dict) -> dict: """Read Individual ID key and the marker names.""" - # TODO: Handle transposed files line_num = 0 with zfile.open(cdata["geno"]) as genofile: for line in filter(lambda line: not line.startswith("#"), @@ -45,25 +44,48 @@ def genotype_metadata(zfile: ZipFile, cdata: dict) -> dict: def genotype_data(zfile: ZipFile, cdata: dict) -> Iterator[dict]: """Load the genotype file, making use of the control data.""" - # TODO: Handle transposed files - with zfile.open(cdata["geno"]) as genofile: - reader = csv.DictReader(filter(lambda line: not line.startswith("#"), - io.TextIOWrapper(genofile)), - delimiter=cdata.get("sep", ",")) - if not cdata.get("geno_transposed", False): + def replace_genotype_codes(val): + return cdata["genotypes"].get(val, val) + + def replace_na_strings(val): + return (None if val in cdata["na.strings"] else val) + + if not cdata.get("geno_transposed", False): + with zfile.open(cdata["geno"]) as genofile: + reader = csv.DictReader( + filter(lambda line: not line.startswith("#"), + io.TextIOWrapper(genofile)), + delimiter=cdata.get("sep", ",")) for row in reader: yield { key: thread_op( value, - # replace genotype codes - lambda val: cdata["genotypes"].get(val, val), - # replace N/A strings - lambda val: ( - None if val in cdata["na.strings"] else val)) + replace_genotype_codes, + replace_na_strings) for key,value in row.items() } + def __merge__(key, samples, line): + marker = line[0] + return ( + dict(zip( + [key, marker], + (thread_op(item, replace_genotype_codes, replace_na_strings) + for item in items))) + for items in zip(samples, line[1:])) + + if cdata.get("geno_transposed", False): + with zfile.open(cdata["geno"]) as genofile: + lines = (line.strip().split(cdata.get("sep", ",")) + for line in filter(lambda line: not line.startswith("#"), + io.TextIOWrapper(genofile))) + id_line = next(lines) + id_key, samples = id_line[0], id_line[1:] + for line in lines: + for row in __merge__(id_key, samples, line): + yield row + 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" @@ -71,10 +93,6 @@ def map_data(zfile: ZipFile, map_type: str, cdata: dict) -> dict: "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" |