diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/db/genotypes.py | 32 |
1 files changed, 16 insertions, 16 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)) |