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authorMuriithi Frederick Muriuki2021-09-01 11:08:38 +0300
committerMuriithi Frederick Muriuki2021-09-01 11:08:38 +0300
commit3ded952f40f486d9aa69746eac2afe7f67fef790 (patch)
tree27847b2c8081a3254b6c28a8c6c7b691c1478947 /gn3/db
parentabfc0410a2385d8c3d6ee1915fc99b708e1d0dbc (diff)
downloadgenenetwork3-3ded952f40f486d9aa69746eac2afe7f67fef790.tar.gz
Fix linting and typing issues
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
Diffstat (limited to 'gn3/db')
-rw-r--r--gn3/db/genotypes.py32
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))