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author | Frederick Muriuki Muriithi | 2021-09-22 08:36:11 +0300 |
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committer | Frederick Muriuki Muriithi | 2021-09-22 08:36:11 +0300 |
commit | 71cc35e5178904b512b9007e33be17a36f6656f2 (patch) | |
tree | 2d059b89aa30ce55d2cafe781915abc3ea31d948 /gn3/db/genotypes.py | |
parent | cd7f301688fd9780df1f842f8bd2b7602775ba1f (diff) | |
download | genenetwork3-71cc35e5178904b512b9007e33be17a36f6656f2.tar.gz |
Fix typing issues
* Ignore some errors
* Update typing definitions for some portions of code
* Add missing imports
Diffstat (limited to 'gn3/db/genotypes.py')
-rw-r--r-- | gn3/db/genotypes.py | 10 |
1 files changed, 6 insertions, 4 deletions
diff --git a/gn3/db/genotypes.py b/gn3/db/genotypes.py index 919c539..9ea9f20 100644 --- a/gn3/db/genotypes.py +++ b/gn3/db/genotypes.py @@ -2,6 +2,8 @@ import os import gzip +from typing import Union, TextIO + from gn3.settings import GENOTYPE_FILES def build_genotype_file( @@ -44,17 +46,17 @@ def __load_genotype_samples_from_geno(genotype_filename: str): """ gzipped_filename = "{}.gz".format(genotype_filename) if os.path.isfile(gzipped_filename): - genofile = gzip.open(gzipped_filename) + genofile: Union[TextIO, gzip.GzipFile] = gzip.open(gzipped_filename) else: genofile = open(genotype_filename) for row in genofile: line = row.strip() - if (not line) or (line.startswith(("#", "@"))): + if (not line) or (line.startswith(("#", "@"))): # type: ignore[arg-type] continue break - headers = line.split("\t") + headers = line.split("\t" ) # type: ignore[arg-type] if headers[3] == "Mb": return headers[4:] return headers[3:] @@ -107,7 +109,7 @@ def parse_genotype_header(line: str, parlist: tuple = tuple()): ("prgy", prgy), ("nprgy", len(prgy))) -def parse_genotype_marker(line: str, geno_obj: dict, parlist: list): +def parse_genotype_marker(line: str, geno_obj: dict, parlist: tuple): """ Parse a data line in a genotype file |