diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/lmdb_matrix.py | 29 |
1 files changed, 16 insertions, 13 deletions
diff --git a/scripts/lmdb_matrix.py b/scripts/lmdb_matrix.py index efd7c58..2d73315 100644 --- a/scripts/lmdb_matrix.py +++ b/scripts/lmdb_matrix.py @@ -12,16 +12,15 @@ guix shell python-click python-lmdb python-wrapper python-numpy -- \ <path-to-lmdb-store> """ +from dataclasses import dataclass from pathlib import Path from subprocess import check_output -import lmdb import json import click +import lmdb import numpy as np -from dataclasses import dataclass - @dataclass class GenotypeMatrix: @@ -32,7 +31,8 @@ class GenotypeMatrix: def count_trailing_newlines(file_path): - with open(file_path, 'rb') as stream: + """Count trailing newlines in a file""" + with open(file_path, 'rb', encoding="utf-8") as stream: stream.seek(0, 2) # Move to the end of the file file_size = stream.tell() if file_size == 0: @@ -111,7 +111,7 @@ def get_genotype_metadata(genotype_file: str) -> tuple[dict, dict]: """ metadata = {} file_metadata = {} - with open(genotype_file, "r") as stream: + with open(genotype_file, "r", encoding="utf-8") as stream: while True: line = stream.readline().strip() match line: @@ -165,7 +165,7 @@ def get_genotype_dimensions(genotype_file: str) -> tuple[int, int]: counter = 0 rows = [] - with open(genotype_file, "r") as stream: + with open(genotype_file, "r", encoding="utf-8") as stream: while True: line = stream.readline() counter += 1 @@ -201,7 +201,7 @@ def read_genotype_headers(genotype_file: str) -> list[str]: ['Chr', 'Locus', 'cM', 'Mb', 'BXD1', 'BXD2', ..., 'BXD220'] """ rows = [] - with open(genotype_file, "r") as stream: + with open(genotype_file, "r", encoding="utf-8") as stream: while True: line = stream.readline() match line: @@ -213,6 +213,7 @@ def read_genotype_headers(genotype_file: str) -> list[str]: return rows +# pylint: disable=too-many-locals def read_genotype_file(genotype_file: str) -> GenotypeMatrix: """Read a genotype file and construct a GenotypeMatrix object. @@ -261,11 +262,9 @@ def read_genotype_file(genotype_file: str) -> GenotypeMatrix: counter = 0 for i, el in enumerate(header): - if el in ["Chr", "Locus", "cM", "Mb"]: - continue - else: - counter = i + if el not in ["Chr", "Locus", "cM", "Mb"]: break + counter = i metadata_columns, individuals = header[:counter], header[counter:] nrows, ncols = get_genotype_dimensions(genotype_file) @@ -286,10 +285,9 @@ def read_genotype_file(genotype_file: str) -> GenotypeMatrix: paternal = metadata.get("pat") heterozygous = metadata.get("het") unknown = metadata.get("unk") - locus, chromosomes = [], [] i = 0 sentinel = True - with open(genotype_file, "r") as stream: + with open(genotype_file, "r", encoding="utf-8") as stream: while True: if i == nrows: break @@ -375,6 +373,8 @@ def genotype_db_get(db: lmdb.Environment) -> GenotypeMatrix: def get_genotype_files(directory: str) -> list[tuple[str, int]]: + """Return a list of all the genotype files from a given + directory.""" geno_files = [ (_file.as_posix(), _file.stat().st_size) for _file in Path(directory).glob("*.geno") if _file.is_file()] @@ -382,6 +382,8 @@ def get_genotype_files(directory: str) -> list[tuple[str, int]]: def __import_directory(directory: str, lmdb_path: str): + """Import all the genotype files from a given directory into + LMDB.""" for genofile, file_size in get_genotype_files(directory): genofile = Path(genofile) size_mb = file_size / (1024 ** 2) @@ -421,6 +423,7 @@ def print_current_matrix(database_directory: str): print(f"File Info: {current.file_info}") +# pylint: disable=missing-function-docstring @click.group() def cli(): pass |