diff options
| -rw-r--r-- | gn3/app.py | 2 | ||||
| -rw-r--r-- | gn3/computations/qtlreaper.py | 6 | ||||
| -rw-r--r-- | gn3/db/genotypes.py | 10 | ||||
| -rw-r--r-- | gn3/db/traits.py | 8 | ||||
| -rw-r--r-- | gn3/heatmaps.py | 8 |
5 files changed, 18 insertions, 16 deletions
@@ -5,7 +5,7 @@ from typing import Dict from typing import Union from flask import Flask -from flask_cors import CORS +from flask_cors import CORS # type: ignore from gn3.api.gemma import gemma from gn3.api.rqtl import rqtl diff --git a/gn3/computations/qtlreaper.py b/gn3/computations/qtlreaper.py index 5d17fed..5ddea76 100644 --- a/gn3/computations/qtlreaper.py +++ b/gn3/computations/qtlreaper.py @@ -4,6 +4,8 @@ computation of QTLs. """ import os import subprocess +from typing import Union + from gn3.random import random_string from gn3.settings import TMPDIR, REAPER_COMMAND @@ -70,9 +72,9 @@ def run_reaper( output_dir, random_string(10)) output_list = ["--main_output", output_filename] if separate_nperm_output: - permu_output_filename = "{}/qtlreaper/permu_output_{}.txt".format( + permu_output_filename: Union[None, str] = "{}/qtlreaper/permu_output_{}.txt".format( output_dir, random_string(10)) - output_list = output_list + ["--permu_output", permu_output_filename] + output_list = output_list + ["--permu_output", permu_output_filename] # type: ignore[list-item] else: permu_output_filename = None 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 diff --git a/gn3/db/traits.py b/gn3/db/traits.py index 747ed27..4fc47c3 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -63,22 +63,22 @@ def update_sample_data(conn: Any, with conn.cursor() as cursor: # Update the Strains table cursor.execute(STRAIN_ID_SQL, (strain_name, strain_id)) - updated_strains: int = cursor.rowcount + updated_strains = cursor.rowcount # Update the PublishData table cursor.execute(PUBLISH_DATA_SQL, (None if value == "x" else value, strain_id, publish_data_id)) - updated_published_data: int = cursor.rowcount + updated_published_data = cursor.rowcount # Update the PublishSE table cursor.execute(PUBLISH_SE_SQL, (None if error == "x" else error, strain_id, publish_data_id)) - updated_se_data: int = cursor.rowcount + updated_se_data = cursor.rowcount # Update the NStrain table cursor.execute(N_STRAIN_SQL, (None if count == "x" else count, strain_id, publish_data_id)) - updated_n_strains: int = cursor.rowcount + updated_n_strains = cursor.rowcount return (updated_strains, updated_published_data, updated_se_data, updated_n_strains) diff --git a/gn3/heatmaps.py b/gn3/heatmaps.py index 9d82fb2..45d0c22 100644 --- a/gn3/heatmaps.py +++ b/gn3/heatmaps.py @@ -7,9 +7,9 @@ from functools import reduce from typing import Any, Dict, Sequence import numpy as np -import plotly.graph_objects as go -import plotly.figure_factory as ff -from plotly.subplots import make_subplots +import plotly.graph_objects as go # type: ignore +import plotly.figure_factory as ff # type: ignore +from plotly.subplots import make_subplots # type: ignore from gn3.settings import TMPDIR from gn3.random import random_string @@ -171,8 +171,6 @@ def build_heatmap(traits_names, conn: Any): clustered = cluster_traits(exported_traits_data_list) slinked = slink(clustered) traits_order = compute_traits_order(slinked) - ordered_traits_names = [ - traits[idx]["trait_fullname"] for idx in traits_order] strains_and_values = retrieve_strains_and_values( traits_order, strains, exported_traits_data_list) traits_filename = "{}/traits_test_file_{}.txt".format( |