refactor: import required modules

Signed-off-by: Josh Loecker <joshloecker@icloud.com>

Author: JoshLoecker

main/como/proteomics_gen.py

@@ -1,15 +1,17 @@
 from __future__ import annotations
 
+import itertools
 import sys
-from io import TextIOWrapper
 from pathlib import Path
+from typing import TextIO, cast
 
 import numpy as np
 import pandas as pd
-from fast_bioservices.biodbnet import BioDBNet, Input, Output
+from bioservices import BioDBNet
+from fast_bioservices.biodbnet import Input, Output  # BioDBNet
 from loguru import logger
 
-from como.data_types import LOG_FORMAT, LogLevel
+from como.data_types import LogLevel
 from como.project import Config
 from como.proteomics_preprocessing import protein_transform_main
 from como.utils import _log_and_raise_error, _set_up_logging, return_placeholder_data

main/como/rnaseq_gen.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import itertools
 import multiprocessing
 import sys
 import time
@@ -8,9 +9,8 @@
 from concurrent.futures import Future, ProcessPoolExecutor, as_completed
 from dataclasses import dataclass, field
 from enum import Enum
-from io import TextIOWrapper
 from pathlib import Path
-from typing import NamedTuple
+from typing import NamedTuple, TextIO, cast
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -22,11 +22,11 @@
 from fast_bioservices.pipeline import ensembl_to_gene_id_and_symbol, gene_symbol_to_ensembl_and_gene_id
 from loguru import logger
 from pandas import DataFrame
-from scipy.signal import find_peaks
-from sklearn.neighbors import KernelDensity
 
 from como.data_types import FilteringTechnique, LogLevel, PeakIdentificationParameters, RNAType
+from como.density import density
 from como.migrations import gene_info_migrations
+from como.peak_finder import find_peaks
 from como.project import Config
 from como.utils import _log_and_raise_error, _num_columns, _read_file, _set_up_logging
 

main/como/rnaseq_preprocess.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import asyncio
+import functools
 import json
 import re
 import sys
@@ -14,7 +15,7 @@
 import numpy as np
 import pandas as pd
 from fast_bioservices.biothings.mygene import MyGene
-from fast_bioservices.pipeline import ensembl_to_gene_id_and_symbol, gene_symbol_to_ensembl_and_gene_id
+from fast_bioservices.pipeline import gene_symbol_to_ensembl_and_gene_id
 from loguru import logger
 
 from como.data_types import PATH_TYPE, LogLevel, RNAType

main/como/utils.py

@@ -2,6 +2,7 @@
 
 import contextlib
 import io
+import itertools
 import sys
 from collections.abc import Iterator
 from pathlib import Path