General cleanup of import statements

pvactools/lib/__init__.py

@@ -1,31 +0,0 @@
-__all__ = [
-    "aggregate_all_epitopes",
-    "binding_filter",
-    "calculate_manufacturability",
-    "call_iedb",
-    "combine_parsed_outputs",
-    "csq_parser",
-    "identify_problematic_amino_acids",
-    "input_file_converter",
-    "download_example_data",
-    "output_parser",
-    'net_chop',
-    "netmhc_stab",
-    "filter",
-    "top_score_filter",
-    "run_utils",
-    "post_processor",
-    "vector_visualization",
-    'filter_regtools_results',
-    'junction_to_fasta',
-    'fasta_to_kmers',
-    'combine_inputs',
-    'load_gtf_data',
-    'junction_to_kmer_pipeline',
-    'variant_to_kmer_pipeline',
-    'fusion_to_kmer_pipeline',
-    'anchor_residue_pass',
-    'aggregate_report_filter',
-]
-
-from . import *

pvactools/lib/identify_problematic_amino_acids.py

@@ -5,7 +5,6 @@
 import textwrap
 import pandas as pd
 
-from pvactools.lib.run_argument_utils import *
 from pvactools.lib.run_utils import supported_amino_acids
 
 

pvactools/lib/print_log.py

@@ -3,9 +3,6 @@
 import yaml
 import importlib.metadata
 
-from pvactools.lib.run_argument_parser import *
-
-
 def print_log(log_dir, args_dict, output_file_prefix):
     os.makedirs(log_dir, exist_ok=True)
     log_file = os.path.join(log_dir, f'{output_file_prefix}.yml')

pvactools/lib/run_pipeline.py

@@ -4,9 +4,9 @@
 import logging
 
 from pvactools.lib.prediction_class import NetMHCIIVersion
-from pvactools.lib.print_log import *
+from pvactools.lib.print_log import print_log
 from pvactools.lib.run_utils import combine_reports, change_permissions_recursive
-from pvactools.lib.prediction_class_utils import *
+from pvactools.lib.prediction_class_utils import split_algorithms, combine_class_ii_alleles, split_alleles
 
 class RunPipeline:
     def __init__(self, **kwargs):

pvactools/tools/__init__.py

@@ -1,11 +0,0 @@
-__all__ = [
-    'allele_specific_cutoffs',
-    'compare',
-    'download_cwls',
-    'download_wdls',
-    'valid_algorithms',
-    'valid_alleles',
-    'valid_netmhciipan_versions',
-]
-
-from . import *

pvactools/tools/main.py

@@ -4,7 +4,16 @@
     from importlib.metadata import version
 except:
     from importlib_metadata import version
-from pvactools.tools import *
+
+from pvactools.tools import (
+    allele_specific_cutoffs,
+    compare,
+    download_cwls,
+    download_wdls,
+    valid_alleles,
+    valid_algorithms,
+    valid_netmhciipan_versions,
+)
 
 def define_parser():
     parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)

pvactools/tools/pvacbind/__init__.py

@@ -1,15 +0,0 @@
-__all__ = [
-    'run',
-    'binding_filter',
-    'download_example_data',
-    'top_score_filter',
-    'net_chop',
-    'netmhc_stab',
-    'calculate_reference_proteome_similarity',
-    'generate_aggregated_report',
-    'identify_problematic_amino_acids',
-    'update_tiers',
-    'aggregate_report_filter',
-]
-
-from . import *

pvactools/tools/pvacbind/main.py

@@ -2,7 +2,20 @@
 import sys
 from subprocess import call
 import os
-from pvactools.tools.pvacbind import *
+
+from pvactools.tools.pvacbind import (
+    run,
+    binding_filter,
+    top_score_filter,
+    aggregate_report_filter,
+    net_chop,
+    netmhc_stab,
+    calculate_reference_proteome_similarity,
+    generate_aggregated_report,
+    identify_problematic_amino_acids,
+    update_tiers,
+    download_example_data,
+)
 
 def define_parser():
     parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)

pvactools/tools/pvacfuse/__init__.py

@@ -1,18 +0,0 @@
-__all__ = [
-    'run',
-    'binding_filter',
-    'coverage_filter',
-    'download_example_data',
-    'top_score_filter',
-    'mark_genes_of_interest',
-    'net_chop',
-    'netmhc_stab',
-    'calculate_reference_proteome_similarity',
-    'generate_protein_fasta',
-    "generate_aggregated_report",
-    'identify_problematic_amino_acids',
-    'update_tiers',
-    'aggregate_report_filter',
-]
-
-from . import *

pvactools/tools/pvacfuse/coverage_filter.py

@@ -5,7 +5,6 @@
 import csv
 
 from pvactools.lib.filter import Filter, FilterCriterion
-from pvactools.lib.run_utils import *
 
 def define_parser():
     parser = argparse.ArgumentParser(

pvactools/tools/pvacfuse/main.py

@@ -1,7 +1,23 @@
 import argparse
 import sys
 import os
-from pvactools.tools.pvacfuse import *
+
+from pvactools.tools.pvacfuse import (
+    run,
+    binding_filter,
+    coverage_filter,
+    top_score_filter,
+    aggregate_report_filter,
+    net_chop,
+    netmhc_stab,
+    calculate_reference_proteome_similarity,
+    generate_protein_fasta,
+    generate_aggregated_report,
+    identify_problematic_amino_acids,
+    mark_genes_of_interest,
+    update_tiers,
+    download_example_data,
+)
 
 def define_parser():
     parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)

pvactools/tools/pvacseq/__init__.py

@@ -1,22 +0,0 @@
-__all__ = [
-    'run',
-    'binding_filter',
-    'download_example_data',
-    'coverage_filter',
-    'generate_protein_fasta',
-    "generate_aggregated_report",
-    'create_peptide_ordering_form',
-    'install_vep_plugin',
-    'top_score_filter',
-    'mark_genes_of_interest',
-    'add_ml_predictions',
-    'net_chop',
-    'netmhc_stab',
-    'calculate_reference_proteome_similarity',
-    'transcript_filter',
-    'identify_problematic_amino_acids',
-    'update_tiers',
-    'aggregate_report_filter',
-]
-
-from . import *

pvactools/tools/pvacseq/main.py

@@ -2,7 +2,28 @@
 import sys
 from subprocess import call
 import os
-from pvactools.tools.pvacseq import *
+
+from pvactools.tools.pvacseq import (
+    run,
+    binding_filter,
+    coverage_filter,
+    transcript_filter,
+    top_score_filter,
+    aggregate_report_filter,
+    net_chop,
+    netmhc_stab,
+    calculate_reference_proteome_similarity,
+    generate_protein_fasta,
+    create_peptide_ordering_form,
+    generate_aggregated_report,
+    identify_problematic_amino_acids,
+    mark_genes_of_interest,
+    add_ml_predictions,
+    update_tiers,
+    download_example_data,
+    install_vep_plugin,
+)
+
 
 def define_parser():
     parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)

pvactools/tools/pvacsplice/__init__.py

@@ -1,19 +0,0 @@
-__all__ = [
-    'binding_filter',
-    'calculate_reference_proteome_similarity',
-    'coverage_filter',
-    'download_example_data',
-    'generate_aggregated_report',
-    'generate_protein_fasta',
-    'identify_problematic_amino_acids',
-    'mark_genes_of_interest',
-    'net_chop',
-    'netmhc_stab',
-    'run',
-    'top_score_filter',
-    'transcript_filter',
-    'update_tiers',
-    'aggregate_report_filter',
-]
-
-from . import *

pvactools/tools/pvacsplice/main.py

@@ -2,7 +2,24 @@
 import sys
 from subprocess import call
 import os
-from pvactools.tools.pvacsplice import *
+
+from pvactools.tools.pvacsplice import (
+    run,
+    binding_filter,
+    coverage_filter,
+    transcript_filter,
+    top_score_filter,
+    aggregate_report_filter,
+    net_chop,
+    netmhc_stab,
+    calculate_reference_proteome_similarity,
+    generate_protein_fasta,
+    generate_aggregated_report,
+    identify_problematic_amino_acids,
+    mark_genes_of_interest,
+    update_tiers,
+    download_example_data,
+)
 
 def define_parser():
     parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)

pvactools/tools/pvacvector/__init__.py

@@ -1,7 +0,0 @@
-__all__ = [
-    'run',
-    'visualize',
-    'download_example_data',
-]
-
-from . import *

pvactools/tools/pvacvector/main.py

@@ -1,6 +1,7 @@
 import argparse
 import sys
-from pvactools.tools.pvacvector import *
+
+from pvactools.tools.pvacvector import run, visualize, download_example_data
 
 def define_parser():
     parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)

pvactools/tools/pvacvector/run.py

@@ -4,25 +4,19 @@
 
 import shutil
 import sys
-import argparse
 import os
-import pandas
 import networkx as nx
 import random
 from Bio import SeqIO
 from Bio.Seq import Seq
 from Bio.SeqRecord import SeqRecord
 import itertools
-import json
-import platform
-import shutil
+import csv
 
 from pvactools.lib.optimal_peptide import OptimalPeptide
 from pvactools.lib.vector_visualization import VectorVisualization
 from pvactools.lib.run_argument_parser import PvacvectorRunArgumentParser
 from pvactools.lib.pvacvector_run_pipeline import PvacvectorRunPipeline
-from pvactools.lib.prediction_class import NetMHCIIVersion
-from pvactools.lib.prediction_class_utils import *
 from pvactools.lib.run_utils import change_permissions_recursive
 
 def define_parser():

pvactools/tools/pvacview/__init__.py

@@ -1,5 +0,0 @@
-__all__ = [
-    'run',
-]
-
-from . import *

pvactools/tools/pvacview/main.py

@@ -2,7 +2,8 @@
 import sys
 from subprocess import call
 import os
-from pvactools.tools.pvacview import *
+
+from pvactools.tools.pvacview import run
 
 def define_parser():
     parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)

tests/test_allele_specific_cutoffs.py

@@ -6,7 +6,7 @@
 from subprocess import PIPE
 from subprocess import run as subprocess_run
 
-from pvactools.tools import *
+from pvactools.tools import allele_specific_cutoffs
 from tests.utils import *
 
 class PvacseqAlleleSpecificCutoffsTests(unittest.TestCase):

tests/test_fasta_to_kmers.py

@@ -6,7 +6,7 @@
 import py_compile
 import pandas as pd
 
-from pvactools.lib.fasta_to_kmers import *
+from pvactools.lib.fasta_to_kmers import JunctionFastaToKmers, FusionFastaToKmers, VariantFastaToKmers
 from tests.utils import *
 
 #python -m unittest tests/test_pvacsplice_filter_regtools_results.py

tests/test_pvacbind.py

@@ -3,25 +3,19 @@
 import os
 import re
 import sys
-import tempfile
 import py_compile
 from subprocess import PIPE
 from subprocess import run as subprocess_run
 from filecmp import cmp
-import yaml
-import datetime
 from mock import patch
-from urllib.request import urlopen
-from shutil import copyfileobj
-from tempfile import NamedTemporaryFile
 import argparse
+import logging
+from testfixtures import LogCapture, StringComparison as S
 
 from pvactools.lib.fasta_to_kmers import SequenceFastaToKmers
 import pvactools.tools.pvacbind.main as pvacbind_main
-from pvactools.tools.pvacbind import *
+from pvactools.tools.pvacbind import run
 from tests.utils import *
-import logging
-from testfixtures import LogCapture, StringComparison as S
 
 def test_data_directory():
     return os.path.join(

tests/test_pvacbind_aggregate_report_filter.py

@@ -7,7 +7,7 @@
 from subprocess import run as subprocess_run
 from tempfile import NamedTemporaryFile
 
-from pvactools.tools.pvacbind import *
+from pvactools.tools.pvacbind import aggregate_report_filter
 from tests.utils import *
 
 def test_data_directory():