From 4abc61b8b6f789d40e69c5a6aa1272ef4c6c4067 Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Wed, 15 Jul 2026 21:55:15 -0500 Subject: [PATCH] General cleanup of import statements --- pvactools/lib/__init__.py | 31 ------------------- .../lib/identify_problematic_amino_acids.py | 1 - pvactools/lib/print_log.py | 3 -- pvactools/lib/run_pipeline.py | 4 +-- pvactools/tools/__init__.py | 11 ------- pvactools/tools/main.py | 11 ++++++- pvactools/tools/pvacbind/__init__.py | 15 --------- pvactools/tools/pvacbind/main.py | 15 ++++++++- pvactools/tools/pvacfuse/__init__.py | 18 ----------- pvactools/tools/pvacfuse/coverage_filter.py | 1 - pvactools/tools/pvacfuse/main.py | 18 ++++++++++- pvactools/tools/pvacseq/__init__.py | 22 ------------- pvactools/tools/pvacseq/main.py | 23 +++++++++++++- pvactools/tools/pvacsplice/__init__.py | 19 ------------ pvactools/tools/pvacsplice/main.py | 19 +++++++++++- pvactools/tools/pvacvector/__init__.py | 7 ----- pvactools/tools/pvacvector/main.py | 3 +- pvactools/tools/pvacvector/run.py | 8 +---- pvactools/tools/pvacview/__init__.py | 5 --- pvactools/tools/pvacview/main.py | 3 +- tests/test_allele_specific_cutoffs.py | 2 +- tests/test_fasta_to_kmers.py | 2 +- tests/test_pvacbind.py | 12 ++----- .../test_pvacbind_aggregate_report_filter.py | 2 +- tests/test_pvacbind_binding_filter.py | 2 +- ...calculate_reference_proteome_similarity.py | 2 +- tests/test_pvacbind_download_example_data.py | 2 +- ...est_pvacbind_generate_aggregated_report.py | 2 +- ...acbind_identify_problematic_amino_acids.py | 2 +- tests/test_pvacbind_net_chop.py | 2 +- tests/test_pvacbind_netmhc_stab.py | 2 +- tests/test_pvacbind_top_score_filter.py | 2 +- tests/test_pvacbind_update_tiers.py | 2 +- tests/test_pvacfuse.py | 2 +- .../test_pvacfuse_aggregate_report_filter.py | 2 +- tests/test_pvacfuse_binding_filter.py | 2 +- ...calculate_reference_proteome_similarity.py | 2 +- tests/test_pvacfuse_coverage_filter.py | 2 +- tests/test_pvacfuse_download_example_data.py | 2 +- ...est_pvacfuse_generate_aggregated_report.py | 2 +- ...acfuse_identify_problematic_amino_acids.py | 2 +- tests/test_pvacfuse_mark_genes_of_interest.py | 2 +- tests/test_pvacfuse_net_chop.py | 2 +- tests/test_pvacfuse_netmhc_stab.py | 2 +- tests/test_pvacfuse_top_score_filter.py | 2 +- tests/test_pvacfuse_update_tiers.py | 2 +- tests/test_pvacseq.py | 2 +- tests/test_pvacseq_add_ml_predictions.py | 2 +- tests/test_pvacseq_aggregate_report_filter.py | 2 +- tests/test_pvacseq_binding_filter.py | 2 +- ...calculate_reference_proteome_similarity.py | 2 +- tests/test_pvacseq_coverage_filter.py | 2 +- tests/test_pvacseq_download_example_data.py | 2 +- ...test_pvacseq_generate_aggregated_report.py | 2 +- ...vacseq_identify_problematic_amino_acids.py | 2 +- tests/test_pvacseq_install_vep_plugin.py | 2 +- tests/test_pvacseq_mark_genes_of_interest.py | 2 +- tests/test_pvacseq_net_chop.py | 2 +- tests/test_pvacseq_netmhc_stab.py | 2 +- tests/test_pvacseq_top_score_filter.py | 2 +- tests/test_pvacseq_transcript_filter.py | 2 +- tests/test_pvacseq_update_tiers.py | 2 +- tests/test_pvacsplice.py | 2 +- ...test_pvacsplice_aggregate_report_filter.py | 2 +- tests/test_pvacsplice_binding_filter.py | 2 +- ...calculate_reference_proteome_similarity.py | 2 +- tests/test_pvacsplice_coverage_filter.py | 2 +- .../test_pvacsplice_download_example_data.py | 2 +- ...t_pvacsplice_generate_aggregated_report.py | 2 +- ...splice_identify_problematic_amino_acids.py | 2 +- .../test_pvacsplice_mark_genes_of_interest.py | 2 +- tests/test_pvacsplice_net_chop.py | 2 +- tests/test_pvacsplice_netmhc_stab.py | 2 +- tests/test_pvacsplice_top_score_filter.py | 2 +- tests/test_pvacsplice_transcript_filter.py | 2 +- tests/test_pvacsplice_update_tiers.py | 2 +- tests/test_pvacvector.py | 2 +- tests/test_pvacview.py | 4 +-- tests/test_valid_algorithms.py | 2 +- tests/test_valid_alleles.py | 2 +- tests/test_valid_netmhciipan_versions.py | 2 +- 81 files changed, 152 insertions(+), 219 deletions(-) diff --git a/pvactools/lib/__init__.py b/pvactools/lib/__init__.py index 6fa95598f..e69de29bb 100644 --- a/pvactools/lib/__init__.py +++ b/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 * diff --git a/pvactools/lib/identify_problematic_amino_acids.py b/pvactools/lib/identify_problematic_amino_acids.py index 36a9ec9ab..f5f9e8ff5 100644 --- a/pvactools/lib/identify_problematic_amino_acids.py +++ b/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 diff --git a/pvactools/lib/print_log.py b/pvactools/lib/print_log.py index c9bb46f8e..9dfd84bea 100644 --- a/pvactools/lib/print_log.py +++ b/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') diff --git a/pvactools/lib/run_pipeline.py b/pvactools/lib/run_pipeline.py index b250dc3ed..4d64c7824 100644 --- a/pvactools/lib/run_pipeline.py +++ b/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): diff --git a/pvactools/tools/__init__.py b/pvactools/tools/__init__.py index 3e77a6dfa..e69de29bb 100644 --- a/pvactools/tools/__init__.py +++ b/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 * diff --git a/pvactools/tools/main.py b/pvactools/tools/main.py index 0c0742c92..8efdcf9ca 100644 --- a/pvactools/tools/main.py +++ b/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) diff --git a/pvactools/tools/pvacbind/__init__.py b/pvactools/tools/pvacbind/__init__.py index 446193213..e69de29bb 100644 --- a/pvactools/tools/pvacbind/__init__.py +++ b/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 * diff --git a/pvactools/tools/pvacbind/main.py b/pvactools/tools/pvacbind/main.py index 5c6e3b47e..6b1b31b00 100644 --- a/pvactools/tools/pvacbind/main.py +++ b/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) diff --git a/pvactools/tools/pvacfuse/__init__.py b/pvactools/tools/pvacfuse/__init__.py index a2506c7ff..e69de29bb 100644 --- a/pvactools/tools/pvacfuse/__init__.py +++ b/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 * diff --git a/pvactools/tools/pvacfuse/coverage_filter.py b/pvactools/tools/pvacfuse/coverage_filter.py index 8ab65ceb0..9b0ce3a47 100644 --- a/pvactools/tools/pvacfuse/coverage_filter.py +++ b/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( diff --git a/pvactools/tools/pvacfuse/main.py b/pvactools/tools/pvacfuse/main.py index 34ecd7fca..69951d59f 100644 --- a/pvactools/tools/pvacfuse/main.py +++ b/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) diff --git a/pvactools/tools/pvacseq/__init__.py b/pvactools/tools/pvacseq/__init__.py index 22ef022fe..e69de29bb 100644 --- a/pvactools/tools/pvacseq/__init__.py +++ b/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 * diff --git a/pvactools/tools/pvacseq/main.py b/pvactools/tools/pvacseq/main.py index c47f814ee..8675c0f0c 100644 --- a/pvactools/tools/pvacseq/main.py +++ b/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) diff --git a/pvactools/tools/pvacsplice/__init__.py b/pvactools/tools/pvacsplice/__init__.py index f5ca4a838..e69de29bb 100644 --- a/pvactools/tools/pvacsplice/__init__.py +++ b/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 * diff --git a/pvactools/tools/pvacsplice/main.py b/pvactools/tools/pvacsplice/main.py index 59f013c17..9df54d386 100644 --- a/pvactools/tools/pvacsplice/main.py +++ b/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) diff --git a/pvactools/tools/pvacvector/__init__.py b/pvactools/tools/pvacvector/__init__.py index 39751f63b..e69de29bb 100644 --- a/pvactools/tools/pvacvector/__init__.py +++ b/pvactools/tools/pvacvector/__init__.py @@ -1,7 +0,0 @@ -__all__ = [ - 'run', - 'visualize', - 'download_example_data', -] - -from . import * diff --git a/pvactools/tools/pvacvector/main.py b/pvactools/tools/pvacvector/main.py index 4dde3629f..32c7c4fa5 100644 --- a/pvactools/tools/pvacvector/main.py +++ b/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) diff --git a/pvactools/tools/pvacvector/run.py b/pvactools/tools/pvacvector/run.py index 001f80281..f01467165 100644 --- a/pvactools/tools/pvacvector/run.py +++ b/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(): diff --git a/pvactools/tools/pvacview/__init__.py b/pvactools/tools/pvacview/__init__.py index 6a7ed93a9..e69de29bb 100644 --- a/pvactools/tools/pvacview/__init__.py +++ b/pvactools/tools/pvacview/__init__.py @@ -1,5 +0,0 @@ -__all__ = [ - 'run', -] - -from . import * diff --git a/pvactools/tools/pvacview/main.py b/pvactools/tools/pvacview/main.py index 5406ace17..cb74c5512 100644 --- a/pvactools/tools/pvacview/main.py +++ b/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) diff --git a/tests/test_allele_specific_cutoffs.py b/tests/test_allele_specific_cutoffs.py index 41545a47d..e84670254 100644 --- a/tests/test_allele_specific_cutoffs.py +++ b/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): diff --git a/tests/test_fasta_to_kmers.py b/tests/test_fasta_to_kmers.py index 2552ea9a1..a4b2a53c5 100644 --- a/tests/test_fasta_to_kmers.py +++ b/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 diff --git a/tests/test_pvacbind.py b/tests/test_pvacbind.py index fdf43bf27..918bf4bff 100644 --- a/tests/test_pvacbind.py +++ b/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( diff --git a/tests/test_pvacbind_aggregate_report_filter.py b/tests/test_pvacbind_aggregate_report_filter.py index dacfb65f3..33996bec9 100644 --- a/tests/test_pvacbind_aggregate_report_filter.py +++ b/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(): diff --git a/tests/test_pvacbind_binding_filter.py b/tests/test_pvacbind_binding_filter.py index 86b6d08be..efde9a51f 100644 --- a/tests/test_pvacbind_binding_filter.py +++ b/tests/test_pvacbind_binding_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 binding_filter from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacbind_calculate_reference_proteome_similarity.py b/tests/test_pvacbind_calculate_reference_proteome_similarity.py index b184024cd..51f8892e9 100644 --- a/tests/test_pvacbind_calculate_reference_proteome_similarity.py +++ b/tests/test_pvacbind_calculate_reference_proteome_similarity.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 calculate_reference_proteome_similarity from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacbind_download_example_data.py b/tests/test_pvacbind_download_example_data.py index 385efe016..c927427c1 100644 --- a/tests/test_pvacbind_download_example_data.py +++ b/tests/test_pvacbind_download_example_data.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import TemporaryDirectory -from pvactools.tools.pvacbind import * +from pvactools.tools.pvacbind import download_example_data from tests.utils import * class PvacbindDownloadExampleDataTests(unittest.TestCase): diff --git a/tests/test_pvacbind_generate_aggregated_report.py b/tests/test_pvacbind_generate_aggregated_report.py index 98c810a9b..da67f8dec 100644 --- a/tests/test_pvacbind_generate_aggregated_report.py +++ b/tests/test_pvacbind_generate_aggregated_report.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 generate_aggregated_report from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacbind_identify_problematic_amino_acids.py b/tests/test_pvacbind_identify_problematic_amino_acids.py index 71d1b9b0c..8897e802b 100644 --- a/tests/test_pvacbind_identify_problematic_amino_acids.py +++ b/tests/test_pvacbind_identify_problematic_amino_acids.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 identify_problematic_amino_acids from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacbind_net_chop.py b/tests/test_pvacbind_net_chop.py index c90663641..e6e20dea7 100644 --- a/tests/test_pvacbind_net_chop.py +++ b/tests/test_pvacbind_net_chop.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 net_chop from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacbind_netmhc_stab.py b/tests/test_pvacbind_netmhc_stab.py index d10d86545..bd8bb9762 100644 --- a/tests/test_pvacbind_netmhc_stab.py +++ b/tests/test_pvacbind_netmhc_stab.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 netmhc_stab from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacbind_top_score_filter.py b/tests/test_pvacbind_top_score_filter.py index 95f768340..8723f1a0d 100644 --- a/tests/test_pvacbind_top_score_filter.py +++ b/tests/test_pvacbind_top_score_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 top_score_filter from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacbind_update_tiers.py b/tests/test_pvacbind_update_tiers.py index 0395f65e1..7656022d6 100644 --- a/tests/test_pvacbind_update_tiers.py +++ b/tests/test_pvacbind_update_tiers.py @@ -6,7 +6,7 @@ from subprocess import PIPE from subprocess import run as subprocess_run -from pvactools.tools.pvacbind import * +from pvactools.tools.pvacbind import update_tiers from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacfuse.py b/tests/test_pvacfuse.py index 93daac109..dcec0bd5e 100644 --- a/tests/test_pvacfuse.py +++ b/tests/test_pvacfuse.py @@ -16,7 +16,7 @@ from shutil import copyfileobj from tempfile import NamedTemporaryFile -from pvactools.tools.pvacfuse import * +from pvactools.tools.pvacfuse import run import pvactools.tools.pvacfuse.main as pvacfuse_main from tests.utils import * diff --git a/tests/test_pvacfuse_aggregate_report_filter.py b/tests/test_pvacfuse_aggregate_report_filter.py index 9464f10ae..ad87ef891 100644 --- a/tests/test_pvacfuse_aggregate_report_filter.py +++ b/tests/test_pvacfuse_aggregate_report_filter.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacfuse import * +from pvactools.tools.pvacfuse import aggregate_report_filter from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacfuse_binding_filter.py b/tests/test_pvacfuse_binding_filter.py index 57d2a4fbf..3bb98f417 100644 --- a/tests/test_pvacfuse_binding_filter.py +++ b/tests/test_pvacfuse_binding_filter.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacfuse import * +from pvactools.tools.pvacfuse import binding_filter from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacfuse_calculate_reference_proteome_similarity.py b/tests/test_pvacfuse_calculate_reference_proteome_similarity.py index 485c320db..236f3fd6c 100644 --- a/tests/test_pvacfuse_calculate_reference_proteome_similarity.py +++ b/tests/test_pvacfuse_calculate_reference_proteome_similarity.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacfuse import * +from pvactools.tools.pvacfuse import calculate_reference_proteome_similarity from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacfuse_coverage_filter.py b/tests/test_pvacfuse_coverage_filter.py index 8d5685af0..5cf3a224d 100644 --- a/tests/test_pvacfuse_coverage_filter.py +++ b/tests/test_pvacfuse_coverage_filter.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacfuse import * +from pvactools.tools.pvacfuse import coverage_filter from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacfuse_download_example_data.py b/tests/test_pvacfuse_download_example_data.py index d5f490d9d..950e01765 100644 --- a/tests/test_pvacfuse_download_example_data.py +++ b/tests/test_pvacfuse_download_example_data.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import TemporaryDirectory -from pvactools.tools.pvacfuse import * +from pvactools.tools.pvacfuse import download_example_data from tests.utils import * class PvacfuseDownloadExampleDataTests(unittest.TestCase): diff --git a/tests/test_pvacfuse_generate_aggregated_report.py b/tests/test_pvacfuse_generate_aggregated_report.py index 5d0d7e320..b5c0cb8e3 100644 --- a/tests/test_pvacfuse_generate_aggregated_report.py +++ b/tests/test_pvacfuse_generate_aggregated_report.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacfuse import * +from pvactools.tools.pvacfuse import generate_aggregated_report from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacfuse_identify_problematic_amino_acids.py b/tests/test_pvacfuse_identify_problematic_amino_acids.py index 123d3f15c..e2d0eb818 100644 --- a/tests/test_pvacfuse_identify_problematic_amino_acids.py +++ b/tests/test_pvacfuse_identify_problematic_amino_acids.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacfuse import * +from pvactools.tools.pvacfuse import identify_problematic_amino_acids from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacfuse_mark_genes_of_interest.py b/tests/test_pvacfuse_mark_genes_of_interest.py index 55e96a4bf..d935b090f 100644 --- a/tests/test_pvacfuse_mark_genes_of_interest.py +++ b/tests/test_pvacfuse_mark_genes_of_interest.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacfuse import * +from pvactools.tools.pvacfuse import mark_genes_of_interest from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacfuse_net_chop.py b/tests/test_pvacfuse_net_chop.py index 2e20bf319..b7c9bb378 100644 --- a/tests/test_pvacfuse_net_chop.py +++ b/tests/test_pvacfuse_net_chop.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacfuse import * +from pvactools.tools.pvacfuse import net_chop from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacfuse_netmhc_stab.py b/tests/test_pvacfuse_netmhc_stab.py index b621f68ed..d08c31f77 100644 --- a/tests/test_pvacfuse_netmhc_stab.py +++ b/tests/test_pvacfuse_netmhc_stab.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacfuse import * +from pvactools.tools.pvacfuse import netmhc_stab from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacfuse_top_score_filter.py b/tests/test_pvacfuse_top_score_filter.py index ee1757a25..332df8156 100644 --- a/tests/test_pvacfuse_top_score_filter.py +++ b/tests/test_pvacfuse_top_score_filter.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacfuse import * +from pvactools.tools.pvacfuse import top_score_filter from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacfuse_update_tiers.py b/tests/test_pvacfuse_update_tiers.py index 88942e42b..e9b5b6463 100644 --- a/tests/test_pvacfuse_update_tiers.py +++ b/tests/test_pvacfuse_update_tiers.py @@ -6,7 +6,7 @@ from subprocess import PIPE from subprocess import run as subprocess_run -from pvactools.tools.pvacfuse import * +from pvactools.tools.pvacfuse import update_tiers from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacseq.py b/tests/test_pvacseq.py index 76941138d..24ac148d6 100644 --- a/tests/test_pvacseq.py +++ b/tests/test_pvacseq.py @@ -16,7 +16,7 @@ from shutil import copyfileobj, copyfile from tempfile import NamedTemporaryFile -from pvactools.tools.pvacseq import * +from pvactools.tools.pvacseq import run import pvactools.tools.pvacseq.main as pvacseq_main from tests.utils import * diff --git a/tests/test_pvacseq_add_ml_predictions.py b/tests/test_pvacseq_add_ml_predictions.py index 4754cd34a..06c38d3e3 100644 --- a/tests/test_pvacseq_add_ml_predictions.py +++ b/tests/test_pvacseq_add_ml_predictions.py @@ -7,7 +7,7 @@ from subprocess import PIPE from subprocess import run as subprocess_run -from pvactools.tools.pvacseq import * +from pvactools.tools.pvacseq import add_ml_predictions from tests.utils import * diff --git a/tests/test_pvacseq_aggregate_report_filter.py b/tests/test_pvacseq_aggregate_report_filter.py index b73683cf7..31b46af79 100644 --- a/tests/test_pvacseq_aggregate_report_filter.py +++ b/tests/test_pvacseq_aggregate_report_filter.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacseq import * +from pvactools.tools.pvacseq import aggregate_report_filter from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacseq_binding_filter.py b/tests/test_pvacseq_binding_filter.py index 8615efb96..8c55c9dfe 100644 --- a/tests/test_pvacseq_binding_filter.py +++ b/tests/test_pvacseq_binding_filter.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacseq import * +from pvactools.tools.pvacseq import binding_filter from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacseq_calculate_reference_proteome_similarity.py b/tests/test_pvacseq_calculate_reference_proteome_similarity.py index d7978bbf9..671a5f1c0 100644 --- a/tests/test_pvacseq_calculate_reference_proteome_similarity.py +++ b/tests/test_pvacseq_calculate_reference_proteome_similarity.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacseq import * +from pvactools.tools.pvacseq import calculate_reference_proteome_similarity from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacseq_coverage_filter.py b/tests/test_pvacseq_coverage_filter.py index bcd3f45b4..41ea3be63 100644 --- a/tests/test_pvacseq_coverage_filter.py +++ b/tests/test_pvacseq_coverage_filter.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacseq import * +from pvactools.tools.pvacseq import coverage_filter from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacseq_download_example_data.py b/tests/test_pvacseq_download_example_data.py index 6037b7f03..884b5b3c3 100644 --- a/tests/test_pvacseq_download_example_data.py +++ b/tests/test_pvacseq_download_example_data.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import TemporaryDirectory -from pvactools.tools.pvacseq import * +from pvactools.tools.pvacseq import download_example_data from tests.utils import * class PvacseqDownloadExampleDataTests(unittest.TestCase): diff --git a/tests/test_pvacseq_generate_aggregated_report.py b/tests/test_pvacseq_generate_aggregated_report.py index a05706456..5d143c06c 100644 --- a/tests/test_pvacseq_generate_aggregated_report.py +++ b/tests/test_pvacseq_generate_aggregated_report.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacseq import * +from pvactools.tools.pvacseq import generate_aggregated_report from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacseq_identify_problematic_amino_acids.py b/tests/test_pvacseq_identify_problematic_amino_acids.py index c27c0600c..b6a501226 100644 --- a/tests/test_pvacseq_identify_problematic_amino_acids.py +++ b/tests/test_pvacseq_identify_problematic_amino_acids.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacseq import * +from pvactools.tools.pvacseq import identify_problematic_amino_acids from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacseq_install_vep_plugin.py b/tests/test_pvacseq_install_vep_plugin.py index 6610e5df1..533f1289b 100644 --- a/tests/test_pvacseq_install_vep_plugin.py +++ b/tests/test_pvacseq_install_vep_plugin.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import TemporaryDirectory -from pvactools.tools.pvacseq import * +from pvactools.tools.pvacseq import install_vep_plugin from tests.utils import * class PvacseqInstallVepPluginTests(unittest.TestCase): diff --git a/tests/test_pvacseq_mark_genes_of_interest.py b/tests/test_pvacseq_mark_genes_of_interest.py index 76d2493a8..d754cb92d 100644 --- a/tests/test_pvacseq_mark_genes_of_interest.py +++ b/tests/test_pvacseq_mark_genes_of_interest.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacseq import * +from pvactools.tools.pvacseq import mark_genes_of_interest from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacseq_net_chop.py b/tests/test_pvacseq_net_chop.py index ff56b634c..9e22e83ea 100644 --- a/tests/test_pvacseq_net_chop.py +++ b/tests/test_pvacseq_net_chop.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacseq import * +from pvactools.tools.pvacseq import net_chop from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacseq_netmhc_stab.py b/tests/test_pvacseq_netmhc_stab.py index bfc1e59a8..bff055b93 100644 --- a/tests/test_pvacseq_netmhc_stab.py +++ b/tests/test_pvacseq_netmhc_stab.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacseq import * +from pvactools.tools.pvacseq import netmhc_stab from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacseq_top_score_filter.py b/tests/test_pvacseq_top_score_filter.py index a2b00f9a7..b39389396 100644 --- a/tests/test_pvacseq_top_score_filter.py +++ b/tests/test_pvacseq_top_score_filter.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacseq import * +from pvactools.tools.pvacseq import top_score_filter from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacseq_transcript_filter.py b/tests/test_pvacseq_transcript_filter.py index 0c9b99a83..851d155d3 100644 --- a/tests/test_pvacseq_transcript_filter.py +++ b/tests/test_pvacseq_transcript_filter.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacseq import * +from pvactools.tools.pvacseq import transcript_filter from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacseq_update_tiers.py b/tests/test_pvacseq_update_tiers.py index f155e011a..2fe38f713 100644 --- a/tests/test_pvacseq_update_tiers.py +++ b/tests/test_pvacseq_update_tiers.py @@ -6,7 +6,7 @@ from subprocess import PIPE from subprocess import run as subprocess_run -from pvactools.tools.pvacseq import * +from pvactools.tools.pvacseq import update_tiers from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacsplice.py b/tests/test_pvacsplice.py index e701b0842..8a49d5d39 100644 --- a/tests/test_pvacsplice.py +++ b/tests/test_pvacsplice.py @@ -16,7 +16,7 @@ from shutil import copyfileobj from tempfile import NamedTemporaryFile -from pvactools.tools.pvacsplice import * +from pvactools.tools.pvacsplice import run import pvactools.tools.pvacsplice.main as pvacsplice_main from tests.utils import * diff --git a/tests/test_pvacsplice_aggregate_report_filter.py b/tests/test_pvacsplice_aggregate_report_filter.py index 705719921..76341219f 100644 --- a/tests/test_pvacsplice_aggregate_report_filter.py +++ b/tests/test_pvacsplice_aggregate_report_filter.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacsplice import * +from pvactools.tools.pvacsplice import aggregate_report_filter from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacsplice_binding_filter.py b/tests/test_pvacsplice_binding_filter.py index 884483258..f879847d9 100644 --- a/tests/test_pvacsplice_binding_filter.py +++ b/tests/test_pvacsplice_binding_filter.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacsplice import * +from pvactools.tools.pvacsplice import binding_filter from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacsplice_calculate_reference_proteome_similarity.py b/tests/test_pvacsplice_calculate_reference_proteome_similarity.py index c7c1bbf40..519f39f39 100644 --- a/tests/test_pvacsplice_calculate_reference_proteome_similarity.py +++ b/tests/test_pvacsplice_calculate_reference_proteome_similarity.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacsplice import * +from pvactools.tools.pvacsplice import calculate_reference_proteome_similarity from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacsplice_coverage_filter.py b/tests/test_pvacsplice_coverage_filter.py index dc82295ae..8a8f2890a 100644 --- a/tests/test_pvacsplice_coverage_filter.py +++ b/tests/test_pvacsplice_coverage_filter.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacsplice import * +from pvactools.tools.pvacsplice import coverage_filter from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacsplice_download_example_data.py b/tests/test_pvacsplice_download_example_data.py index 64e3363ac..c5b9952ab 100644 --- a/tests/test_pvacsplice_download_example_data.py +++ b/tests/test_pvacsplice_download_example_data.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import TemporaryDirectory -from pvactools.tools.pvacsplice import * +from pvactools.tools.pvacsplice import download_example_data from tests.utils import * class PvacspliceDownloadExampleDataTests(unittest.TestCase): diff --git a/tests/test_pvacsplice_generate_aggregated_report.py b/tests/test_pvacsplice_generate_aggregated_report.py index a3fa04ca0..b5203e1ac 100644 --- a/tests/test_pvacsplice_generate_aggregated_report.py +++ b/tests/test_pvacsplice_generate_aggregated_report.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacsplice import * +from pvactools.tools.pvacsplice import generate_aggregated_report from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacsplice_identify_problematic_amino_acids.py b/tests/test_pvacsplice_identify_problematic_amino_acids.py index 93ff8339c..3d85db418 100644 --- a/tests/test_pvacsplice_identify_problematic_amino_acids.py +++ b/tests/test_pvacsplice_identify_problematic_amino_acids.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacsplice import * +from pvactools.tools.pvacsplice import identify_problematic_amino_acids from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacsplice_mark_genes_of_interest.py b/tests/test_pvacsplice_mark_genes_of_interest.py index 6fccde63f..54443e09d 100644 --- a/tests/test_pvacsplice_mark_genes_of_interest.py +++ b/tests/test_pvacsplice_mark_genes_of_interest.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacsplice import * +from pvactools.tools.pvacsplice import mark_genes_of_interest from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacsplice_net_chop.py b/tests/test_pvacsplice_net_chop.py index 6ae236abc..62db3e977 100644 --- a/tests/test_pvacsplice_net_chop.py +++ b/tests/test_pvacsplice_net_chop.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacsplice import * +from pvactools.tools.pvacsplice import net_chop from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacsplice_netmhc_stab.py b/tests/test_pvacsplice_netmhc_stab.py index 87eb32ad7..e2c379bcd 100644 --- a/tests/test_pvacsplice_netmhc_stab.py +++ b/tests/test_pvacsplice_netmhc_stab.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacsplice import * +from pvactools.tools.pvacsplice import netmhc_stab from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacsplice_top_score_filter.py b/tests/test_pvacsplice_top_score_filter.py index 0406cd03b..3d9ff1b20 100644 --- a/tests/test_pvacsplice_top_score_filter.py +++ b/tests/test_pvacsplice_top_score_filter.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacsplice import * +from pvactools.tools.pvacsplice import top_score_filter from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacsplice_transcript_filter.py b/tests/test_pvacsplice_transcript_filter.py index 0bfaa659f..4b1b2768a 100644 --- a/tests/test_pvacsplice_transcript_filter.py +++ b/tests/test_pvacsplice_transcript_filter.py @@ -7,7 +7,7 @@ from subprocess import run as subprocess_run from tempfile import NamedTemporaryFile -from pvactools.tools.pvacsplice import * +from pvactools.tools.pvacsplice import transcript_filter from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacsplice_update_tiers.py b/tests/test_pvacsplice_update_tiers.py index 6f5ee07c3..0f5667a9b 100644 --- a/tests/test_pvacsplice_update_tiers.py +++ b/tests/test_pvacsplice_update_tiers.py @@ -6,7 +6,7 @@ from subprocess import PIPE from subprocess import run as subprocess_run -from pvactools.tools.pvacsplice import * +from pvactools.tools.pvacsplice import update_tiers from tests.utils import * def test_data_directory(): diff --git a/tests/test_pvacvector.py b/tests/test_pvacvector.py index 36288328e..32d8ea8de 100644 --- a/tests/test_pvacvector.py +++ b/tests/test_pvacvector.py @@ -12,7 +12,7 @@ from mock import patch import argparse -from pvactools.tools.pvacvector import * +from pvactools.tools.pvacvector import run, visualize, download_example_data import pvactools.tools.pvacvector.main as pvacvector_main from tests.utils import * diff --git a/tests/test_pvacview.py b/tests/test_pvacview.py index 8078819cc..d7a4567e7 100644 --- a/tests/test_pvacview.py +++ b/tests/test_pvacview.py @@ -12,7 +12,7 @@ import socket import argparse -from pvactools.tools.pvacview import * +from pvactools.tools.pvacview import run import pvactools.tools.pvacview.main as pvacview_main from tests.utils import * @@ -46,7 +46,7 @@ def test_pvacview_commands(self): "run", '-h' ], shell=False, stdout=PIPE) - self.assertFalse(result.returncode, "Failed `pvacseq run -h`") + self.assertFalse(result.returncode, "Failed `pvacview run -h`") self.assertRegex(result.stdout.decode(), usage_search) def test_run_compiles(self): diff --git a/tests/test_valid_algorithms.py b/tests/test_valid_algorithms.py index d7134d1e4..ff5ecc69c 100644 --- a/tests/test_valid_algorithms.py +++ b/tests/test_valid_algorithms.py @@ -7,7 +7,7 @@ from subprocess import PIPE from subprocess import run as subprocess_run -from pvactools.tools import * +from pvactools.tools import valid_algorithms from tests.utils import * class ValidAlgorithmsTests(unittest.TestCase): diff --git a/tests/test_valid_alleles.py b/tests/test_valid_alleles.py index 803fc7ed7..f25ba48e0 100644 --- a/tests/test_valid_alleles.py +++ b/tests/test_valid_alleles.py @@ -7,7 +7,7 @@ from subprocess import PIPE from subprocess import run as subprocess_run -from pvactools.tools import * +from pvactools.tools import valid_alleles from tests.utils import * class ValidAllelesTests(unittest.TestCase): diff --git a/tests/test_valid_netmhciipan_versions.py b/tests/test_valid_netmhciipan_versions.py index 94c3f7e77..8e42ea0a9 100644 --- a/tests/test_valid_netmhciipan_versions.py +++ b/tests/test_valid_netmhciipan_versions.py @@ -6,7 +6,7 @@ from subprocess import PIPE from subprocess import run as subprocess_run -from pvactools.tools import * +from pvactools.tools import valid_netmhciipan_versions from tests.utils import * class PvacseqValidNetmhciipanVersionsTests(unittest.TestCase):