diff --git a/unit-tests/Data4Test.py b/unit-tests/Data4Test.py index 3ab4de944f609d978406d9de9e209ecfbda191d9..20ebf2a53283b50477383838de5effdfdad3e77e 100755 --- a/unit-tests/Data4Test.py +++ b/unit-tests/Data4Test.py @@ -1,7 +1,7 @@ import os -from _modules.IData_handling import genomeFastaRecovery,totReads -from _modules.main_utils import inputRawDataArgs,functionalParms,InputDerivedDataArgs,technicalParms +from phagetermvirome.IData_handling import genomeFastaRecovery,totReads +from phagetermvirome.main_utils import inputRawDataArgs,functionalParms,InputDerivedDataArgs,technicalParms TEST_DIR_PATH = os.path.dirname(os.path.abspath(__file__)) TEST_DATA_PATH = os.path.join(TEST_DIR_PATH, "..", "test-data") diff --git a/unit-tests/test_functions_PhageTerm_for_multi.py b/unit-tests/test_functions_PhageTerm_for_multi.py index 7e84e1181ee9f542068cf86921298d32aaf641e0..bfcec8993907046887d54b63cb6d3eb6bc2427a7 100755 --- a/unit-tests/test_functions_PhageTerm_for_multi.py +++ b/unit-tests/test_functions_PhageTerm_for_multi.py @@ -6,7 +6,7 @@ import sys sys.path.append("..") -sys.path.append("../_modules") +sys.path.append("../phagetermvirome") import unittest import numpy as np @@ -14,9 +14,9 @@ import os import shutil from Data4Test import buildTestData, Data4Test -from _modules.functions_PhageTerm import readsCoverage -from _modules.readsCoverage_res import loadRCRes,RCRes,RCCheckpoint_handler -from _modules.debug_utils import ReadMappingInfoLogger +from phagetermvirome.functions_PhageTerm import readsCoverage +from phagetermvirome.readsCoverage_res import loadRCRes,RCRes,RCCheckpoint_handler +from phagetermvirome.debug_utils import ReadMappingInfoLogger @@ -71,7 +71,7 @@ class Test_functions_Phageterm (unittest.TestCase): # # # VL: start basic testing of sum_reads_coverage_for_seq for multimachine mode def test_basic_sum_readsCoverage_for_seq(self): - from _modules.seq_processing import sum_readsCoverage_for_seq + from phagetermvirome.seq_processing import sum_readsCoverage_for_seq d=Data4Test("data/G-janv_S2_R1_001.fastq.500","data/seq1_2_3.fasta", paired="data/G-janv_S2_R2_001.fastq.500", \ hostseq="", seed=20, edge=500, insert_max=1000, limit_coverage=11, virome=0) dir_cov_res=os.path.join(os.getcwd(),"data")