From aa1595a97837835ecaa9d07f44830e0c52a6cc08 Mon Sep 17 00:00:00 2001 From: Ulthran Date: Tue, 14 May 2024 16:32:32 -0400 Subject: [PATCH] Update test refs to lib --- src/dnabc/main.py | 2 -- src/dnabc/seqfile.py | 3 --- tests/test_assigner.py | 2 +- tests/test_main.py | 2 +- tests/test_sample.py | 2 +- tests/test_seqfile.py | 4 ++-- tests/test_writer.py | 2 +- 7 files changed, 6 insertions(+), 11 deletions(-) diff --git a/src/dnabc/main.py b/src/dnabc/main.py index 1702097..7fd8dde 100644 --- a/src/dnabc/main.py +++ b/src/dnabc/main.py @@ -1,7 +1,5 @@ import argparse -from cmath import log import gzip -import json import os from .writer import PairedFastqWriter diff --git a/src/dnabc/seqfile.py b/src/dnabc/seqfile.py index 39d812b..2c2cfac 100644 --- a/src/dnabc/seqfile.py +++ b/src/dnabc/seqfile.py @@ -1,6 +1,3 @@ -import itertools - - # Factory function for SequenceFile classes def SequenceFile(fwd, rev, fwd_idx=None, rev_idx=None): if fwd_idx and rev_idx: diff --git a/tests/test_assigner.py b/tests/test_assigner.py index 38cffce..f91159a 100644 --- a/tests/test_assigner.py +++ b/tests/test_assigner.py @@ -1,7 +1,7 @@ from collections import namedtuple, Counter import unittest -from dnabclib.assigner import ( +from src.dnabc.assigner import ( BarcodeAssigner, deambiguate, reverse_complement, diff --git a/tests/test_main.py b/tests/test_main.py index e1f02e2..070053e 100644 --- a/tests/test_main.py +++ b/tests/test_main.py @@ -4,7 +4,7 @@ import tempfile import unittest -from dnabclib.main import main +from src.dnabc.main import main class FastqDemultiplexTests(unittest.TestCase): diff --git a/tests/test_sample.py b/tests/test_sample.py index 69a5e6f..216e186 100644 --- a/tests/test_sample.py +++ b/tests/test_sample.py @@ -1,6 +1,6 @@ import unittest -from dnabclib.sample import ( +from src.dnabc.sample import ( SampleBarcode, load_sample_barcodes, check_sample_names, diff --git a/tests/test_seqfile.py b/tests/test_seqfile.py index 73b20c4..be95c09 100644 --- a/tests/test_seqfile.py +++ b/tests/test_seqfile.py @@ -3,12 +3,12 @@ import os.path import unittest -from dnabclib.seqfile import ( +from src.dnabc.seqfile import ( IndexFastqSequenceFile, NoIndexFastqSequenceFile, parse_fastq, ) -from dnabclib.assigner import BarcodeAssigner +from src.dnabc.assigner import BarcodeAssigner class MockWriter(object): diff --git a/tests/test_writer.py b/tests/test_writer.py index 00df240..50d57c4 100644 --- a/tests/test_writer.py +++ b/tests/test_writer.py @@ -4,7 +4,7 @@ import tempfile import unittest -from dnabclib.writer import FastaWriter, FastqWriter, PairedFastqWriter +from src.dnabc.writer import FastaWriter, FastqWriter, PairedFastqWriter MockFastaRead = namedtuple("Read", "desc seq") MockFastqRead = namedtuple("Read", "desc seq qual")