From c31f516982afde9bf381a213cc62749faf3365f9 Mon Sep 17 00:00:00 2001
From: uym2 <ceciliamaitouyen@gmail.com>
Date: Tue, 9 Jul 2024 14:39:07 -0400
Subject: [PATCH] modify laml_libs/preprocess/*.py so that they import libs
 from lamlinstead of cassiopeia

---
 laml_libs/preprocess/UMI_utils.py             | 4 ++--
 laml_libs/preprocess/cassiopeia_preprocess.py | 6 +++---
 laml_libs/preprocess/doublet_utils.py         | 4 ++--
 laml_libs/preprocess/setup_utilities.py       | 6 +++---
 laml_libs/preprocess/utilities.py             | 2 +-
 5 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/laml_libs/preprocess/UMI_utils.py b/laml_libs/preprocess/UMI_utils.py
index 05ffbd0..8a270ce 100755
--- a/laml_libs/preprocess/UMI_utils.py
+++ b/laml_libs/preprocess/UMI_utils.py
@@ -22,8 +22,8 @@
 from tqdm.auto import tqdm
 import warnings
 
-from cassiopeia.mixins import logger, PreprocessError, PreprocessWarning
-from cassiopeia.preprocess import constants
+from laml_libs.mixins import logger, PreprocessError, PreprocessWarning
+from laml_libs.preprocess import constants
 
 from .collapse_cython import (
     hq_mismatches_from_seed,
diff --git a/laml_libs/preprocess/cassiopeia_preprocess.py b/laml_libs/preprocess/cassiopeia_preprocess.py
index afb9b12..375df67 100755
--- a/laml_libs/preprocess/cassiopeia_preprocess.py
+++ b/laml_libs/preprocess/cassiopeia_preprocess.py
@@ -3,7 +3,7 @@
 
 This file stores the main entry point for Cassiopeia-preprocess, and makes
 heavy use of the high level functionality in
-cassiopeia.preprocess.pipeline. Here, we assume that the user
+laml_libs.preprocess.pipeline. Here, we assume that the user
 has already run CellRanger Count, or some equivalent, to obtain a BAM file that
 relates cell barcodes and UMIs to sequences.
 
@@ -16,8 +16,8 @@
 import pandas as pd
 from typing import Any, Dict
 
-from cassiopeia.mixins import logger, PreprocessError
-from cassiopeia.preprocess import pipeline, setup_utilities, utilities
+from laml_libs.mixins import logger, PreprocessError
+from laml_libs.preprocess import pipeline, setup_utilities, utilities
 
 STAGES = {
     "convert": pipeline.convert_fastqs_to_unmapped_bam,
diff --git a/laml_libs/preprocess/doublet_utils.py b/laml_libs/preprocess/doublet_utils.py
index 1d73520..fabfdce 100644
--- a/laml_libs/preprocess/doublet_utils.py
+++ b/laml_libs/preprocess/doublet_utils.py
@@ -7,8 +7,8 @@
 
 import pandas as pd
 
-from cassiopeia.mixins import logger
-from cassiopeia.preprocess import utilities
+from laml_libs.mixins import logger
+from laml_libs.preprocess import utilities
 
 
 @utilities.log_molecule_table
diff --git a/laml_libs/preprocess/setup_utilities.py b/laml_libs/preprocess/setup_utilities.py
index df84d10..28b1f1a 100755
--- a/laml_libs/preprocess/setup_utilities.py
+++ b/laml_libs/preprocess/setup_utilities.py
@@ -1,7 +1,7 @@
 """"
 A file that stores general functionality for setting up a Cassiopeia
 preprocessing instance. This file supports the command line interface entrypoint
-in cassiopeia_preprocess.py.
+in laml_libs_preprocess.py.
 """
 import os
 
@@ -10,8 +10,8 @@
 import logging
 from typing import Any, Dict
 
-from cassiopeia.mixins import logger, UnspecifiedConfigParameterError
-from cassiopeia.preprocess import constants
+from laml_libs.mixins import logger, UnspecifiedConfigParameterError
+from laml_libs.preprocess import constants
 
 
 def setup(output_directory_location: str, verbose: bool) -> None:
diff --git a/laml_libs/preprocess/utilities.py b/laml_libs/preprocess/utilities.py
index 9517e08..418996f 100755
--- a/laml_libs/preprocess/utilities.py
+++ b/laml_libs/preprocess/utilities.py
@@ -18,7 +18,7 @@
 import re
 from tqdm.auto import tqdm
 
-from cassiopeia.mixins import is_ambiguous_state, logger, PreprocessWarning
+from laml_libs.mixins import is_ambiguous_state, logger, PreprocessWarning
 
 
 def log_molecule_table(wrapped: Callable):