levseq 1.2.6__tar.gz → 1.2.7__tar.gz

{levseq-1.2.6/levseq.egg-info → levseq-1.2.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: levseq
-Version: 1.2.6
+Version: 1.2.7
 Home-page: https://github.com/fhalab/levseq/
 Author: Yueming Long, Emreay Gursoy, Ariane Mora, Francesca-Zhoufan Li
 Author-email: ylong@caltech.edu
@@ -54,7 +54,7 @@ Figure 1: Overview of the LevSeq variant sequencing workflow using Nanopore tech
 
 
 - Data to reproduce the results and to test are available on zenodo [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13694463.svg)](https://doi.org/10.5281/zenodo.13694463)
-- A dockerized website and database for labs to locally host and visualize their data: website is available [here](https://github.com/ArianeMora/LevSeq_vis/) and code to host locally at: https://github.com/fhalab/LevSeq_VDB/
+- A dockerized website and database for labs to locally host and visualize their data: website is available [here](https://levseqdb.streamlit.app/) and code to host locally [here](https://github.com/fhalab/LevSeq_db)
 
 ## Setup
 
@@ -172,3 +172,7 @@ For more details or trouble shooting please look at our [computational_protocols
 #### Citing
 
 If you have found LevSeq useful, please cite out [paper](https://doi.org/10.1101/2024.09.04.611255).
+
+#### Contact
+
+Leave a feature request in the issues or reach us via [email](mailto:levseqdb@gmail.com). 

{levseq-1.2.6 → levseq-1.2.7}/README.md

@@ -7,7 +7,7 @@ Figure 1: Overview of the LevSeq variant sequencing workflow using Nanopore tech
 
 
 - Data to reproduce the results and to test are available on zenodo [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13694463.svg)](https://doi.org/10.5281/zenodo.13694463)
-- A dockerized website and database for labs to locally host and visualize their data: website is available [here](https://github.com/ArianeMora/LevSeq_vis/) and code to host locally at: https://github.com/fhalab/LevSeq_VDB/
+- A dockerized website and database for labs to locally host and visualize their data: website is available [here](https://levseqdb.streamlit.app/) and code to host locally [here](https://github.com/fhalab/LevSeq_db)
 
 ## Setup
 
@@ -125,3 +125,7 @@ For more details or trouble shooting please look at our [computational_protocols
 #### Citing
 
 If you have found LevSeq useful, please cite out [paper](https://doi.org/10.1101/2024.09.04.611255).
+
+#### Contact
+
+Leave a feature request in the issues or reach us via [email](mailto:levseqdb@gmail.com). 

{levseq-1.2.6 → levseq-1.2.7}/levseq/__init__.py

@@ -18,7 +18,7 @@
 __title__ = 'levseq'
 __description__ = 'LevSeq nanopore sequencing'
 __url__ = 'https://github.com/fhalab/levseq/'
-__version__ = '1.2.6'
+__version__ = '1.2.7'
 __author__ = 'Yueming Long, Emreay Gursoy, Ariane Mora, Francesca-Zhoufan Li'
 __author_email__ = 'ylong@caltech.edu'
 __license__ = 'GPL3'

{levseq-1.2.6 → levseq-1.2.7}/levseq/run_levseq.py

@@ -275,11 +275,11 @@ def create_df_v(variants_df):
     )
     # Fill in 'Deletion' in 'aa_variant' column
     df_variants_.loc[
-        df_variants_["nc_variant"] == "Deletion", "aa_variant"
-    ] = "Deletion"
+        df_variants_["nc_variant"] == "#DEL#", "aa_variant"
+    ] = "#DEL#"
     df_variants_.loc[
-        df_variants_["nc_variant"] == "Insertion", "aa_variant"
-    ] = "Insertion"
+        df_variants_["nc_variant"] == "#INS#", "aa_variant"
+    ] = "#INS#"
 
     # Compare aa_variant with translated refseq and generate Substitutions column
     df_variants_["Substitutions"] = df_variants_.apply(get_mutations, axis=1)
@@ -291,7 +291,7 @@ def create_df_v(variants_df):
     # Fill in Deletion into Substitutions Column, keep #N.A.# unchanged
     for i in df_variants_.index:
         if df_variants_["nc_variant"].iloc[i] == "Deletion":
-            df_variants_.Substitutions.iat[i] = df_variants_.Substitutions.iat[i].replace("", "-")
+            df_variants_.Substitutions.iat[i] = df_variants_.Substitutions.iat[i].replace("", "#DEL#")
         elif df_variants_["nc_variant"].iloc[i] == "#N.A.#":
             df_variants_.Substitutions.iat[i] = "#N.A.#"
 
@@ -363,9 +363,9 @@ def create_nc_variant(variant, refseq):
     elif variant == "#PARENT#":
         return refseq
     elif "DEL" in variant:
-        return "Deletion"
+        return "#DEL#"
     elif variant == '+':
-        return "Insertion"
+        return "#INS#"
     else:
         mutations = variant.split("_")
         nc_variant = list(refseq)
@@ -465,7 +465,7 @@ def process_ref_csv(cl_args, tqdm_fn=tqdm.tqdm):
             logging.info(f"Fasta file for {name} already exists. Skipping write.")
         
         barcode_path = filter_bc(cl_args, name_folder, i)
-        output_dir = Path(result_folder) / "basecalled_reads"
+        output_dir = Path(result_folder) / f"{cl_args['name']}_fastq"
         output_dir.mkdir(parents=True, exist_ok=True)
 
         if not cl_args["skip_demultiplexing"]:
@@ -491,17 +491,25 @@ def process_ref_csv(cl_args, tqdm_fn=tqdm.tqdm):
                 continue
     
     variant_df.to_csv(variant_csv_path, index=False)
-    return variant_df
+    return variant_df, ref_df
 
 # Main function to run LevSeq and ensure saving of intermediate results if an error occurs
 def run_LevSeq(cl_args, tqdm_fn=tqdm.tqdm):
     result_folder = create_result_folder(cl_args)
+    # Ref folder for saving ref csv file
+    ref_folder = os.path.join(result_folder, "ref")
+    os.makedirs(ref_folder, exist_ok=True)
+    
     configure_logging(result_folder)
+    logging.info("Logging configured. Starting program.")
 
     variant_df = pd.DataFrame(columns=["barcode_plate", "name", "refseq", "variant"])
     
     try:
-        variant_df = process_ref_csv(cl_args, tqdm_fn)
+        variant_df, ref_df = process_ref_csv(cl_args, tqdm_fn)
+        ref_df_path = os.path.join(ref_folder, cl_args["name"]+".csv")
+        ref_df.to_csv(ref_df_path, index=False)
+
         if variant_df.empty:
             logging.warning("No data found during CSV processing. The CSV is empty.")
     except Exception as e:

{levseq-1.2.6 → levseq-1.2.7}/levseq/variantcaller.py

@@ -37,11 +37,12 @@ The variant caller starts from demultiplexed fastq files.
 3) Call variant with soft alignment
 
 '''
-# Set up logging with a default level of WARNING
-logging.basicConfig(level=logging.WARNING, format='%(asctime)s - %(levelname)s - %(message)s')
+
 logger = logging.getLogger(__name__)
-# Suppress numpy warnings
-warnings.filterwarnings("ignore", category=RuntimeWarning)
+logger.setLevel(logging.WARNING)  # Set default level for this module
+# Use the logger in this file
+logger.warning("This is a warning message.")
+logger.info("This won't show unless logging is configured to INFO elsewhere.")
 
 class VariantCaller:
     """

{levseq-1.2.6 → levseq-1.2.7/levseq.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: levseq
-Version: 1.2.6
+Version: 1.2.7
 Home-page: https://github.com/fhalab/levseq/
 Author: Yueming Long, Emreay Gursoy, Ariane Mora, Francesca-Zhoufan Li
 Author-email: ylong@caltech.edu
@@ -54,7 +54,7 @@ Figure 1: Overview of the LevSeq variant sequencing workflow using Nanopore tech
 
 
 - Data to reproduce the results and to test are available on zenodo [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13694463.svg)](https://doi.org/10.5281/zenodo.13694463)
-- A dockerized website and database for labs to locally host and visualize their data: website is available [here](https://github.com/ArianeMora/LevSeq_vis/) and code to host locally at: https://github.com/fhalab/LevSeq_VDB/
+- A dockerized website and database for labs to locally host and visualize their data: website is available [here](https://levseqdb.streamlit.app/) and code to host locally [here](https://github.com/fhalab/LevSeq_db)
 
 ## Setup
 
@@ -172,3 +172,7 @@ For more details or trouble shooting please look at our [computational_protocols
 #### Citing
 
 If you have found LevSeq useful, please cite out [paper](https://doi.org/10.1101/2024.09.04.611255).
+
+#### Contact
+
+Leave a feature request in the issues or reach us via [email](mailto:levseqdb@gmail.com).