levseq 1.4.1__tar.gz → 1.4.3__tar.gz

{levseq-1.4.1/levseq.egg-info → levseq-1.4.3}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: levseq
-Version: 1.4.1
+Version: 1.4.3
 Home-page: https://github.com/fhalab/levseq/
 Author: Yueming Long, Ariane Mora, Francesca-Zhoufan Li, Emre Gursoy
 Author-email: ylong@caltech.edu
@@ -44,6 +44,18 @@ Requires-Dist: scikit-learn
 Requires-Dist: statsmodels
 Requires-Dist: tqdm
 Requires-Dist: biopandas
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: project-url
+Dynamic: requires-dist
+Dynamic: requires-python
 
 # Variant Sequencing with Nanopore (LevSeq)
 
@@ -51,9 +63,21 @@ LevSeq provides a streamlined pipeline for sequencing and analyzing genetic vari
 
 ![Figure 1: LevSeq Workflow](manuscript/figures/LevSeq_Figure-1.jpeg)
 Figure 1: Overview of the LevSeq variant sequencing workflow using Nanopore technology. This diagram illustrates the key steps in the process, from sample preparation to data analysis and visualization.
+## Notes
+
+LevSeq was designed for epPCR and SSM experiments, however, we are currently extending it to work for other enzyme engineering designs as well, the current features are under development:
+
+1. Insertion handling (see version 4.1.3) - thanks to  Brian Zhong for his contributions to this section!
+2. Gene calling (handling different genes, use the `--oligopool` flag)
+
+If you notice any issues with new features or have adapted the LevSeq code for your own use cases, we would love community contributions! Please submit either an issue, or a pull request and we will aim to incorperate the changes.
 
 ## Quick Start
 
+Note the current stable version is: `1.4.2`, the latest version is `1.4.3`. 
+
+For stable releases these are made available via docker and pip. For latest versions, please clone the repo and install locally (see *Local development or install of latest version* below).
+
 ### Docker Installation (Recommended)
 
 1. Install Docker: [https://docs.docker.com/engine/install/](https://docs.docker.com/engine/install/)
@@ -69,7 +93,10 @@ Figure 1: Overview of the LevSeq variant sequencing workflow using Nanopore tech
    ```bash
    docker run --rm -v "/full/path/to/data:/levseq_results" yueminglong/levseq:levseq-1.4-arm64 my_experiment levseq_results/ levseq_results/ref.csv
    ```
-
+4. Connect function data to your sequence data
+   ```bash
+   docker run --rm -v "/full/path/to/data:/levseq_results" yueminglong/levseq:levseq-1.4-arm64 my_experiment levseq_results/ levseq_results/ref.csv --fitness_files "levseq_results/20250712_epPCR_Q06714_37.csv,levseq_results/20250712_epPCR_Q06714_39.csv,levseq_results/20250712_epPCR_Q06714_40.csv" --smiles 'O=P(OC1=CC=CC=C1)(OC2=CC=CC=C2)OC3=CC=CC=C3>>O=P(O)(OC4=CC=CC=C4)OC5=CC=CC=C5' --compound dPPi --variant_df "levseq_results/visualization_partial.csv"
+   ```
 ### Pip Installation (Mac/Linux only)
 
 **IMPORTANT**: On Mac M-series chips (M1-M4), gcc 13 and 14 are **REQUIRED**:
@@ -98,6 +125,18 @@ brew install gcc@13 gcc@14
    levseq my_experiment /path/to/data/ /path/to/ref.csv
    ```
 
+5. Combine function data:
+   ```bash
+   levseq my_experiment /path/to/data/ /path/to/ref.csv  "LCMS_file_{barcode1}.csv,LCMS_file_{barcode2}.csv," --smiles 'reaction_smiles_string' --compound "name_of_compound_in_LCMS_file" --variant_df "visualization_partial.csv"
+   ```
+
+Note for function data we currently expect a LCMS file e.g. with the columns: 
+- `Sample Vial Number` (corresponding to the well that the sample was from). 
+- `Area` (which becomes fitness value). 
+- `Compound Name` which is the name of the compound we filter for that is passed as a parameter.
+- The last `_X.csv` needs to be the barcode number to match that sample to your plate e.g. if you ran LevSeq with barcode 33 for plate 2 you need to have `_33.csv` for the fitness file for plate 2. e.g. `some_fitnes_for_plate_2_33.csv`.
+
+
 ## Data and Visualization
 
 - **Test Data**: Sample data is available on Zenodo [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13694463.svg)](https://doi.org/10.5281/zenodo.13694463)
@@ -168,6 +207,16 @@ For the wet lab protocol:
 - **Advanced Usage**: See the [manuscript notebook](https://github.com/fhalab/LevSeq/blob/main/manuscript/notebooks/epPCR_10plates.ipynb)
 - **Troubleshooting**: See our [computational protocols wiki](https://github.com/fhalab/LevSeq/wiki/Computational-protocols)
 
+### Local development or install of latest version
+
+```
+conda create --name levseq python=3.10
+git clone git@github.com:fhalab/LevSeq.git
+cd LevSeq
+python setup.py sdist bdist_wheel
+pip install dist/levseq-1.4.3.tar.gz
+```
+
 ## Citing LevSeq
 
 If you find LevSeq useful, please cite our paper:

{levseq-1.4.1 → levseq-1.4.3}/README.md

@@ -4,9 +4,21 @@ LevSeq provides a streamlined pipeline for sequencing and analyzing genetic vari
 
 ![Figure 1: LevSeq Workflow](manuscript/figures/LevSeq_Figure-1.jpeg)
 Figure 1: Overview of the LevSeq variant sequencing workflow using Nanopore technology. This diagram illustrates the key steps in the process, from sample preparation to data analysis and visualization.
+## Notes
+
+LevSeq was designed for epPCR and SSM experiments, however, we are currently extending it to work for other enzyme engineering designs as well, the current features are under development:
+
+1. Insertion handling (see version 4.1.3) - thanks to  Brian Zhong for his contributions to this section!
+2. Gene calling (handling different genes, use the `--oligopool` flag)
+
+If you notice any issues with new features or have adapted the LevSeq code for your own use cases, we would love community contributions! Please submit either an issue, or a pull request and we will aim to incorperate the changes.
 
 ## Quick Start
 
+Note the current stable version is: `1.4.2`, the latest version is `1.4.3`. 
+
+For stable releases these are made available via docker and pip. For latest versions, please clone the repo and install locally (see *Local development or install of latest version* below).
+
 ### Docker Installation (Recommended)
 
 1. Install Docker: [https://docs.docker.com/engine/install/](https://docs.docker.com/engine/install/)
@@ -22,7 +34,10 @@ Figure 1: Overview of the LevSeq variant sequencing workflow using Nanopore tech
    ```bash
    docker run --rm -v "/full/path/to/data:/levseq_results" yueminglong/levseq:levseq-1.4-arm64 my_experiment levseq_results/ levseq_results/ref.csv
    ```
-
+4. Connect function data to your sequence data
+   ```bash
+   docker run --rm -v "/full/path/to/data:/levseq_results" yueminglong/levseq:levseq-1.4-arm64 my_experiment levseq_results/ levseq_results/ref.csv --fitness_files "levseq_results/20250712_epPCR_Q06714_37.csv,levseq_results/20250712_epPCR_Q06714_39.csv,levseq_results/20250712_epPCR_Q06714_40.csv" --smiles 'O=P(OC1=CC=CC=C1)(OC2=CC=CC=C2)OC3=CC=CC=C3>>O=P(O)(OC4=CC=CC=C4)OC5=CC=CC=C5' --compound dPPi --variant_df "levseq_results/visualization_partial.csv"
+   ```
 ### Pip Installation (Mac/Linux only)
 
 **IMPORTANT**: On Mac M-series chips (M1-M4), gcc 13 and 14 are **REQUIRED**:
@@ -51,6 +66,18 @@ brew install gcc@13 gcc@14
    levseq my_experiment /path/to/data/ /path/to/ref.csv
    ```
 
+5. Combine function data:
+   ```bash
+   levseq my_experiment /path/to/data/ /path/to/ref.csv  "LCMS_file_{barcode1}.csv,LCMS_file_{barcode2}.csv," --smiles 'reaction_smiles_string' --compound "name_of_compound_in_LCMS_file" --variant_df "visualization_partial.csv"
+   ```
+
+Note for function data we currently expect a LCMS file e.g. with the columns: 
+- `Sample Vial Number` (corresponding to the well that the sample was from). 
+- `Area` (which becomes fitness value). 
+- `Compound Name` which is the name of the compound we filter for that is passed as a parameter.
+- The last `_X.csv` needs to be the barcode number to match that sample to your plate e.g. if you ran LevSeq with barcode 33 for plate 2 you need to have `_33.csv` for the fitness file for plate 2. e.g. `some_fitnes_for_plate_2_33.csv`.
+
+
 ## Data and Visualization
 
 - **Test Data**: Sample data is available on Zenodo [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13694463.svg)](https://doi.org/10.5281/zenodo.13694463)
@@ -121,6 +148,16 @@ For the wet lab protocol:
 - **Advanced Usage**: See the [manuscript notebook](https://github.com/fhalab/LevSeq/blob/main/manuscript/notebooks/epPCR_10plates.ipynb)
 - **Troubleshooting**: See our [computational protocols wiki](https://github.com/fhalab/LevSeq/wiki/Computational-protocols)
 
+### Local development or install of latest version
+
+```
+conda create --name levseq python=3.10
+git clone git@github.com:fhalab/LevSeq.git
+cd LevSeq
+python setup.py sdist bdist_wheel
+pip install dist/levseq-1.4.3.tar.gz
+```
+
 ## Citing LevSeq
 
 If you find LevSeq useful, please cite our paper:

{levseq-1.4.1 → levseq-1.4.3}/levseq/__init__.py

@@ -18,7 +18,7 @@
 __title__ = 'levseq'
 __description__ = 'LevSeq nanopore sequencing'
 __url__ = 'https://github.com/fhalab/levseq/'
-__version__ = '1.4.1'
+__version__ = '1.4.3'
 __author__ = 'Yueming Long, Ariane Mora, Francesca-Zhoufan Li, Emre Gursoy'
 __author_email__ = 'ylong@caltech.edu'
 __license__ = 'GPL3'

{levseq-1.4.1 → levseq-1.4.3}/levseq/interface.py

@@ -21,6 +21,8 @@ Contain argument parsers used for command line interface and web interface
 import os
 import tqdm
 import argparse
+import pandas as pd
+
 # Import local packages
 from levseq.run_levseq import run_LevSeq
 
@@ -68,16 +70,73 @@ def build_cli_parser():
                                      help="Whether this experiment came from an oligopool, default is false.")
     optional_args_group.add_argument("--show_msa",
                                      default=False,
-                                     help="Skip showing msa")                                 
+                                     help="Skip showing msa")  
+    # if cl_args.get('fitness_files') and cl_args.get('smiles'):
+    optional_args_group.add_argument("--fitness_files",
+                                    default=None,
+                                    help="A comma separated list of fitness files (full path) with string quotation marks around them.")
+    optional_args_group.add_argument("--smiles",
+                                default=None,
+                                help="A smiles string of the reaction with quotation marks around.")
+    optional_args_group.add_argument("--compound",
+                            default=None,
+                            help="The compound in the fitness files (e.g. pDT or pdt - case sensitive).")     
+    optional_args_group.add_argument("--variant_df",
+                        default=None,
+                        help="The variant dataframe to combine with fitness data.")                                   
     return parser
 
 
+def combine_seq_func_data(cl_args):
+    # Also check if we have any fitness data 
+    if cl_args.get('fitness_files') and cl_args.get('smiles') and cl_args.get('variant_df'):
+        variant_filename = cl_args.get('variant_df')
+        variant_df = pd.read_csv(variant_filename)
+        # Combine the fitness data with the plate data (note the barcode has to be the last _[barcode])
+        # The smiles has to be the reaction smiles
+        function_files = cl_args.get('fitness_files')
+        compound_name = cl_args.get('compound') if cl_args.get('compound') else 'pdt'
+        print(function_files, compound_name)
+        all_function_df = pd.DataFrame()
+        for function_file in function_files.split(','):
+            barcode = function_file.split('.csv')[0].split('_')[-1]
+            function_df = pd.read_csv(f'{function_file}')
+            function_df.columns = [c.replace('\n', ' ') for c in function_df.columns]
+            function_df['function_well'] = [x.split('-')[-1] if isinstance(x, str) else None for x in function_df['Sample Vial Number'].values]
+            function_df['function_barcode_plate'] = barcode
+            function_df = function_df[function_df['Compound Name'] == compound_name] # We only use pdt or Pdt
+            # Convert it to numeric 
+            function_df['Area'] = pd.to_numeric(function_df['Area'], errors='coerce')
+
+            function_df['barcode_well'] = [f'{p}_{w}' for w, p in function_df[['function_well', 'function_barcode_plate']].values]
+            function_df['filename'] = function_file
+            print(function_df.head())
+            all_function_df = pd.concat([all_function_df, function_df])
+        # Join this with the variant_df barcode plate
+        variant_df['barcode_well'] = [f'{p}_{w}' for w, p in variant_df[['Well', 'barcode_plate']].values]
+        # Join the two
+        variant_df.set_index('barcode_well', inplace=True)
+        all_function_df.set_index('barcode_well', inplace=True)
+        variant_df = variant_df.join(all_function_df, how='left')
+        reaction_smiles = cl_args.get('smiles')
+        variant_df['smiles_string'] = reaction_smiles.split('>>')[-1]
+        variant_df['reaction_smiles'] = reaction_smiles
+        variant_df.columns = [c.lower().replace(' ', '_') for c in variant_df.columns]
+        variant_df.rename(columns={'area': 'fitness_value'}, inplace=True)
+        variant_df.to_csv(f'{variant_filename.replace(".csv", "_seqfunc.csv")}')
+        
+        # levseq levseq_4.1 ref.csv fitness --fitness_files "20250712_epPCR_Q06714_37.csv,20250712_epPCR_Q06714_38.csv,20250712_epPCR_Q06714_39.csv,20250712_epPCR_Q06714_40.csv" --smiles 'O=P(OC1=CC=CC=C1)(OC2=CC=CC=C2)OC3=CC=CC=C3>>O=P(O)(OC4=CC=CC=C4)OC5=CC=CC=C5'  --compound dPPi --variant_df visualization_partial.csv
+        return variant_df
+        
 # Execute LevSeq
 def execute_LevSeq():
     # Build parser
     parser = build_cli_parser()
     # Parse the arguments
     CL_ARGS = vars(parser.parse_args())
+    if CL_ARGS.get('fitness_files') and CL_ARGS.get('smiles') and CL_ARGS.get('variant_df'):
+        print('Combining LevSeq')
+        return combine_seq_func_data(CL_ARGS)
     # Set up progres bar
     tqdm_fn = tqdm.tqdm
     # Run LevSeq

{levseq-1.4.1 → levseq-1.4.3}/levseq/run_levseq.py

@@ -602,6 +602,7 @@ def process_ref_csv(cl_args, tqdm_fn=tqdm.tqdm):
                 continue
     
     variant_df.to_csv(variant_csv_path, index=False)
+
     return variant_df, ref_df
 
 

{levseq-1.4.1 → levseq-1.4.3}/levseq/utils.py

@@ -205,7 +205,7 @@ def calculate_mutation_significance_across_well(seq_df):
         seq_df.at[i, 'p(g)'] = p_g
         seq_df.at[i, 'p(c)'] = p_c
         seq_df.at[i, 'p(n)'] = p_n
-        seq_df.at[i, 'p(i)'] = p_n
+        seq_df.at[i, 'p(i)'] = p_i
         seq_df.at[i, 'p_value'] = p_value
         seq_df.at[i, 'percent_most_freq_mutation'] = val
         seq_df.at[i, 'most_frequent'] = actual_seq
@@ -324,6 +324,8 @@ def get_reads_for_well(parent_name, bam_file_path: str, ref_str: str, msa_path=N
                               'C', 'p(c)', 'N', 'p(n)', 'I', 'p(i)', 'Warnings']
             return calculate_mutation_significance_across_well(seq_df), alignment_count
     return None, 0
+
+
 def make_row_from_read_pileup_across_well(well_df, ref_str, label, insert_map):
     """
     Given a pileup of reads, we want to get some summary information about that sequence
@@ -349,12 +351,12 @@ def make_row_from_read_pileup_across_well(well_df, ref_str, label, insert_map):
                 warning = f'WARNING: INSERT.'
             rows.append([label, col, ref_seq, actual_seq, freq_non_ref, total_other, total_reads, 1.0, 0.0,
                          len(vc[vc == 'A']), 1.0, len(vc[vc == 'T']), 1.0, len(vc[vc == 'G']), 1.0,
-                         len(vc[vc == 'C']), 1.0, len(vc[vc == '-']), 1.0, len(insert_map.get(col)),
+                         len(vc[vc == 'C']), 1.0, len(vc[vc == '-']), 1.0, len(vc[vc == 'I']),
                          1.0, warning])
-        if ref_seq != '-':
+        elif ref_seq != '-':
             rows.append([label, col, ref_seq, actual_seq, freq_non_ref, total_other, total_reads, 1.0, 0.0,
                          len(vc[vc == 'A']), 1.0, len(vc[vc == 'T']), 1.0, len(vc[vc == 'G']), 1.0,
-                         len(vc[vc == 'C']), 1.0, len(vc[vc == '-']), 1.0, 0,
+                         len(vc[vc == 'C']), 1.0, len(vc[vc == '-']), 1.0, len(vc[vc == 'I']),
                          1.0, warning])
     return rows
 

{levseq-1.4.1 → levseq-1.4.3/levseq.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: levseq
-Version: 1.4.1
+Version: 1.4.3
 Home-page: https://github.com/fhalab/levseq/
 Author: Yueming Long, Ariane Mora, Francesca-Zhoufan Li, Emre Gursoy
 Author-email: ylong@caltech.edu
@@ -44,6 +44,18 @@ Requires-Dist: scikit-learn
 Requires-Dist: statsmodels
 Requires-Dist: tqdm
 Requires-Dist: biopandas
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: project-url
+Dynamic: requires-dist
+Dynamic: requires-python
 
 # Variant Sequencing with Nanopore (LevSeq)
 
@@ -51,9 +63,21 @@ LevSeq provides a streamlined pipeline for sequencing and analyzing genetic vari
 
 ![Figure 1: LevSeq Workflow](manuscript/figures/LevSeq_Figure-1.jpeg)
 Figure 1: Overview of the LevSeq variant sequencing workflow using Nanopore technology. This diagram illustrates the key steps in the process, from sample preparation to data analysis and visualization.
+## Notes
+
+LevSeq was designed for epPCR and SSM experiments, however, we are currently extending it to work for other enzyme engineering designs as well, the current features are under development:
+
+1. Insertion handling (see version 4.1.3) - thanks to  Brian Zhong for his contributions to this section!
+2. Gene calling (handling different genes, use the `--oligopool` flag)
+
+If you notice any issues with new features or have adapted the LevSeq code for your own use cases, we would love community contributions! Please submit either an issue, or a pull request and we will aim to incorperate the changes.
 
 ## Quick Start
 
+Note the current stable version is: `1.4.2`, the latest version is `1.4.3`. 
+
+For stable releases these are made available via docker and pip. For latest versions, please clone the repo and install locally (see *Local development or install of latest version* below).
+
 ### Docker Installation (Recommended)
 
 1. Install Docker: [https://docs.docker.com/engine/install/](https://docs.docker.com/engine/install/)
@@ -69,7 +93,10 @@ Figure 1: Overview of the LevSeq variant sequencing workflow using Nanopore tech
    ```bash
    docker run --rm -v "/full/path/to/data:/levseq_results" yueminglong/levseq:levseq-1.4-arm64 my_experiment levseq_results/ levseq_results/ref.csv
    ```
-
+4. Connect function data to your sequence data
+   ```bash
+   docker run --rm -v "/full/path/to/data:/levseq_results" yueminglong/levseq:levseq-1.4-arm64 my_experiment levseq_results/ levseq_results/ref.csv --fitness_files "levseq_results/20250712_epPCR_Q06714_37.csv,levseq_results/20250712_epPCR_Q06714_39.csv,levseq_results/20250712_epPCR_Q06714_40.csv" --smiles 'O=P(OC1=CC=CC=C1)(OC2=CC=CC=C2)OC3=CC=CC=C3>>O=P(O)(OC4=CC=CC=C4)OC5=CC=CC=C5' --compound dPPi --variant_df "levseq_results/visualization_partial.csv"
+   ```
 ### Pip Installation (Mac/Linux only)
 
 **IMPORTANT**: On Mac M-series chips (M1-M4), gcc 13 and 14 are **REQUIRED**:
@@ -98,6 +125,18 @@ brew install gcc@13 gcc@14
    levseq my_experiment /path/to/data/ /path/to/ref.csv
    ```
 
+5. Combine function data:
+   ```bash
+   levseq my_experiment /path/to/data/ /path/to/ref.csv  "LCMS_file_{barcode1}.csv,LCMS_file_{barcode2}.csv," --smiles 'reaction_smiles_string' --compound "name_of_compound_in_LCMS_file" --variant_df "visualization_partial.csv"
+   ```
+
+Note for function data we currently expect a LCMS file e.g. with the columns: 
+- `Sample Vial Number` (corresponding to the well that the sample was from). 
+- `Area` (which becomes fitness value). 
+- `Compound Name` which is the name of the compound we filter for that is passed as a parameter.
+- The last `_X.csv` needs to be the barcode number to match that sample to your plate e.g. if you ran LevSeq with barcode 33 for plate 2 you need to have `_33.csv` for the fitness file for plate 2. e.g. `some_fitnes_for_plate_2_33.csv`.
+
+
 ## Data and Visualization
 
 - **Test Data**: Sample data is available on Zenodo [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13694463.svg)](https://doi.org/10.5281/zenodo.13694463)
@@ -168,6 +207,16 @@ For the wet lab protocol:
 - **Advanced Usage**: See the [manuscript notebook](https://github.com/fhalab/LevSeq/blob/main/manuscript/notebooks/epPCR_10plates.ipynb)
 - **Troubleshooting**: See our [computational protocols wiki](https://github.com/fhalab/LevSeq/wiki/Computational-protocols)
 
+### Local development or install of latest version
+
+```
+conda create --name levseq python=3.10
+git clone git@github.com:fhalab/LevSeq.git
+cd LevSeq
+python setup.py sdist bdist_wheel
+pip install dist/levseq-1.4.3.tar.gz
+```
+
 ## Citing LevSeq
 
 If you find LevSeq useful, please cite our paper:

{levseq-1.4.1 → levseq-1.4.3}/tests/test_variant_calling.py

@@ -283,7 +283,7 @@ class TestVariantCalling(TestClass):
 
     def test_calling_variant_with_insert(self):
         u.dp(["Testing calling variants using SSM with error"])
-
+        # ToDo: Update this with new calling need a new test for this
         parent_sequence = "ATGAGT"
         mutated_sequence = 'ATGAGT' # Not actually mutated
         parent_name = 'parent'