levseq 1.4.2__tar.gz → 1.4.3__tar.gz

{levseq-1.4.2/levseq.egg-info → levseq-1.4.3}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: levseq
-Version: 1.4.2
+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/)
@@ -183,6 +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-1.4.2 → 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/)
@@ -136,6 +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-1.4.2 → levseq-1.4.3}/levseq/__init__.py

@@ -18,7 +18,7 @@
 __title__ = 'levseq'
 __description__ = 'LevSeq nanopore sequencing'
 __url__ = 'https://github.com/fhalab/levseq/'
-__version__ = '1.4.2'
+__version__ = '1.4.3'
 __author__ = 'Yueming Long, Ariane Mora, Francesca-Zhoufan Li, Emre Gursoy'
 __author_email__ = 'ylong@caltech.edu'
 __license__ = 'GPL3'

{levseq-1.4.2 → 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-1.4.2 → levseq-1.4.3/levseq.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: levseq
-Version: 1.4.2
+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/)
@@ -183,6 +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-1.4.2 → 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'