edms 0.0.post176__tar.gz

edms-0.0.post176/.gitignore

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+# Byte-compiled / optimized / DLL files
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+*.py[cod]
+*$py.class
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+# C extensions
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+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
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+# pdm
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+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
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edms-0.0.post176/LICENSE

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+MIT License
+
+Copyright (c) 2024 marczepeda
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

edms-0.0.post176/MANIFEST.in

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+include README.md LICENSE
+recursive-include src/edms/resources *.csv

edms-0.0.post176/PKG-INFO

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+Metadata-Version: 2.4
+Name: edms
+Version: 0.0.post176
+Summary: Endogenous Deep Mutational Scans
+Author-email: Marcanthony Zepeda <mzepeda@g.harvard.edu>
+License: MIT License
+        
+        Copyright (c) 2024 marczepeda
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Homepage, https://github.com/marczepeda/edms
+Project-URL: Repository, https://github.com/marczepeda/edms
+Project-URL: Issues, https://github.com/marczepeda/edms/issues
+Project-URL: Documentation, https://github.com/marczepeda/edms#readme
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: matplotlib
+Requires-Dist: seaborn
+Requires-Dist: pandas
+Requires-Dist: biopython
+Requires-Dist: requests
+Requires-Dist: scipy
+Requires-Dist: statsmodels
+Requires-Dist: scikit-learn
+Requires-Dist: Levenshtein
+Requires-Dist: ViennaRNA
+Requires-Dist: adjustText
+Requires-Dist: pillow
+Requires-Dist: dna-features-viewer
+Requires-Dist: openpyxl
+Requires-Dist: psutil
+Requires-Dist: argcomplete
+Dynamic: license-file
+
+# Endogenous Deep Mutational Scans (EDMS)
+## Command Line Interface
+```shell
+edms -h # or edms <TAB>
+```
+## Package Organization
+- gen: input/output, data wrangling, generating plots, and statistics.
+    ```shell
+    import edms.gen.cli as cli
+    import edms.gen.image as im
+    import edms.gen.io as io
+    import edms.gen.plot as p
+    import edms.gen.stat as st
+    import edms.gen.tidy as t
+    ```
+- bio: molecular biology & tissue culture workflows.
+    ```shell
+    import edms.bio.clone as cl
+    import edms.bio.fastq as fq
+    import edms.bio.genbank as gb
+    import edms.bio.ngs as ngs
+    import edms.bio.pe as pe
+    import edms.bio.pegLIT as pegLIT
+    import edms.bio.primedesign as primedesign
+    import edms.bio.qPCR as qPCR
+    import edms.bio.sanger as sanger
+    import edms.bio.signature as signature
+    import edms.bio.transfect as tf
+    ```
+- dat: interacting with databases.
+    ```shell
+    import edms.dat.cosmic as co
+    import edms.dat.cvar as cv
+    import edms.dat.ncbi as ncbi
+    ```
+
+## Instructions
+### Install
+1. Download Anaconda:
+    - Mac: https://docs.anaconda.com/anaconda/install/mac-os/
+    - Windows: https://docs.anaconda.com/anaconda/install/windows/
+    - Linux: https://docs.anaconda.com/anaconda/install/linux/
+2. Download Git: https://github.com/git-guides/install-git
+3. Clone edms from github:
+    ```shell
+    cd ~
+    mkdir git
+    cd git
+    git clone https://github.com/marczepeda/edms.git
+    cd edms 
+    ```
+4. Make the environment and install edms:
+    ```shell
+    conda env create -f edms.yml # When conda asks you to proceed, type "y"
+    conda activate edms
+    pip install -e . # Include the "."
+    bash autocomplete.sh # Optional: follow CLI instructions
+    conda deactivate
+    ```
+5. Optional: fastq.py UMI methods need umi_tools, cutadapt, samtools, bowtie2, and fgbio in a seperate environment
+    ```shell
+    conda create -n umi_tools umi_tools cutadapt samtools bowtie2 fgbio
+    ```
+
+### Update
+1. Enter the environment and uninstall edms:
+    ```shell
+    cd ~/git/edms
+    conda activate edms
+    pip uninstall -y edms
+    rm -rf build/ dist/ *.egg-info
+
+    ```
+2. Pull latest version from github and install edms:
+    ```shell
+    git pull origin main
+    pip install -e . # Include the "."
+    conda deactivate
+    ```
+
+## PE Strategies
+| Strategy | Description | Reference |
+|----------|-------------|---------- |
+| PE1 | Cas9(H840A) - M-MLV RT<br>+ pegRNA | [Search-and-replace genome editing without double-strand breaks or donor DNA](https://www.nature.com/articles/s41586-019-1711-4) |
+| PE2 | Cas9(H840A) – M-MLV RT(D200N/L603W/T330P/T306K/W313F)<br>+ pegRNA | [Search-and-replace genome editing without double-strand breaks or donor DNA](https://www.nature.com/articles/s41586-019-1711-4) |
+| PE3 | Cas9(H840A) – M-MLV RT(D200N/L603W/T330P/T306K/W313F)<br>+ ngRNA (targets non-edited strand) | [Search-and-replace genome editing without double-strand breaks or donor DNA](https://www.nature.com/articles/s41586-019-1711-4) |
+| PE4 | Cas9(H840A) – M-MLV RT(D200N/L603W/T330P/T306K/W313F)<br>+ MLH1dn (MMR evasion) | [Enhanced prime editing systems by manipulating cellular determinants of editing outcomes](https://www.cell.com/cell/fulltext/S0092-8674(21)01065-5?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867421010655%3Fshowall%3Dtrue) |
+| PE5 | Cas9(H840A) – M-MLV RT(D200N/L603W/T330P/T306K/W313F)<br>+ MLH1dn (MMR evasion)<br>+ ngRNA (targets non-edited strand) | [Enhanced prime editing systems by manipulating cellular determinants of editing outcomes](https://www.cell.com/cell/fulltext/S0092-8674(21)01065-5?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867421010655%3Fshowall%3Dtrue) |
+| PE6a-d | Cas9(H840A) – ...<br>PEa: ... - evo-Ec48 RT<br>PEb: ... - evo-Tf1 RT<br>PEc: ... - Tf1 RT variant<br>PEd: ... - M-MLV RT variant | [Phage-assisted evolution and protein engineering yield compact, efficient prime editors](https://www.cell.com/cell/fulltext/S0092-8674(23)00854-1?uuid=uuid%3Acdb9bfe9-fd83-4a51-8a65-51f2e8e5cfe2) |
+| PE6e-f | Cas9(H840A) variants – ...<br>M-MLV RT(ΔRNAseH) | [Phage-assisted evolution and protein engineering yield compact, efficient prime editors](https://www.cell.com/cell/fulltext/S0092-8674(23)00854-1?uuid=uuid%3Acdb9bfe9-fd83-4a51-8a65-51f2e8e5cfe2) |
+| PE7 | Cas9(H840A) – M-MLV RT(D200N/L603W/T330P/T306K/W313F) - La (RNA binding protein that stabilizes pegRNA)<br>+/- ngRNA (targets non-edited strand) | [Improving prime editing with an endogenous small RNA-binding protein](https://www.nature.com/articles/s41586-024-07259-6) |
+| PEmax | Mammalian codon-optimized PE | [Enhanced prime editing systems by manipulating cellular determinants of editing outcomes](https://www.cell.com/cell/fulltext/S0092-8674(21)01065-5?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867421010655%3Fshowall%3Dtrue) |
+| pegRNA | spacer - scaffold - RTT - PBS (makes the edit) | [Search-and-replace genome editing without double-strand breaks or donor DNA](https://www.nature.com/articles/s41586-019-1711-4) |
+| epegRNA | spacer - scaffold - RTT - PBS - linker - tevoPreQ (makes the edit; more stable pegRNA) | [Engineered pegRNAs improve prime editing efficiency](https://www.nature.com/articles/s41587-021-01039-7) |
+| ngRNA | spacer - scaffold (targets non-edited strand) | [Search-and-replace genome editing without double-strand breaks or donor DNA](https://www.nature.com/articles/s41586-019-1711-4) |
+| MLH1dn | Dominant negative MLH1 (MMR evasion) | [Enhanced prime editing systems by manipulating cellular determinants of editing outcomes](https://www.cell.com/cell/fulltext/S0092-8674(21)01065-5?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867421010655%3Fshowall%3Dtrue) |
+| silent mutations | Larger prime edits are more efficient through bypassing MMR | [Enhanced prime editing systems by manipulating cellular determinants of editing outcomes](https://www.cell.com/cell/fulltext/S0092-8674(21)01065-5?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867421010655%3Fshowall%3Dtrue) |
+| La | Small RNA binding protein that stabilizes pegRNA | [Improving prime editing with an endogenous small RNA-binding protein](https://www.nature.com/articles/s41586-024-07259-6) |
+| PE-eVLP | Engineered Virus-Like Particle for Prime Editors | [Engineered virus-like particles for transient delivery of prime editor ribonucleoprotein complexes in vivo](https://www.nature.com/articles/s41587-023-02078-y) |
+| dNTPs | HSCs have low dNTP levels, limiting reverse transcription | [Enhancing prime editing in hematopoietic stem and progenitor cells by modulating nucleotide metabolism](https://www.nature.com/articles/s41587-024-02266-4) |
+| Vpx | HSCs express SAMHD1 (triphosphohydrolase), which depletes dNTPs. Accessory lentiviral protein Vpx, encoded by HIV-2 and simian immunodeficiency viruses (SIVs), associates with the CRL4-DCAF1 E3 ubiquitin ligase to target SAMHD1 for proteasomal degradation. | [Enhancing prime editing in hematopoietic stem and progenitor cells by modulating nucleotide metabolism](https://www.nature.com/articles/s41587-024-02266-4) |
+| MLH-SB | Small protein binder that disrupts MLH1 & PMS2 binding (MMR evasion) | [AI-generated small binder improves prime editing (Preprint)](https://www.biorxiv.org/content/10.1101/2024.09.11.612443v1.full) |

edms-0.0.post176/README.md

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+# Endogenous Deep Mutational Scans (EDMS)
+## Command Line Interface
+```shell
+edms -h # or edms <TAB>
+```
+## Package Organization
+- gen: input/output, data wrangling, generating plots, and statistics.
+    ```shell
+    import edms.gen.cli as cli
+    import edms.gen.image as im
+    import edms.gen.io as io
+    import edms.gen.plot as p
+    import edms.gen.stat as st
+    import edms.gen.tidy as t
+    ```
+- bio: molecular biology & tissue culture workflows.
+    ```shell
+    import edms.bio.clone as cl
+    import edms.bio.fastq as fq
+    import edms.bio.genbank as gb
+    import edms.bio.ngs as ngs
+    import edms.bio.pe as pe
+    import edms.bio.pegLIT as pegLIT
+    import edms.bio.primedesign as primedesign
+    import edms.bio.qPCR as qPCR
+    import edms.bio.sanger as sanger
+    import edms.bio.signature as signature
+    import edms.bio.transfect as tf
+    ```
+- dat: interacting with databases.
+    ```shell
+    import edms.dat.cosmic as co
+    import edms.dat.cvar as cv
+    import edms.dat.ncbi as ncbi
+    ```
+
+## Instructions
+### Install
+1. Download Anaconda:
+    - Mac: https://docs.anaconda.com/anaconda/install/mac-os/
+    - Windows: https://docs.anaconda.com/anaconda/install/windows/
+    - Linux: https://docs.anaconda.com/anaconda/install/linux/
+2. Download Git: https://github.com/git-guides/install-git
+3. Clone edms from github:
+    ```shell
+    cd ~
+    mkdir git
+    cd git
+    git clone https://github.com/marczepeda/edms.git
+    cd edms 
+    ```
+4. Make the environment and install edms:
+    ```shell
+    conda env create -f edms.yml # When conda asks you to proceed, type "y"
+    conda activate edms
+    pip install -e . # Include the "."
+    bash autocomplete.sh # Optional: follow CLI instructions
+    conda deactivate
+    ```
+5. Optional: fastq.py UMI methods need umi_tools, cutadapt, samtools, bowtie2, and fgbio in a seperate environment
+    ```shell
+    conda create -n umi_tools umi_tools cutadapt samtools bowtie2 fgbio
+    ```
+
+### Update
+1. Enter the environment and uninstall edms:
+    ```shell
+    cd ~/git/edms
+    conda activate edms
+    pip uninstall -y edms
+    rm -rf build/ dist/ *.egg-info
+
+    ```
+2. Pull latest version from github and install edms:
+    ```shell
+    git pull origin main
+    pip install -e . # Include the "."
+    conda deactivate
+    ```
+
+## PE Strategies
+| Strategy | Description | Reference |
+|----------|-------------|---------- |
+| PE1 | Cas9(H840A) - M-MLV RT<br>+ pegRNA | [Search-and-replace genome editing without double-strand breaks or donor DNA](https://www.nature.com/articles/s41586-019-1711-4) |
+| PE2 | Cas9(H840A) – M-MLV RT(D200N/L603W/T330P/T306K/W313F)<br>+ pegRNA | [Search-and-replace genome editing without double-strand breaks or donor DNA](https://www.nature.com/articles/s41586-019-1711-4) |
+| PE3 | Cas9(H840A) – M-MLV RT(D200N/L603W/T330P/T306K/W313F)<br>+ ngRNA (targets non-edited strand) | [Search-and-replace genome editing without double-strand breaks or donor DNA](https://www.nature.com/articles/s41586-019-1711-4) |
+| PE4 | Cas9(H840A) – M-MLV RT(D200N/L603W/T330P/T306K/W313F)<br>+ MLH1dn (MMR evasion) | [Enhanced prime editing systems by manipulating cellular determinants of editing outcomes](https://www.cell.com/cell/fulltext/S0092-8674(21)01065-5?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867421010655%3Fshowall%3Dtrue) |
+| PE5 | Cas9(H840A) – M-MLV RT(D200N/L603W/T330P/T306K/W313F)<br>+ MLH1dn (MMR evasion)<br>+ ngRNA (targets non-edited strand) | [Enhanced prime editing systems by manipulating cellular determinants of editing outcomes](https://www.cell.com/cell/fulltext/S0092-8674(21)01065-5?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867421010655%3Fshowall%3Dtrue) |
+| PE6a-d | Cas9(H840A) – ...<br>PEa: ... - evo-Ec48 RT<br>PEb: ... - evo-Tf1 RT<br>PEc: ... - Tf1 RT variant<br>PEd: ... - M-MLV RT variant | [Phage-assisted evolution and protein engineering yield compact, efficient prime editors](https://www.cell.com/cell/fulltext/S0092-8674(23)00854-1?uuid=uuid%3Acdb9bfe9-fd83-4a51-8a65-51f2e8e5cfe2) |
+| PE6e-f | Cas9(H840A) variants – ...<br>M-MLV RT(ΔRNAseH) | [Phage-assisted evolution and protein engineering yield compact, efficient prime editors](https://www.cell.com/cell/fulltext/S0092-8674(23)00854-1?uuid=uuid%3Acdb9bfe9-fd83-4a51-8a65-51f2e8e5cfe2) |
+| PE7 | Cas9(H840A) – M-MLV RT(D200N/L603W/T330P/T306K/W313F) - La (RNA binding protein that stabilizes pegRNA)<br>+/- ngRNA (targets non-edited strand) | [Improving prime editing with an endogenous small RNA-binding protein](https://www.nature.com/articles/s41586-024-07259-6) |
+| PEmax | Mammalian codon-optimized PE | [Enhanced prime editing systems by manipulating cellular determinants of editing outcomes](https://www.cell.com/cell/fulltext/S0092-8674(21)01065-5?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867421010655%3Fshowall%3Dtrue) |
+| pegRNA | spacer - scaffold - RTT - PBS (makes the edit) | [Search-and-replace genome editing without double-strand breaks or donor DNA](https://www.nature.com/articles/s41586-019-1711-4) |
+| epegRNA | spacer - scaffold - RTT - PBS - linker - tevoPreQ (makes the edit; more stable pegRNA) | [Engineered pegRNAs improve prime editing efficiency](https://www.nature.com/articles/s41587-021-01039-7) |
+| ngRNA | spacer - scaffold (targets non-edited strand) | [Search-and-replace genome editing without double-strand breaks or donor DNA](https://www.nature.com/articles/s41586-019-1711-4) |
+| MLH1dn | Dominant negative MLH1 (MMR evasion) | [Enhanced prime editing systems by manipulating cellular determinants of editing outcomes](https://www.cell.com/cell/fulltext/S0092-8674(21)01065-5?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867421010655%3Fshowall%3Dtrue) |
+| silent mutations | Larger prime edits are more efficient through bypassing MMR | [Enhanced prime editing systems by manipulating cellular determinants of editing outcomes](https://www.cell.com/cell/fulltext/S0092-8674(21)01065-5?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867421010655%3Fshowall%3Dtrue) |
+| La | Small RNA binding protein that stabilizes pegRNA | [Improving prime editing with an endogenous small RNA-binding protein](https://www.nature.com/articles/s41586-024-07259-6) |
+| PE-eVLP | Engineered Virus-Like Particle for Prime Editors | [Engineered virus-like particles for transient delivery of prime editor ribonucleoprotein complexes in vivo](https://www.nature.com/articles/s41587-023-02078-y) |
+| dNTPs | HSCs have low dNTP levels, limiting reverse transcription | [Enhancing prime editing in hematopoietic stem and progenitor cells by modulating nucleotide metabolism](https://www.nature.com/articles/s41587-024-02266-4) |
+| Vpx | HSCs express SAMHD1 (triphosphohydrolase), which depletes dNTPs. Accessory lentiviral protein Vpx, encoded by HIV-2 and simian immunodeficiency viruses (SIVs), associates with the CRL4-DCAF1 E3 ubiquitin ligase to target SAMHD1 for proteasomal degradation. | [Enhancing prime editing in hematopoietic stem and progenitor cells by modulating nucleotide metabolism](https://www.nature.com/articles/s41587-024-02266-4) |
+| MLH-SB | Small protein binder that disrupts MLH1 & PMS2 binding (MMR evasion) | [AI-generated small binder improves prime editing (Preprint)](https://www.biorxiv.org/content/10.1101/2024.09.11.612443v1.full) |

edms-0.0.post176/autocomplete.sh

@@ -0,0 +1,36 @@
+#!/usr/bin/env bash
+
+CLI_COMMAND="edms"
+RC_FILE=""
+SHELL_TYPE="$(basename "$SHELL")"
+
+# Determine shell and config file
+if [[ "$SHELL_TYPE" == "bash" ]]; then
+    RC_FILE="$HOME/.bashrc"
+    AUTOCOMP_LINE="eval \"\$(register-python-argcomplete $CLI_COMMAND)\""
+elif [[ "$SHELL_TYPE" == "zsh" ]]; then
+    RC_FILE="$HOME/.zshrc"
+    AUTOCOMP_LINE="eval \"\$(register-python-argcomplete $CLI_COMMAND)\""
+    COMPINIT_LINE="autoload -U compinit && compinit"
+else
+    echo "Unsupported shell: $SHELL_TYPE"
+    exit 1
+fi
+
+# Add compinit if needed (for Zsh)
+if [[ "$SHELL_TYPE" == "zsh" ]]; then
+    if ! grep -q "compinit" "$RC_FILE"; then
+        echo "Adding compinit to $RC_FILE..."
+        echo -e "\n$COMPINIT_LINE" >> "$RC_FILE"
+    fi
+fi
+
+# Add autocomplete line if not already present
+if ! grep -Fq "$AUTOCOMP_LINE" "$RC_FILE"; then
+    echo "Adding autocomplete line to $RC_FILE..."
+    echo -e "\n$AUTOCOMP_LINE" >> "$RC_FILE"
+else
+    echo "Autocomplete already enabled in $RC_FILE."
+fi
+
+echo "Done. Please run: source $RC_FILE"

edms-0.0.post176/edms.yml

@@ -0,0 +1,159 @@
+name: edms
+channels:
+  - anaconda
+  - defaults
+  - conda-forge
+  - bioconda
+  - https://repo.anaconda.com/pkgs/main
+  - https://repo.anaconda.com/pkgs/r
+dependencies:
+  - adjusttext=1.3.0=pyhd8ed1ab_0
+  - appnope=0.1.4=pyhd8ed1ab_1
+  - asttokens=3.0.0=pyhd8ed1ab_1
+  - biopython=1.85=py312hea69d52_1
+  - blas=2.131=openblas
+  - blas-devel=3.9.0=31_h11c0a38_openblas
+  - brotli=1.1.0=hd74edd7_2
+  - brotli-bin=1.1.0=hd74edd7_2
+  - brotli-python=1.1.0=py312hde4cb15_2
+  - bzip2=1.0.8=h80987f9_6
+  - c-ares=1.34.5=h5505292_0
+  - ca-certificates=2025.8.3=hbd8a1cb_0
+  - certifi=2025.8.3=pyhd8ed1ab_0
+  - cffi=1.17.1=py312h0fad829_0
+  - charset-normalizer=3.4.1=pyhd8ed1ab_0
+  - comm=0.2.2=pyhd8ed1ab_1
+  - contourpy=1.3.2=py312hb23fbb9_0
+  - cycler=0.12.1=pyhd8ed1ab_1
+  - debugpy=1.8.14=py312hd8f9ff3_0
+  - decorator=5.2.1=pyhd8ed1ab_0
+  - et_xmlfile=2.0.0=pyhd8ed1ab_1
+  - exceptiongroup=1.2.2=pyhd8ed1ab_1
+  - executing=2.2.0=pyhd8ed1ab_0
+  - expat=2.7.0=h286801f_0
+  - fonttools=4.57.0=py312h998013c_0
+  - freetype=2.13.3=hce30654_1
+  - git=2.49.0=pl5321hd71a902_0
+  - h2=4.2.0=pyhd8ed1ab_0
+  - hpack=4.1.0=pyhd8ed1ab_0
+  - hyperframe=6.1.0=pyhd8ed1ab_0
+  - idna=3.10=pyhd8ed1ab_1
+  - importlib-metadata=8.6.1=pyha770c72_0
+  - ipykernel=6.29.5=pyh57ce528_0
+  - ipython=9.2.0=pyhfb0248b_0
+  - ipython_pygments_lexers=1.1.1=pyhd8ed1ab_0
+  - jedi=0.19.2=pyhd8ed1ab_1
+  - jupyter_client=8.6.3=pyhd8ed1ab_1
+  - jupyter_core=5.7.2=pyh31011fe_1
+  - kiwisolver=1.4.8=py312h2c4a281_0
+  - krb5=1.21.3=h237132a_0
+  - lcms2=2.17=h7eeda09_0
+  - lerc=4.0.0=hd64df32_1
+  - levenshtein=0.27.1=py312hd8f9ff3_0
+  - libblas=3.9.0=31_h10e41b3_openblas
+  - libbrotlicommon=1.1.0=hd74edd7_2
+  - libbrotlidec=1.1.0=hd74edd7_2
+  - libbrotlienc=1.1.0=hd74edd7_2
+  - libcblas=3.9.0=31_hb3479ef_openblas
+  - libcurl=8.14.1=h73640d1_0
+  - libcxx=20.1.3=ha82da77_0
+  - libdeflate=1.22=hd74edd7_0
+  - libedit=3.1.20191231=hc8eb9b7_2
+  - libev=4.33=h93a5062_2
+  - libexpat=2.7.0=h286801f_0
+  - libffi=3.4.4=hca03da5_1
+  - libfreetype=2.13.3=hce30654_1
+  - libfreetype6=2.13.3=h1d14073_1
+  - libgfortran=14.2.0=heb5dd2a_105
+  - libgfortran5=14.2.0=h2c44a93_105
+  - libiconv=1.18=hfe07756_1
+  - libintl=0.23.1=h493aca8_0
+  - libjpeg-turbo=3.1.0=h5505292_0
+  - liblapack=3.9.0=31_hc9a63f6_openblas
+  - liblapacke=3.9.0=31_hbb7bcf8_openblas
+  - liblzma=5.8.1=h39f12f2_0
+  - libnghttp2=1.64.0=h6d7220d_0
+  - libopenblas=0.3.29=openmp_hf332438_0
+  - libpng=1.6.47=h3783ad8_0
+  - libsodium=1.0.20=h99b78c6_0
+  - libsqlite=3.45.2=h091b4b1_0
+  - libssh2=1.11.1=h1590b86_0
+  - libtiff=4.7.0=ha962b0a_2
+  - libwebp-base=1.5.0=h2471fea_0
+  - libxcb=1.17.0=hdb1d25a_0
+  - libzlib=1.3.1=h8359307_2
+  - llvm-openmp=20.1.3=hdb05f8b_0
+  - matplotlib-base=3.10.1=py312hdbc7e53_0
+  - matplotlib-inline=0.1.7=pyhd8ed1ab_1
+  - munkres=1.1.4=pyh9f0ad1d_0
+  - ncurses=6.4=h313beb8_0
+  - nest-asyncio=1.6.0=pyhd8ed1ab_1
+  - numpy=2.0.1=py312h7f4fdc5_1
+  - numpy-base=2.0.1=py312he047099_1
+  - openblas=0.3.29=openmp_hea878ba_0
+  - openjpeg=2.5.3=h8a3d83b_0
+  - openpyxl=3.1.5=py312hf6e0af7_1
+  - openssl=3.5.2=he92f556_0
+  - packaging=25.0=pyh29332c3_1
+  - pandas=2.2.3=py312hcb1e3ce_3
+  - parso=0.8.4=pyhd8ed1ab_1
+  - patsy=1.0.1=pyhd8ed1ab_1
+  - pcre2=10.44=ha881caa_2
+  - perl=5.32.1=7_h4614cfb_perl5
+  - pexpect=4.9.0=pyhd8ed1ab_1
+  - pickleshare=0.7.5=pyhd8ed1ab_1004
+  - pillow=11.1.0=py312h50aef2c_0
+  - pip=25.1=pyh8b19718_0
+  - platformdirs=4.3.7=pyh29332c3_0
+  - prompt-toolkit=3.0.51=pyha770c72_0
+  - psutil=7.0.0=py312hea69d52_0
+  - pthread-stubs=0.4=hd74edd7_1002
+  - ptyprocess=0.7.0=pyhd8ed1ab_1
+  - pure_eval=0.2.3=pyhd8ed1ab_1
+  - pycparser=2.22=pyh29332c3_1
+  - pygments=2.19.1=pyhd8ed1ab_0
+  - pyparsing=3.2.3=pyhd8ed1ab_1
+  - pysocks=1.7.1=pyha55dd90_7
+  - python=3.12.2=hdf0ec26_0_cpython
+  - python-dateutil=2.9.0.post0=pyhff2d567_1
+  - python-levenshtein=0.27.1=pyhff2d567_0
+  - python-tzdata=2025.2=pyhd8ed1ab_0
+  - python_abi=3.12=7_cp312
+  - pytz=2025.2=pyhd8ed1ab_0
+  - pyzmq=26.4.0=py312hf4875e0_0
+  - qhull=2020.2=h420ef59_5
+  - rapidfuzz=3.13.0=py312hd8f9ff3_0
+  - readline=8.2=h1a28f6b_0
+  - requests=2.32.3=py312hca03da5_1
+  - scipy=1.15.2=py312h99a188d_0
+  - setuptools=75.8.0=py312hca03da5_0
+  - six=1.17.0=pyhd8ed1ab_0
+  - sqlite=3.45.2=hf2abe2d_0
+  - stack_data=0.6.3=pyhd8ed1ab_1
+  - statsmodels=0.14.4=py312h755e627_0
+  - tk=8.6.13=h5083fa2_1
+  - tornado=6.4.2=py312hea69d52_0
+  - traitlets=5.14.3=pyhd8ed1ab_1
+  - typing_extensions=4.13.2=pyh29332c3_0
+  - tzdata=2025a=h04d1e81_0
+  - unicodedata2=16.0.0=py312hea69d52_0
+  - urllib3=2.4.0=pyhd8ed1ab_0
+  - wcwidth=0.2.13=pyhd8ed1ab_1
+  - wheel=0.45.1=py312hca03da5_0
+  - xorg-libxau=1.0.12=h5505292_0
+  - xorg-libxdmcp=1.1.5=hd74edd7_0
+  - xz=5.6.4=h80987f9_1
+  - zeromq=4.3.5=hc1bb282_7
+  - zipp=3.21.0=pyhd8ed1ab_1
+  - zlib=1.3.1=h8359307_2
+  - zstandard=0.23.0=py312hea69d52_2
+  - zstd=1.5.7=h6491c7d_2
+  - pip:
+      - argcomplete==3.6.2
+      - dna-features-viewer==3.1.4
+      - joblib==1.4.2
+      - scikit-learn==1.6.1
+      - seaborn==0.13.2
+      - threadpoolctl==3.6.0
+      - viennarna==2.7.0
+prefix: /opt/anaconda3/envs/edms