ArraySplitter 1.0.9__tar.gz → 1.1.1__tar.gz

ArraySplitter-1.1.1/PKG-INFO

@@ -0,0 +1,59 @@
+Metadata-Version: 2.1
+Name: ArraySplitter
+Version: 1.1.1
+Summary: De Novo Decomposition of Satellite DNA Arrays into Monomers within Telomere-to-Telomere Assemblies
+Home-page: https://github.com/aglabx/ArraySplitter
+Author: Aleksey Komissarov
+Author-email: ad3002@gmail.com
+License: BSD
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+# ArraySplitter: De Novo Decomposition of Satellite DNA Arrays
+
+Decomposes satellite DNA arrays into monomers within telomere-to-telomere (T2T) assemblies. Ideal for analyzing centromeric and pericentromeric regions on monomeric level.
+
+**Status:** In development. Optimized for 100Kb scale arrays; longer arrays will work but may take longer to process. Signigicanlty longerer time.
+
+## Installation
+
+**Prerequisites**
+
+* Python 3.6 or later
+
+**Installation with pip:**
+
+```bash
+pip install arraysplitter
+```
+
+## Usage
+
+**Basic Example**
+
+```bash
+time arraysplitter --input chr1.arrays.fa --output chr1.arrays
+```
+
+**Explanation**
+
+* **`--input chr1.arrays.fa`:**  FASTA file of satDNA arrays.
+* **`--output chr1.arrays`:** Output FASTA containing decomposed monomers (separated by spaces).
+
+**All Options** 
+
+```bash
+arraysplitter --help 
+```
+
+## Contact
+
+For questions or support: ad3002@gmail.com

ArraySplitter-1.1.1/README.md

@@ -0,0 +1,40 @@
+# ArraySplitter: De Novo Decomposition of Satellite DNA Arrays
+
+Decomposes satellite DNA arrays into monomers within telomere-to-telomere (T2T) assemblies. Ideal for analyzing centromeric and pericentromeric regions on monomeric level.
+
+**Status:** In development. Optimized for 100Kb scale arrays; longer arrays will work but may take longer to process. Signigicanlty longerer time.
+
+## Installation
+
+**Prerequisites**
+
+* Python 3.6 or later
+
+**Installation with pip:**
+
+```bash
+pip install arraysplitter
+```
+
+## Usage
+
+**Basic Example**
+
+```bash
+time arraysplitter --input chr1.arrays.fa --output chr1.arrays
+```
+
+**Explanation**
+
+* **`--input chr1.arrays.fa`:**  FASTA file of satDNA arrays.
+* **`--output chr1.arrays`:** Output FASTA containing decomposed monomers (separated by spaces).
+
+**All Options** 
+
+```bash
+arraysplitter --help 
+```
+
+## Contact
+
+For questions or support: ad3002@gmail.com

{ArraySplitter-1.0.9 → ArraySplitter-1.1.1}/src/ArraySplitter/__init__.py

@@ -5,6 +5,6 @@
 # @author: Aleksey Komissarov
 # @contact: ad3002@gmail.com
 
-__version__ = "1.0.9"
+__version__ = "1.1.1"
 
 # __all__ = []

ArraySplitter-1.1.1/src/ArraySplitter.egg-info/PKG-INFO

@@ -0,0 +1,59 @@
+Metadata-Version: 2.1
+Name: ArraySplitter
+Version: 1.1.1
+Summary: De Novo Decomposition of Satellite DNA Arrays into Monomers within Telomere-to-Telomere Assemblies
+Home-page: https://github.com/aglabx/ArraySplitter
+Author: Aleksey Komissarov
+Author-email: ad3002@gmail.com
+License: BSD
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+# ArraySplitter: De Novo Decomposition of Satellite DNA Arrays
+
+Decomposes satellite DNA arrays into monomers within telomere-to-telomere (T2T) assemblies. Ideal for analyzing centromeric and pericentromeric regions on monomeric level.
+
+**Status:** In development. Optimized for 100Kb scale arrays; longer arrays will work but may take longer to process. Signigicanlty longerer time.
+
+## Installation
+
+**Prerequisites**
+
+* Python 3.6 or later
+
+**Installation with pip:**
+
+```bash
+pip install arraysplitter
+```
+
+## Usage
+
+**Basic Example**
+
+```bash
+time arraysplitter --input chr1.arrays.fa --output chr1.arrays
+```
+
+**Explanation**
+
+* **`--input chr1.arrays.fa`:**  FASTA file of satDNA arrays.
+* **`--output chr1.arrays`:** Output FASTA containing decomposed monomers (separated by spaces).
+
+**All Options** 
+
+```bash
+arraysplitter --help 
+```
+
+## Contact
+
+For questions or support: ad3002@gmail.com

ArraySplitter-1.0.9/PKG-INFO

@@ -1,56 +0,0 @@
-Metadata-Version: 2.1
-Name: ArraySplitter
-Version: 1.0.9
-Summary: De Novo Decomposition of Satellite DNA Arrays into Monomers within Telomere-to-Telomere Assemblies
-Home-page: https://github.com/aglabx/ArraySplitter
-Author: Aleksey Komissarov
-Author-email: ad3002@gmail.com
-License: BSD
-Classifier: Development Status :: 4 - Beta
-Classifier: Environment :: Console
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: BSD License
-Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown
-License-File: LICENSE
-
-# ArraySplitter
-ArraySplitter: De Novo Decomposition of Satellite DNA Arrays into Monomers within Telomere-to-Telomere Assemblies
-
-## Introduction
-
-ArraySplitter is a tool for the de novo decomposition of satellite DNA arrays into monomers within telomere-to-telomere assemblies. It is designed to work with a very long satDNA arrays from T2T assemblies, such as those found in centromeric and pericentromeric regions. ArraySplitter is implemented in Python and is available as a standalone tool.
-
-## Installation
-
-ArraySplitter is implemented in Python and requires Python 3.6 or later. 
-
-To install ArraySplitter, clone the repository from GitHub and install the required dependencies using pip:
-
-```bash
-pip install -r requirements.txt
-
-python setup.py install
-```
-
-## Usage
-
-ArraySplitter is a command-line tool. To see the available options, run:
-
-```bash
-time python ./ArraySplitter/main.py --help
-```
-
-The main input to ArraySplitter is a FASTA file containing the telomere-to-telomere assembly. The output is a FASTA file containing the monomers of the satellite DNA arrays seperated by spaces.
-
-## Example
-
-To run ArraySplitter on the provided test data, run:
-
-```bash
-time python ./ArraySplitter/main.py --input ./test_data/chr1.fa --output ./test_data/chr1_monomers
-```
-

ArraySplitter-1.0.9/README.md

@@ -1,37 +0,0 @@
-# ArraySplitter
-ArraySplitter: De Novo Decomposition of Satellite DNA Arrays into Monomers within Telomere-to-Telomere Assemblies
-
-## Introduction
-
-ArraySplitter is a tool for the de novo decomposition of satellite DNA arrays into monomers within telomere-to-telomere assemblies. It is designed to work with a very long satDNA arrays from T2T assemblies, such as those found in centromeric and pericentromeric regions. ArraySplitter is implemented in Python and is available as a standalone tool.
-
-## Installation
-
-ArraySplitter is implemented in Python and requires Python 3.6 or later. 
-
-To install ArraySplitter, clone the repository from GitHub and install the required dependencies using pip:
-
-```bash
-pip install -r requirements.txt
-
-python setup.py install
-```
-
-## Usage
-
-ArraySplitter is a command-line tool. To see the available options, run:
-
-```bash
-time python ./ArraySplitter/main.py --help
-```
-
-The main input to ArraySplitter is a FASTA file containing the telomere-to-telomere assembly. The output is a FASTA file containing the monomers of the satellite DNA arrays seperated by spaces.
-
-## Example
-
-To run ArraySplitter on the provided test data, run:
-
-```bash
-time python ./ArraySplitter/main.py --input ./test_data/chr1.fa --output ./test_data/chr1_monomers
-```
-

ArraySplitter-1.0.9/src/ArraySplitter.egg-info/PKG-INFO

@@ -1,56 +0,0 @@
-Metadata-Version: 2.1
-Name: ArraySplitter
-Version: 1.0.9
-Summary: De Novo Decomposition of Satellite DNA Arrays into Monomers within Telomere-to-Telomere Assemblies
-Home-page: https://github.com/aglabx/ArraySplitter
-Author: Aleksey Komissarov
-Author-email: ad3002@gmail.com
-License: BSD
-Classifier: Development Status :: 4 - Beta
-Classifier: Environment :: Console
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: BSD License
-Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown
-License-File: LICENSE
-
-# ArraySplitter
-ArraySplitter: De Novo Decomposition of Satellite DNA Arrays into Monomers within Telomere-to-Telomere Assemblies
-
-## Introduction
-
-ArraySplitter is a tool for the de novo decomposition of satellite DNA arrays into monomers within telomere-to-telomere assemblies. It is designed to work with a very long satDNA arrays from T2T assemblies, such as those found in centromeric and pericentromeric regions. ArraySplitter is implemented in Python and is available as a standalone tool.
-
-## Installation
-
-ArraySplitter is implemented in Python and requires Python 3.6 or later. 
-
-To install ArraySplitter, clone the repository from GitHub and install the required dependencies using pip:
-
-```bash
-pip install -r requirements.txt
-
-python setup.py install
-```
-
-## Usage
-
-ArraySplitter is a command-line tool. To see the available options, run:
-
-```bash
-time python ./ArraySplitter/main.py --help
-```
-
-The main input to ArraySplitter is a FASTA file containing the telomere-to-telomere assembly. The output is a FASTA file containing the monomers of the satellite DNA arrays seperated by spaces.
-
-## Example
-
-To run ArraySplitter on the provided test data, run:
-
-```bash
-time python ./ArraySplitter/main.py --input ./test_data/chr1.fa --output ./test_data/chr1_monomers
-```
-