Metadata-Version: 2.1
Name: AlignmentUtilis
Version: 0.0.2
Summary: Simple application of sequence alignment algorithms
Home-page: https://github.com/Youpu-Chen/Myscripts/tree/main/Sequence_Handle/sequencealignment
Author: Youpu Chen
Author-email: otis.hongpu@gmail.com
License: MIT
Description: # SequenceAlignment
        
        `sequencealignment` is a collection utilities of sequence alignment algorithms,
        
        - Needleman-Wunsch and Smith-Watermen algorithms to conduct sequence alignment with affine gap penalty
        - Naive exact matching to conduct reads alignment problem
        - ...
        
        ## How to get it?
        
        ```shell
        pip3 install Alignment-Utilis
        ```
        
        
        
        ## How to use it?
        
        ```shell
        # 1. PairwiseSequenceAlignment
        from sequencealignment import PairwiseSequenceAlignment
        # Test
        seq1 = "TCGTAGACGA"
        seq2 = "ATAGAATGCGG"
        # Run Global Alignment
        Runalignment(seq1, seq2, 1, -1, -2, -1, local=False)
        # Run Local Alignment
        Runalignment(seq1, seq2, 1, -1, -2, -1, local=True)
        
        # 2. Naive exact matching
        from sequencealignment import Naive, runCMD, getExampleDatasets
        ```
        
        
        
        ## License
        
        MIT License
        Copyright (c) 2022 Youpu Chen
        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.
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Information Technology
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Description-Content-Type: text/markdown
