Metadata-Version: 2.1
Name: trviz
Version: 1.2.0
Summary: A python library for decomposing and visualizing tandem repeat sequences
Home-page: https://github.com/Jong-hun-Park/trviz
Author: Jonghun Park
Author-email: jop002@ucsd.edu
License: UNKNOWN
Description: ```
          _______ _______      _______ ______
         |__   __|  __ \ \    / /_   _|___  /
            | |  | |__) \ \  / /  | |    / / 
            | |  |  _  / \ \/ /   | |   / /  
            | |  | | \ \  \  /   _| |_ / /__ 
            |_|  |_|  \_\  \/   |_____/_____|
        
        ```
        TRviz is a python library for analyzing tandem repeat sequences. TRviz includes modules for 
        decomposing, encoding, aligning, and visualizing tandem repeat sequences.
        
        Full documentation is available at [readthedocs](https://trviz.readthedocs.io/)
        
        # Overview of TRviz
        ![](https://github.com/Jong-hun-Park/trviz/blob/main/examples/figures/TRviz_main_figure.png?raw=true)
        
        # Getting Started
        
        ## Prerequisite
        > **Note**
        > TRviz requires [MAFFT](https://mafft.cbrc.jp/alignment/software/). Tested with MAFFT v7.505.
        
        Install the library with pip or from source.
        ## with pip
        ```
        pip install trviz
        ```
        
        ## from source
        ```
        git clone https://github.com/Jong-hun-Park/trviz.git
        cd trviz/
        pip install .
        ```
        
        ## Input
        1. Tandem repeat sequences (alleles)
        2. A set of motifs for decomposition
        
        ## Output
        1. A plot showing the motif composition of the input sequences
        2. A plot mapping color to motif
        3. Aligned and labeled motifs
        4. Motif map, a set of motifs detected in the samples and their labels and frequencies 
        
        # Code samples and examples
        > **Note**
        > Please see the [jupyter notebook](https://github.com/Jong-hun-Park/trviz/blob/main/examples/sample_code.ipynb) for code examples.
        
        TRviz has four modules:
        1. Decomposition
        2. Encoding
        3. Alignment
        4. Visualization
        
        See full documentation at [readthedocs](https://trviz.readthedocs.io/en/latest/)
        
        ## Generating a plot
        
        ```python
        from trviz.main import TandemRepeatVizWorker
        from trviz.utils import get_sample_and_sequence_from_fasta
        
        tr_visualizer = TandemRepeatVizWorker()
        sample_ids, tr_sequences = get_sample_and_sequence_from_fasta(fasta_file_path)
        tr_id = "CACNA1C"
        motifs = ['GACCCTGACCTGACTAGTTTACAATCACAC']
        
        tr_visualizer.generate_trplot(tr_id, sample_ids, tr_sequences, motifs)
        ``` 
        
        ## Motif decomposition
        ```python
        from trviz.decomposer import Decomposer
        
        tr_decomposer = Decomposer()
        tr_sequence = "ACCTTGACCTTGACCTTGACCTTG"
        motifs = ["ACCTTG"]
        tr_decomposer.decompose(tr_sequence, motifs)
        # >>> ["ACCTTG", "ACCTTG", "ACCTTG", "ACCTTG"]
        ``` 
        
        ## Citation:
        Jonghun Park, Eli Kaufman, Paul N Valdmanis, Vineet Bafna, [TRviz: a Python library for decomposing and visualizing tandem repeat sequences](https://doi.org/10.1093/bioadv/vbad058), Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad058 
        
        # Contact Us
        Please submit an issue on the [TRviz github](https://github.com/Jong-hun-Park/trviz/issues)
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
