Metadata-Version: 2.1
Name: rsnapsim
Version: 0.0.28
Summary: A package for mRNA sequence translation stochastic simulations
Home-page: UNKNOWN
Author: Dr. Luis Aguilera, William Raymond, Dr. Brian Munsky
Author-email: wsraymon@rams.colostate.edu
License: UNKNOWN
Description: Python 2.7 or 3.5+ Version of the Single Molecule Translation Simulator (MatLab) by Dr. Luis Aguilera 
        
        [Computational Design and Interpretation of Single-RNA Translation Experiments](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6816579/)
        
        Translated by Will Raymond - 2018/2019
        
        ------------------------------
        ### **rSNAPsim** - **R**NA **S**equence to **NA**scent **P**rotein **Sim**ulation
        -------------------------------
        ### Project Goal
        
        Provide a Python module that takes nucleotide sequence as an input and does the following: 
           * Choose a file or pull a file from GeneBank
           * Analyzes the sequence and identifies proteins 
           * Detects or adds fluorescent tags
           * Simulates translation trajectories and converts to intensity vectors of A.U. under various conditions
              * Constructs with Rare codons only or Common codons, FRAP or Harringtonite assays
           * Provides analyses of the trajectories 
           * Allows the user to save or export the data
           * Commandline / GUI implementations
        
        ---------------------------------
        ### Documentation
        
        Tutorials, Module Documentation, Installiation and more [LINK TO MUNSKY GROUP WEBSITE]
        
        Dependencies: 
         * [NumPy](https://www.numpy.org/) 
         * [SciPy](https://www.scipy.org/)
         * [BioPython](https://biopython.org/)
         * [matplotlib](https://matplotlib.org/)
         * [pandas](https://pandas.pydata.org/)
         * [SnapGene Reader](https://github.com/IsaacLuo/SnapGeneFileReader)
         
        -----------------------------------
        ### Instillation 
        
        #### Within a conda enviroment:
        
        ```conda install eigen ```
        
        ```pip install -i https://test.pypi.org/simple/ rsnapsim-ssa-cpp ```
        
        ```pip install -i https://test.pypi.org/simple/ rsnapsim```
        
        ##### Compilation of the C++ 
        
        The c++ model should attempt to compile when you pip install the ssa-cpp module, however in the event that it cannot here are some common errors:
        
        * cannot include eigen3/Eigen/Dense
          * This means eigen was not installed correctly from the conda installiation, you may have to manually download [eigen](http://eigen.tuxfamily.org/index.php?title=Main_Page) and pass the argument to the setup.py command. ```python setup.py build_ext --inplace -I[PATH TO EIGEN FOLDER]```
          
        * gcc not found
        
        -------------------------------------
        
        #### Future work
        
        - Example notebooks of all functions
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
