Metadata-Version: 2.1
Name: RNAtweaks
Version: 0.0.2
Summary: Package including ViennaRNA helper functions and classes
Home-page: https://github.com/domonik/RNAtweaks
Author: Dominik Rabsch
Author-email: rabsch@informatik.uni-freiburg.de
License: LICENSE.txt
Description: # RNAtweaks
        
        ## Installation
        In addition to the RNAtweaks package you also need the viennarna package from anaconda
        
        ```bash
        pip install RNAtweaks
        conda install viennarna
        ```
        
        ## Usage
        ### RNAplfold
        For RNAplfold usage two different wrappers exist. One uses the command line version of RNAplfold and the other 
        uses the ViennaRNA API
        ```python
        import RNAtweaks.RNAtweaks as RNAtweaks
        sequence = "AAATTTTGGGGGGCCCC"
        window = 3  # winsize option of RNAplfold
        span = 3   # span option of RNAplfold
        region = 3  # ulength option of RNAplfold
        constraint = ("paired", 3, 5)
        api_result = RNAtweaks.api_rnaplfold(sequence, window, span, region=region, temperature=37.0, constraint=[constraint])
        cmd_result = RNAtweaks.cmd_rnaplfold(sequence, window, span, region=region, temperature=37.0, constraint=[constraint])
        ```
        
        For now only paired and unpaired constraints are supported. The constraints must be a list of 
        Tuples in the format `("paired"/"unpaired", start, end)` in contrast to the ViennaRNA constraints these are zero based.
        Both calls will produce an identical PLFoldOutput object that reflects the ViennaRNA `_lunp` file.
        
        ### PLFoldOutput
        Object that reflects the ViennaRNA `_lunp` file. The objects supports various functions to get different representations
        of the file. The recommended usage is to produce an numpy array as follows:
        
        ```python
        array = api_result.numpy_array
        ```
        
        However, it is also possible to get the text representation of the file, which is usually produced by RNAplfold via:
        
        ```python
        array = api_result.get_text(nan="NA", truncated=False)
        ```
        Hereby nan replaced the non float values with `"NA"` and the truncated flag is used to either keep or drop the header 
        lines beginning with "#".
        
        
        
Platform: UNKNOWN
Description-Content-Type: text/markdown
