Metadata-Version: 1.0
Name: BWTsearch
Version: 0.1.15
Summary: Burrows Wheeler Transform (BWT) search
Home-page: UNKNOWN
Author: UNKNOWN
Author-email: UNKNOWN
License: MIT
Description: 
        **Burrows Wheeler Transform (BWT) search**
        
        Import the `BWT` class into your namespace for convenience:
        
        ```
        from BWTsearch import BWT
        ```
        
        Initialize a BWT of text with instantiating the BWT class:
        
        ```
        text = "AGATA"
        ```
        
        ```
        bwt = BWT(text)
        ```
        
        The instance bwt now will contain all necessary indices for efficiently searching:
        
        - `bwt.bwt` ... contains the BWT string
        - `bwt.position_list` ... contains the start positions of the rotations for each character of bwt
        - `bwt.ranks` ... contains rank indices for each character of the alphabet in bwt
        - `bwt.cnums` ... contains number of character occurances of the alphabet in bwt
        
        Use the `search()` function to obtain a list of positions of exact matches for pattern in text:
        
        ```
        pattern = "AT"
        ```
        
        ```
        bwt.search(pattern)
        ```
        
        This returns a list with indexes into text where an exact match occurs. Empty list if none.
        The pattern will be searched case-sensitive and should not contain $.
        
        Use the `get_text()` function to retrieve the original text from the BWT instance:
        
        ```
        bwt.get_text()
        ```
        
        If a sequence file is available, a genome can be loaded from a FASTA file:
        
        ```
        phix = BWT.from_fast_file("phix.fa")
        ```
        
        ```
        phix.search("AGATA")
        ```
        
Platform: UNKNOWN
