Burrows Wheeler Transform (BWT) search
Project 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") `
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