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Burrows Wheeler Transform (BWT) search

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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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