edlib 1.3.9.post1

align()

align(query, target, [mode], [task], [k], [additionalEqualities])

Aligns query against target with edit distance.

query and target can be strings, bytes, or any iterables of hashable objects, as long as all together they don’t have more than 256 unique values.

Output of help(edlib.align):

cython_function_or_method in module edlib

align(query, target, mode='NW', task='distance', k=-1, additionalEqualities=None)
    Align query with target using edit distance.
    @param {str or bytes or iterable of hashable objects} query, combined with target must have no more
           than 256 unique values
    @param {str or bytes or iterable of hashable objects} target, combined with query must have no more
           than 256 unique values
    @param {string} mode  Optional. Alignment method do be used. Possible values are:
            - 'NW' for global (default)
            - 'HW' for infix
            - 'SHW' for prefix.
    @param {string} task  Optional. Tells edlib what to calculate. The less there is to calculate,
            the faster it is. Possible value are (from fastest to slowest):
            - 'distance' - find edit distance and end locations in target. Default.
            - 'locations' - find edit distance, end locations and start locations.
            - 'path' - find edit distance, start and end locations and alignment path.
    @param {int} k  Optional. Max edit distance to search for - the lower this value,
            the faster is calculation. Set to -1 (default) to have no limit on edit distance.
    @param {list} additionalEqualities  Optional.
            List of pairs of characters or hashable objects, where each pair defines two values as equal.
            This way you can extend edlib's definition of equality (which is that each character is equal only
            to itself).
            This can be useful e.g. when you want edlib to be case insensitive, or if you want certain
            characters to act as a wildcards.
            Set to None (default) if you do not want to extend edlib's default equality definition.
    @return Dictionary with following fields:
            {int} editDistance  Integer, -1 if it is larger than k.
            {int} alphabetLength Integer, length of unique characters in 'query' and 'target'
            {[(int, int)]} locations  List of locations, in format [(start, end)].
            {string} cigar  Cigar is a standard format for alignment path.
                Here we are using extended cigar format, which uses following symbols:
                Match: '=', Insertion to target: 'I', Deletion from target: 'D', Mismatch: 'X'.
                e.g. cigar of "5=1X1=1I" means "5 matches, 1 mismatch, 1 match, 1 insertion (to target)".

getNiceAlignment()

getNiceAlignment(alignResult, query, target)

Represents alignment from align() in a visually attractive format.

Output of help(edlib.getNiceAlignment):

cython_function_or_method in module edlib

getNiceAlignment(alignResult, query, target, gapSymbol='-')
    Output alignments from align() in NICE format
    @param {dictionary} alignResult, output of the method align()
        NOTE: The method align() requires the argument task="path"
    @param {string} query, the exact query used for alignResult
    @param {string} target, the exact target used for alignResult
    @param {string} gapSymbol, default "-"
        String used to represent gaps in the alignment between query and target
    @return Alignment in NICE format, which is human-readable visual representation of how the query and target align to each other.
        e.g., for "telephone" and "elephant", it would look like:
           telephone
            |||||.|.
           -elephant
        It is represented as dictionary with following fields:
          - {string} query_aligned
          - {string} matched_aligned ('|' for match, '.' for mismatch, ' ' for insertion/deletion)
          - {string} target_aligned
        Normally you will want to print these three in order above joined with newline character.