Skip to main content
`Ctrl`+`K`

# skbio.alignment.StripedSmithWaterman

class skbio.alignment.StripedSmithWaterman

  Performs a striped (banded) Smith Waterman Alignment.

  First a StripedSmithWaterman object must be instantiated with a query sequence. The resulting object is then callable with a target sequence and may be reused on a large collection of target sequences.

  Parameters:
    query_sequence string

      The query sequence, this may be upper or lowercase from the set of {A, C, G, T, N} (nucleotide) or from the set of {A, R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, V, B, Z, X, * } (protein)

    gap_open_penalty int, optional

      The penalty applied to creating a gap in the alignment. This CANNOT be 0. Default is 5.

    gap_extend_penalty int, optional

      The penalty applied to extending a gap in the alignment. This CANNOT be 0. Default is 2.

    score_size int, optional

      If your estimated best alignment score is < 255 this should be 0. If your estimated best alignment score is >= 255, this should be 1. If you don’t know, this should be 2. Default is 2.

    mask_length int, optional

      The distance between the optimal and suboptimal alignment ending position >= mask_length. We suggest to use len(query_sequence)/2, if you don’t have special concerns. Detailed description of mask_length: After locating the optimal alignment ending position, the suboptimal alignment score can be heuristically found by checking the second largest score in the array that contains the maximal score of each column of the SW matrix. In order to avoid picking the scores that belong to the alignments sharing the partial best alignment, SSW C library masks the reference loci nearby (mask length = mask_length) the best alignment ending position and locates the second largest score from the unmasked elements. Default is 15.

    mask_auto bool, optional

      This will automatically set the used mask length to be max(int(len(query_sequence)/2), mask_length). Default is True.

    score_only bool, optional

      This will prevent the best alignment beginning positions (BABP) and the cigar from being returned as a result. This overrides any setting on score_filter, distance_filter, and override_skip_babp. It has the highest precedence. Default is False.

    score_filter int, optional

      If set, this will prevent the cigar and best alignment beginning positions (BABP) from being returned if the optimal alignment score is less than score_filter saving some time computationally. This filter may be overridden by score_only (prevents BABP and cigar, regardless of other arguments), distance_filter (may prevent cigar, but will cause BABP to be calculated), and override_skip_babp (will ensure BABP) returned. Default is None.

    distance_filter int, optional

      If set, this will prevent the cigar from being returned if the length of the query_sequence or the target_sequence is less than distance_filter saving some time computationally. The results of this filter may be overridden by score_only (prevents BABP and cigar, regardless of other arguments), and score_filter (may prevent cigar). override_skip_babp has no effect with this filter applied, as BABP must be calculated to perform the filter. Default is None.

    override_skip_babp bool, optional

      When True, the best alignment beginning positions (BABP) will always be returned unless score_only is set to True. Default is False.

    protein bool, optional

      When True, the query_sequence and target_sequence will be read as protein sequence. When False, the query_sequence and target_sequence will be read as nucleotide sequence. If True, a substitution_matrix must be supplied. Default is False.

    match_score int, optional

      When using a nucleotide sequence, the match_score is the score added when a match occurs. This is ignored if substitution_matrix is provided. Default is 2.

    mismatch_score int, optional

      When using a nucleotide sequence, the mismatch is the score subtracted when a mismatch occurs. This should be a negative integer. This is ignored if substitution_matrix is provided. Default is -3.

    substitution_matrix 2D dict, optional

      Provides the score for each possible substitution of sequence characters. This may be used for protein or nucleotide sequences. The entire set of possible combinations for the relevant sequence type MUST be enumerated in the dict of dicts. This will override match_score and mismatch_score. Required when protein is True. Default is None.

    suppress_sequences bool, optional

      If True, the query and target sequences will not be returned for convenience. Default is False.

    zero_index bool, optional

      If True, all inidices will start at 0. If False, all inidices will start at 1. Default is True.

  Notes

  This is a wrapper for the SSW package [1].

  mask_length has to be >= 15, otherwise the suboptimal alignment information will NOT be returned.

  match_score is a positive integer and mismatch_score is a negative integer.

  match_score and mismatch_score are only meaningful in the context of nucleotide sequences.

  A substitution matrix must be provided when working with protein sequences.

  References

  [1]

  Zhao, Mengyao, Wan-Ping Lee, Erik P. Garrison, & Gabor T. Marth. “SSW Library: An SIMD Smith-Waterman C/C++ Library for Applications”. PLOS ONE (2013). Web. 11 July 2014. http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082138

  Built-ins

  `__call__` | Align target_sequence to query_sequence
  `__eq__`(value, /) | Return self==value.
  `__ge__`(value, /) | Return self>=value.
  `__getstate__`(/) | Helper for pickle.
  `__gt__`(value, /) | Return self>value.
  `__hash__`(/) | Return hash(self).
  `__le__`(value, /) | Return self<=value.
  `__lt__`(value, /) | Return self<value.
  `__ne__`(value, /) | Return self!=value.
  `__setstate__` |
  `__str__`(/) | Return str(self).

  Methods