skbio.alignment.Alignment.start_end_positions

Alignment.start_end_positions()[source]

Returns the (start, end) positions for each aligned sequence.

Returns:

list, None

The list of sequence start/end positions, or None if this was not provided on object construction.

Notes

The start/end positions indicate the range of the unaligned sequences in the alignment. For example, if local alignment were performed on the sequences ACA and TACAT, depending on the specific algorithm that was used to perform the alignment, the start/end positions would likely be: [(0,2), (1,3)]. This indicates that the first and last positions of the second sequence were not included in the alignment, and the aligned sequences were therefore: ACA ACA

This value will often be None, as it is generally only going to be provided on construction if the alignment itself was built within scikit-bio.