remove_terminal_gaps
#
- biotite.sequence.align.remove_terminal_gaps(alignment)[source]#
Remove terminal gaps from an alignment.
Terminal gaps are gaps that appear before all sequences start and after any sequence ends.
- Parameters:
- alignmentAlignment
The alignment, where the terminal gaps should be removed from.
- Returns:
- truncated_alignmentAlignment
A shallow copy of the input alignment with an truncated trace, that does not contain alignment columns with terminal gaps.
See also
Examples
>>> sequences = [ ... NucleotideSequence(seq_string) for seq_string in ( ... "AAAAACTGATTC", ... "AAACTGTTCA", ... "CTGATTCAAA" ... ) ... ] >>> trace = np.transpose([ ... ( 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, -1, -1, -1), ... (-1, -1, 0, 1, 2, 3, 4, 5, -1, 6, 7, 8, 9, -1, -1), ... (-1, -1, -1, -1, -1, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9), ... ]) >>> alignment = Alignment(sequences, trace) >>> print(alignment) AAAAACTGATTC--- --AAACTG-TTCA-- -----CTGATTCAAA >>> truncated_alignment = remove_terminal_gaps(alignment) >>> print(truncated_alignment) CTGATTC CTG-TTC CTGATTC