find_subsequence#

biotite.sequence.find_subsequence(sequence, query)[source]#

Find a subsequence in a sequence.

Parameters:
sequenceSequence

The sequence to find the subsequence in.

querySequence

The potential subsequence. Its alphabet must extend the sequence alphabet.

Returns:
match_indicesndarray

The starting indices in sequence, where query has been found. The array is empty if no match has been found.

Raises:
ValueError

If the query alphabet does not extend the sequence alphabet.

Examples

>>> main_seq = NucleotideSequence("ACTGAATGA")
>>> sub_seq = NucleotideSequence("TGA")
>>> print(find_subsequence(main_seq, sub_seq))
[2 6]