Three-way is mate comparison about dnaio HOT 2 CLOSED

I support this! I haven’t seen R3 files, yet, but there’s been requests for demultiplexing support in Cutadapt by using I1 files. An are_mates function would be a good step towards support for reading three input files. The only alternative name I can up with at the moment is is_trio, but that evokes the wrong connotation. I think are_mates is fine. (Edit: Or is_triple)

from dnaio.

I think we should implement as follows:

def are_mates(self, *args) where args is a tuple of SequenceRecord objects. Since we cannot do three-way comparison of memory in C anyway, we need to compare two times. This can be done in a simple loop where self is compared to any number of sequence records in args. That way we are immediately future proofed against any number of comparisons, and the name are_mates nicely reflects that.

The advantage here is that we only have to do the costly strcspn function once per comparison.

from dnaio.