Should numbers greater than len raise errors in __get_item__?

[manulera]

I see that it does not raise an error on Seq, but what should it mean on a circular molecule?

• Should it be made as if it was until the end like in Seq?
• Should numbers greater than the length be folded (% len)?
• Current behaviour
• Raise an error?

print(Seq('AAAA')[0:8])
# AAAA

print(SeqRecord(Seq('AAAA'))[0:8].seq)
# AAAA

print(Dseq('AAAA', circular=False)[0:8])
# AAAA

print(Dseq('AAAA', circular=True)[0:8])
# empty sequence

print(Dseqrecord('AAAA', circular=False)[0:8].seq)
# AAAA

print(Dseqrecord('AAAA', circular=True)[0:8].seq)
# empty sequence

[BjornFJohansson]

I would expect this to return the sequence or going around as much as needed. Perhaps the former as I cant think of a reason for the latter right now. I agree that the empty string is wrong.

[manulera]

I think the going around would be good, but it should not be allowed to be more than a full circle, I think. For example, in a circular sequence:

seq = Dseq('ACGTA')

seq[3:6] # I would expect TAA
seq[3:8] # I would expect TAACG
seq[3:10] # I would expect TAACG or an error

I think this is more similar to what one would expect from a circular string