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I was playing around with the crispr module and came across a weird error where the cut coordinates of a cas9 object were way larger than the target sequence.
from pydna.dseqrecord import Dseqrecord
from pydna.crispr import cas9
guide = Dseqrecord("GTTACTTTACCCGACGTCCC")
target = Dseqrecord("GTTACTTTACCCGACGTCCCaGG")
# Create an enzyme object with the guide RNA
enzyme = cas9(str(guide.seq))
# Search for a cutsite in the target sequence
print(enzyme.search(target)) # prints [148] (should be 18)
print(len(target)) # prints 23
The problem was that I was passing a Dseqrecord object and not a string. I am not very familiar yet with the rest of pydna so do most functions require a string or a Dseq / Dseqrecord object? Should we check the input type within the functions or add type hinting?
Let me know if I can help.
The text was updated successfully, but these errors were encountered:
Hi and thanks for your interest in pydna. I have been busy with this years round of grant proposals, nomrally I try to respond quicker.
The crispr module right now is a minimally working example.
I think the way to go here is to specify something that intuitively describes a linear ssDNA molecule.
In pydna, Dseq and Dseqrecords are used for dsDNA.
I think better type hinting at the least and perhaps accepting pydna.seqrecord.SeqRecord would make sense?
I was playing around with the
crispr
module and came across a weird error where the cut coordinates of acas9
object were way larger than the target sequence.The problem was that I was passing a
Dseqrecord
object and not astring
. I am not very familiar yet with the rest ofpydna
so do most functions require astring
or aDseq
/Dseqrecord
object? Should we check the input type within the functions or add type hinting?Let me know if I can help.
The text was updated successfully, but these errors were encountered: