Dseqrecord: error transferring features when cutting a plasmid open

[manulera]

Hi @BjornFJohansson I noticed this when making further tests for the cuts. My implementation makes the exact same mistake, but the code below is with current pydna code. Will make a fix for this in the new implementation, but wanted to document it somewhere.

cc: @hiyama341 (maybe related to the error in the transfer of features that you mentioned)

The example below uses the following circular sequence with 4 features:

• full_overlap (blue): spans only the overhang
• left_side (green): spans the overhang and a bp from the left side
• right_side (pink): spans the overhang and a bp from the right side
• throughout (orange): spans from left to right.

In the image below, the overhang of EcoRI is highlighted with the selector

The expected behaviour would be that when you cut with EcoRI, you would end up with something like this:

However, the result gives wrong coordinates for left_side and keeps throughout when it should not (see print of the script).

from Bio.Restriction import EcoRI
from pydna.dseqrecord import Dseqrecord
from Bio.SeqFeature import SeqFeature, SimpleLocation

seq = Dseqrecord("acgtGAATTCaatt", circular=True)
seq.features.append(SeqFeature(SimpleLocation(5, 9), id='full_overlap', type='CDS', qualifiers={'label': 'full_overlap'}))
seq.features.append(SeqFeature(SimpleLocation(3, 9), id='left_side', type='CDS', qualifiers={'label': 'left_side'}))
seq.features.append(SeqFeature(SimpleLocation(5, 10), id='right_side', type='CDS', qualifiers={'label': 'right_side'}))
seq.features.append(SeqFeature(SimpleLocation(3, 10), id='throughout', type='CDS', qualifiers={'label': 'throughout'}))

open_seq = seq.cut(EcoRI)[0]

print(*open_seq.features, sep='\n')
print(open_seq.seq.__repr__())

Prints:

type: CDS
location: [0:4]
id: full_overlap
qualifiers:
    Key: label, Value: full_overlap

type: CDS
location: join{[0:4], [12:14]}
id: left_side
qualifiers:
    Key: label, Value: left_side

type: CDS
location: [0:5]
id: right_side
qualifiers:
    Key: label, Value: right_side

type: CDS
location: join{[0:5], [12:14]}
id: throughout
qualifiers:
    Key: label, Value: throughout

Dseq(-18)
AATTCaattacgtG
    GttaatgcaCTTAA