genome-minimal-fail.gff

##gff-version 3
scaffold_28	prediction	gene	1	402	0	+	.	ID=545184;Name=545184
scaffold_28	prediction	gene	805	981	0	-	.	ID=93782;Name=93782
scaffold_28	prediction	gene	2030	2721	0	+	.	ID=545205;Name=545205
scaffold_28	prediction	gene	3273	3545	0	-	.	Name=YOL159C-A;Synteny=no_synteny;SystematicGeneName=YOL159C-A;ID=38792
scaffold_28	prediction	gene	5318	5833	0	-	.	Name=YOL159C;Synteny=no_synteny;SystematicGeneName=YOL159C;ID=38793
scaffold_28	prediction	gene	6780	8600	0	-	.	Name=ENB1;Synteny=no_synteny;SystematicGeneName=YOL158C;StandardGeneName=ENB1;ID=38794
scaffold_28	prediction	gene	9698	11467	0	-	.	Name=IMA4;Synteny=no_synteny;SystematicGeneName=YJL221C;StandardGeneName=IMA4;ID=38795

minimal-fail-2.py

import gffutils
import os

def generatorShiftFeatures(features, shift):
    for feature in features:
        print("original position: " + str(feature.start) + " " + str(feature.end))
        feature.start += shift
        feature.end += shift
        print("new position: " + str(feature.start) + " " + str(feature.end))
        yield feature

def updateGenome():
    genomeGFF="genome-minimal-fail.gff"
    genomeGFFdb = genomeGFF.replace(".gff", ".db")

    #create database for genome
    db = gffutils.create_db(genomeGFF, dbfn=genomeGFFdb, force=True, merge_strategy="merge")

    #shift coordinates of features that follow the original integration site by deletion size
    downstreamGenomeFeatures = list(db.region('scaffold_28:6001-11467', completely_within=True))
    db.delete(db.region('scaffold_28:6001-11467', completely_within=True))
    
    db.update(generatorShiftFeatures(downstreamGenomeFeatures,10000), merge_strategy="replace")

    allFeatures = db.all_features()

    for feature in allFeatures:
        print(feature.start)
    return

updateGenome()

Edit: this comment relates to the initial version of the gist at https://gist.github.com/rmzelle/22fc9c537ddf8f40de4b/fb3c0e885cbdaac4189155893836d0046300ef46

Gives output:

original position: 6780 8600
new position: 16780 18600
original position: 9698 11467
new position: 19698 21467
1
805
2030
3273
5318
6780
9698

The last two values should be "16790" and "19698", but they're still at their original values.

Edit: this comment relates to the second version of the gist at https://gist.github.com/rmzelle/22fc9c537ddf8f40de4b/0813fd6c8594647b5e934c84621475a4f7166998
(see the diff at https://gist.github.com/rmzelle/22fc9c537ddf8f40de4b/revisions)

@daler, I was able to fix this by creating a list with all the features I wanted to shift, and then deleting the original features from the database. See https://gist.github.com/rmzelle/22fc9c537ddf8f40de4b/revisions

This now gives the desired output:

original position: 6780 8600
new position: 16780 18600
original position: 9698 11467
new position: 19698 21467
1
805
2030
3273
5318
16780
19698

It seems to me that this shouldn't be necessary, though. It looks like db.update() with merge_strategy="replace" doesn't update the feature coordinates when they change.