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.py

import gffutils
import os

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

    #create database for genome
    if os.path.isfile(genomeGFFdb):
        db = gffutils.FeatureDB(genomeGFFdb)
    else:
        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 = db.region('scaffold_28:6001-11467', completely_within=True)

    for feature in downstreamGenomeFeatures:
        print(feature["Name"][0])
        feature.start += 10000
        feature.end += 10000
        print(feature.end)

    db.update(downstreamGenomeFeatures, merge_strategy="replace")

    return

updateGenome()

Thanks a lot. Could you please check my new example, though, at https://gist.github.com/rmzelle/22fc9c537ddf8f40de4b

I'm trying to shift the last two features of the GFF file downstream by 10000 bp. While the generator shows that the coordinates change, somehow the changes don't make it into the database after running db.update().