minimal-failure.py

import gffutils
import os

genomeGFF = 'test.gff'
genomeGFFdb = 'test.db'

db = gffutils.create_db(genomeGFF, dbfn=genomeGFFdb, force=True, merge_strategy="merge")

def generatorModifyFeatures(featureFamilies):
    for featureFamily in featureFamilies:
        print featureFamily
        print type(featureFamily)
        yield featureFamily

featureFamilies = list(db.iter_by_parent_childs())

db.update(generatorModifyFeatures(featureFamilies), merge_strategy="replace")

output.txt

>>> ================================ RESTART ================================
>>> 
[<Feature gene (scaffold10_size537661:22073-23956[-]) at 0x2c87f60L>, <Feature CDS (scaffold10_size537661:22076-23956[-]) at 0x2d7a6d8L>, <Feature exon (scaffold10_size537661:22076-23956[-]) at 0x2d7a9e8L>, <Feature mRNA (scaffold10_size537661:22073-23956[-]) at 0x2c93160L>]
<type 'list'>

Traceback (most recent call last):
  File "...\minimal-failure.py", line 17, in <module>
    db.update(generatorModifyFeatures(featureFamilies), merge_strategy="replace")
  File "...\WinPython-64bit-2.7.9.1\python-2.7.9.amd64\lib\site-packages\gffutils\interface.py", line 809, in update
    data = iterators.DataIterator(data, **_iterator_kwargs)
  File "...\WinPython-64bit-2.7.9.1\python-2.7.9.amd64\lib\site-packages\gffutils\iterators.py", line 278, in DataIterator
    return _FeatureIterator(**_kwargs)
  File "...\WinPython-64bit-2.7.9.1\python-2.7.9.amd64\lib\site-packages\gffutils\iterators.py", line 93, in __init__
    self._observed_dialects = [i.dialect for i in self.peek]
AttributeError: 'list' object has no attribute 'dialect'
>>> 

test.gff

##gff-version 3
##sequence-region scaffold10_size537661 1 537661
scaffold10_size537661	AUGUSTUS	gene	22073	23956	.	-	0	ID=95_g3576;Name=ARN1;
scaffold10_size537661	AUGUSTUS	mRNA	22073	23956	.	-	0	Parent=95_g3576;product=Siderophore iron transporter ARN1
scaffold10_size537661	AUGUSTUS	exon	22076	23956	1	-	0	Parent=95_g3576;
scaffold10_size537661	AUGUSTUS	CDS	22076	23956	1	-	0	Parent=95_g3576;Name=ARN1;