Attributes

The last field of a GFF or GTF file contains attributes. As described in Dialects, these can be inconsistently formatted, but we try to the best we can. Once the attributes have been parsed, they can be accessed via Feature.attributes or using getitem syntax on the Feature itself.

An attributes.Attributes object behaves much like a dictionary, except that all of its values are stored internally as a list. By default, all attribute values are returned as lists, even 1-item lists. However, this can be changed using the constants.always_return_list setting.

Let’s get an example Attributes object to work with, by parsing a GFF line:

>>> f = gffutils.feature.feature_from_line(
... 'chr2L\tFlyBase\texon\t8193\t8589\t.\t+\t.\tID=exon1; Parent=FBtr0300689,FBtr0300690')

The attributes.Attributes object is accessed like this:

>>> f.attributes
<gffutils.attributes.Attributes object at ...>

It behaves like a dictionary of lists:

>>> for i in sorted(f.attributes.items()):
...     print('{i[0]}: {i[1]}'.format(i=i))
ID: ['exon1']
Parent: ['FBtr0300689', 'FBtr0300690']

>>> f.attributes['ID']
['exon1']

Usually it’s more convenient to access the attributes directly from the feature, like this:

>>> f['ID']
['exon1']

We can add attributes, again directly from the feature:

>>> f['parent_type'] = 'mRNA'

By default, a list is always returned, even for 1-item lists:

>>> f['parent_type'] == f.attributes['parent_type'] == ['mRNA']
True

However, we can change this behavior like so:

>>> gffutils.constants.always_return_list = False

Now the single values are returned as strings rather than 1-item lists:

>>> for i in sorted(f.attributes.items()):
...     print('{i[0]}: {i[1]}'.format(i=i))
ID: exon1
Parent: ['FBtr0300689', 'FBtr0300690']
parent_type: mRNA

Reset back to the original behavior:

>>> gffutils.constants.always_return_list = True