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"""
Module for integration with BioPython, specifically SeqRecords and SeqFeature
objects.
"""
try:
from Bio.SeqFeature import SeqFeature, FeatureLocation
except ImportError:
import warnings
warnings.warn("BioPython must be installed to use this module")
from .feature import Feature, feature_from_line
_biopython_strand = {
"+": 1,
"-": -1,
".": None,
"?": 0,
}
_feature_strand = dict((v, k) for k, v in _biopython_strand.items())
def to_seqfeature(feature):
"""
Converts a gffutils.Feature object to a Bio.SeqFeature object.
The GFF fields `source`, `score`, `seqid`, and `frame` are stored as
qualifiers. GFF `attributes` are also stored as qualifiers.
Parameters
----------
feature : Feature object, or string
If string, assume it is a GFF or GTF-format line; otherwise just use
the provided feature directly.
"""
if isinstance(feature, str):
feature = feature_from_line(feature)
qualifiers = {
"source": [feature.source],
"score": [feature.score],
"seqid": [feature.seqid],
"frame": [feature.frame],
}
qualifiers.update(feature.attributes)
return SeqFeature(
# Convert from GFF 1-based to standard Python 0-based indexing used by
# BioPython
FeatureLocation(
feature.start - 1, feature.stop, strand=_biopython_strand[feature.strand]
),
id=feature.id,
type=feature.featuretype,
qualifiers=qualifiers,
)
def from_seqfeature(s, **kwargs):
"""
Converts a Bio.SeqFeature object to a gffutils.Feature object.
The GFF fields `source`, `score`, `seqid`, and `frame` are assumed to be
stored as qualifiers. Any other qualifiers will be assumed to be GFF
attributes.
"""
source = s.qualifiers.get("source", ".")[0]
score = s.qualifiers.get("score", ".")[0]
seqid = s.qualifiers.get("seqid", ".")[0]
frame = s.qualifiers.get("frame", ".")[0]
strand = _feature_strand[s.location.strand]
# BioPython parses 1-based GenBank positions into 0-based for use within
# Python. We need to convert back to 1-based GFF format here.
start = s.location.start + 1
stop = s.location.end
featuretype = s.type
id = s.id
attributes = dict(s.qualifiers)
attributes.pop("source", ".")
attributes.pop("score", ".")
attributes.pop("seqid", ".")
attributes.pop("frame", ".")
return Feature(
seqid,
source,
featuretype,
start,
stop,
score,
strand,
frame,
attributes,
id=id,
**kwargs
)
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