initial support for biopython SeqFeatures

see #42

gffutils/__init__.py

@@ -5,5 +5,4 @@
 from gffutils.helpers import example_filename
 from gffutils.exceptions import FeatureNotFoundError, DuplicateIDError
 from gffutils.version import version as __version__
-
-
+from gffutils import biopython_integration

gffutils/biopython_integration.py

@@ -0,0 +1,66 @@
+"""
+Module for integration with BioPython, specifically SeqRecords and SeqFeature
+objects.
+"""
+try:
+    from Bio.SeqFeature import SeqFeature, FeatureLocation
+except ImportError:
+    raise ImportError(
+        "BioPython must be installed to use this module")
+from . import Feature
+
+_biopython_strand = {
+    '+':  1,
+    '-': -1,
+    '.':  0,
+}
+_feature_strand = dict((v, k) for k, v in _biopython_strand.items())
+
+
+def to_seqfeature(f):
+    """
+    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.
+    """
+    qualifiers = {
+        'source': [f.source],
+        'score': [f.score],
+        'seqid': [f.seqid],
+        'frame': [f.frame],
+    }
+    qualifiers.update(f.attributes)
+    return SeqFeature(
+        FeatureLocation(f.start, f.stop),
+        id=f.id,
+        type=f.featuretype,
+        strand=_biopython_strand[f.strand],
+        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.strand]
+    start = s.location.start.position
+    stop = s.location.end.position
+    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, **kwargs)

gffutils/test/test_biopython_integration.py

@@ -0,0 +1,16 @@
+from gffutils import example_filename, create, parser, feature
+import gffutils
+import gffutils.biopython_integration as bp
+
+def test_roundtrip():
+    """
+    Feature -> SeqFeature -> Feature should be invariant.
+    """
+    db_fname = gffutils.example_filename("gff_example1.gff3")
+    db = gffutils.create_db(db_fname, ':memory:')
+    feature = db['ENSMUSG00000033845']
+    feature.keep_order = True
+    dialect = feature.dialect
+    s = bp.to_seqfeature(feature)
+    f = bp.from_seqfeature(s, dialect=dialect, keep_order=True)
+    assert feature == f