add test for #213

gffutils/test/test_issues.py

@@ -568,3 +568,40 @@ def _check(txt, expected_keys, dialect_trailing_semicolon):
  ],
  dialect_trailing_semicolon=False,
  )
+
+
+def test_issue_213():
+ # GFF header directives seem to be not parsed when building a db from
+ # a file, even though it seems to work fine from a string.
+ data = dedent(
+ """
+ ##gff-version 3
+ . . . . . . . .
+ . . . . . . . .
+ . . . . . . . .
+ . . . . . . . .
+ """
+ )
+
+ # Ensure directives are parsed from DataIterator
+ it = gffutils.iterators.DataIterator(data, from_string=True)
+ assert it.directives == ["gff-version 3"]
+
+
+ # Ensure they're parsed into the db from a string
+ db = gffutils.create_db(data, dbfn=":memory:", from_string=True, verbose=False)
+ assert db.directives == ["gff-version 3"], db.directives
+
+ # Ensure they're parsed into the db from a file
+ tmp = tempfile.NamedTemporaryFile(delete=False).name
+ with open(tmp, "w") as fout:
+ fout.write(data + "\n")
+ db = gffutils.create_db(tmp, ":memory:")
+ assert db.directives == ["gff-version 3"], db.directives
+ assert len(db.directives) == 1
+
+ # Ensure they're parsed into the db from a file, and going to a file (to
+ # exactly replicate example in #213)
+ db = gffutils.create_db(tmp, dbfn='issue_213.db', force=True)
+ assert db.directives == ["gff-version 3"], db.directives
+ assert len(db.directives) == 1