def test_020_gff3_i0(self):
"""check functions for retreiving input filename, and reading and validating a GFF3 file and separate FASTA file"""
newmunger = GFFMunger(None)
newmunger.input_file_arg = test_gff_no_fasta
newmunger.fasta_file_arg = test_fasta_file
newmunger.output_file = self.output_file
self.assertEqual(test_gff_no_fasta, newmunger.get_gff3_source())
self.assertTrue(newmunger.validate_GFF3(test_gff_no_fasta))
self.assertTrue(newmunger.validate_FASTA(test_fasta_file))
self.assertEqual(newmunger.gffutils_db_filename,
newmunger.import_gff3())
self.assertEqual(newmunger.gffutils_db_filename,
newmunger.import_gff3(test_gff_no_fasta))
# when FASTA is in separate file, GFFMunger.extract_GFF3_components() should read only metadata
self.assertEqual(expected_num_metadata_lines,
newmunger.extract_GFF3_components())
self.assertEqual(expected_num_metadata_lines,
newmunger.extract_GFF3_components(test_gff_no_fasta))
with warnings.catch_warnings():
warnings.filterwarnings("ignore", "unclosed file <_io\.FileIO",
ResourceWarning, "six", 581)
warnings.filterwarnings("ignore", "", ResourceWarning, "gffutils",
0)
self.assertIsInstance(newmunger.import_fasta(), pyfaidx.Fasta)
self.assertIsInstance(newmunger.import_fasta(test_fasta_file),
pyfaidx.Fasta)
try:
newmunger.move_polypeptide_annotations()
except:
self.fail("Failed to process valid GFF3 file " +
test_gff_no_fasta)
warnings.resetwarnings()
self.assertTrue(newmunger.export_gff3())
os.remove(newmunger.output_file)
newmunger.clean_up()
def test_000_gff3_with_fasta_io(self):
"""check functions for reading and validating a GFF3 file including FASTA, and writing it as output"""
gffmunger = GFFMunger(None)
gffmunger.input_file_arg = test_gff_file
gffmunger.output_file = self.output_file
self.assertEqual(test_gff_file, gffmunger.get_gff3_source())
self.assertTrue(gffmunger.validate_GFF3(test_gff_file))
self.assertEqual(gffmunger.gffutils_db_filename,
gffmunger.import_gff3())
self.assertEqual(gffmunger.gffutils_db_filename,
gffmunger.import_gff3(test_gff_file))
self.assertEqual(expected_num_input_lines,
gffmunger.extract_GFF3_components())
self.assertEqual(expected_num_input_lines,
gffmunger.extract_GFF3_components(test_gff_file))
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
"unclosed file <_io\.TextIOWrapper",
ResourceWarning, "gffutils", 668)
try:
gffmunger.move_polypeptide_annotations()
except:
self.fail("Failed to process valid GFF3 file " + test_gff_file)
warnings.resetwarnings()
self.assertTrue(gffmunger.export_gff3())
os.remove(gffmunger.output_file)
gffmunger.clean_up()