示例#1
0
    def maybe_make_db(self):
        """Get GFFutils database from file or create from a gtf"""
        if self.gffutils_db is not None:
            copied_db = os.path.join(self.gtf_folder,
                                     os.path.basename(self.gffutils_db))
            util.progress('Copying gffutils database from {} to {} '
                          '...'.format(self.gffutils_db, copied_db))
            shutil.copyfile(self.gffutils_db, copied_db)
            util.done()

            util.progress('Reading gffutils database from {} ...'.format(
                copied_db))
            db = gffutils.FeatureDB(copied_db)
            util.done()
        else:
            basename = os.path.basename(self.gtf_filename)
            db_filename = os.path.join(self.gtf_folder,
                                       '{}.db'.format(basename))
            util.progress("Found GTF file in {}".format(self.gtf_filename))
            try:
                db = gffutils.FeatureDB(db_filename)
                util.progress(
                    "Found existing built outrigger-built gffutils database "
                    "file in {}".format(db_filename))
            except (ValueError, TypeError):
                util.progress(
                    'Creating a "gffutils" '
                    'database {} ...'.format(db_filename))
                db = gtf.create_db(self.gtf_filename, db_filename)
                util.done()
        return db
示例#2
0
def test_create_db(gtf_filename, db, snap25_exon_id):
    from outrigger.io import gtf

    true = db
    test = gtf.create_db(gtf_filename, 'test.gtf.db')

    # Check that all the true db features are in the test database
    for featuretype in true.featuretypes():
        for feature in true.features_of_type(featuretype=featuretype):
            try:
                test[feature.id]
            except gffutils.FeatureNotFoundError:
                pytest.fail('Feature in true database not found in test '
                            'database')

    # Check that all the test db features are in the true database
    for featuretype in test.featuretypes():
        for feature in test.features_of_type(featuretype=featuretype):
            try:
                true[feature.id]
            except gffutils.FeatureNotFoundError:
                pytest.fail('Feature in test database not found in true '
                            'database')

    # SNAP25 should be in both the true and test databases
    assert true[snap25_exon_id] is not None
    assert test[snap25_exon_id] is not None