def _get_bax2bam_inputs(): """Little hackery to get the setup class Inputs and to avoid calls to setupclass if skiptest is used Nat: we want to test that this behaves properly when multiple movies are supplied as input, so we make an HdfSubreadSet on the fly from various bax files in testdata """ if HAVE_DATA_AND_BAX2BAM: hdf_subread_xml = tempfile.NamedTemporaryFile( suffix=".hdfsubreadset.xml").name bax_files = ( SIV_DATA_DIR + "/SA3-RS/lambda/2372215/0007_tiny/Analysis_Results/m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.bax.h5", pbcore.data.getBaxH5_v23()[0]) ds = HdfSubreadSet(*bax_files) ds.name = "lambda_rsii" assert len(set([f.movieName for f in ds.resourceReaders()])) == 2 ds.write(hdf_subread_xml) return [hdf_subread_xml] else: # Assume the test data isn't found and the test won't be run return ["/path/to/this-test-should-be-skipped.txt"]
def _get_bax2bam_inputs(): """Little hackery to get the setup class Inputs and to avoid calls to setupclass if skiptest is used Nat: we want to test that this behaves properly when multiple movies are supplied as input, so we make an HdfSubreadSet on the fly from various bax files in testdata """ if HAVE_DATA_AND_BAX2BAM: hdf_subread_xml = tempfile.NamedTemporaryFile(suffix=".hdfsubreadset.xml").name bax_files = (SIV_DATA_DIR + "/SA3-RS/lambda/2372215/0007_tiny/Analysis_Results/m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.bax.h5", pbtestdata.get_file("rsii-bax-h5")) ds = HdfSubreadSet(*bax_files) ds.name = "lambda_rsii" assert len(set([f.movieName for f in ds.resourceReaders()])) == 2 ds.write(hdf_subread_xml) return [hdf_subread_xml] else: # Assume the test data isn't found and the test won't be run return ["/path/to/this-test-should-be-skipped.txt"]