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"]
