def test_fix(self):
"""The 'fix' command."""
# Extract fake target/antitarget bins from a combined file
ref = cnvlib.read('formats/reference-tr.cnn')
is_bg = (ref["gene"] == "Background")
tgt_bins = ref[~is_bg]
tgt_bins.log2 += np.random.randn(len(tgt_bins)) / 5
anti_bins = ref[is_bg]
anti_bins.log2 += np.random.randn(len(anti_bins)) / 5
blank_bins = cnary.CopyNumArray([])
# Typical usage (hybrid capture)
cnr = commands.do_fix(tgt_bins, anti_bins, ref)
self.assertTrue(0 < len(cnr) <= len(ref))
# Blank antitargets (WGS or amplicon)
cnr = commands.do_fix(tgt_bins, blank_bins, ref[~is_bg])
self.assertTrue(0 < len(cnr) <= len(tgt_bins))
def test_fix(self):
"""The 'fix' command."""
# Extract fake target/antitarget bins from a combined file
ref = cnvlib.read('formats/reference-tr.cnn')
is_bg = (ref["gene"] == "Background")
tgt_bins = ref[~is_bg]
tgt_bins.log2 += np.random.randn(len(tgt_bins)) / 5
anti_bins = ref[is_bg]
anti_bins.log2 += np.random.randn(len(anti_bins)) / 5
blank_bins = cnary.CopyNumArray([])
# Typical usage (hybrid capture)
cnr = commands.do_fix(tgt_bins, anti_bins, ref)
self.assertTrue(0 < len(cnr) <= len(ref))
# Blank antitargets (WGS or amplicon)
cnr = commands.do_fix(tgt_bins, blank_bins, ref[~is_bg])
self.assertTrue(0 < len(cnr) <= len(tgt_bins))
