def test_on_protein(self):
from multicov.alignment import Alignment
from multicov.alphabet import protein_alphabet
from multicov.filtering import filter_rows
threshold = 1 / 21
align = Alignment([
'WKHNAYDMLSSDCQFESSHKHTQVCSAGMGYCAKPNNWGYW-LIVKMMW-CDYKQKLIYIAPLN',
'KHRCDANC-MLAN-SVIKYTHSACALIWTWNS-KIIRYFFVGAWFKEHFDSVPTAQACVCDSTP',
'LGVVGYYFKPCT-EVPSYSRFNVFHRIFPYLVYRVEE-NHTGHHVQ-KIVRNQYELRSIFDEHG',
'LIGDDHRN-LALCPS-T-GTTCCNWKWRSEWTMHSDTNCNPVAE--SYSKRCNDIGYITWINYA',
'CMPRYWYTYQYDCIFGWRFYSVYWPCLDDMFWQPYVDSMELF-NPMVATEWIMENCQGWG-N-K',
'QWFWRARPFE--FSC-C-PGP-GWVNLIDWMSCNKAMETLMRPYCNPYLKIQLPRSKNLLDDDG',
'VTMPEGHHCPAM-PLDLNGQR-KMWGSDFKKEDCKGYPEKFDCENLIDMDICLSLNTRPED-QR',
'LNYINMHVD-IGP-PCPQYDL--KFKCMYW-GQIEDV-NMQ-WKK-RTMDAVEQIVSMYHMSVE',
'WHV-EWKPVLC-PHWQFYM-VITEYVAMFQWCPPKGMASPKKGNLPRMFQSAKAIGAHRSDM-Y',
'PIWGGFNFPWID-GSQRQQR-EVTTGCDDFEHKYNPYLVPG-WEFGKYSNCWT-RCWRVNHDTV',
'PPCWVEAPYKPMGMWN-GRKV-NVAVWHHVIVL-DMYGLHLLRDWTMVKNAAHIFSHNMEMSNI',
'E-MWRGLIWSKGAY-YQNDNGTFNWPKQKHP-ARCSF-PTVNKDQNPGP-MVQMREFKSQQGQQ',
'RFGKFTCMGFRWKEYFTKQ-NPYKYRGIVHVKVQMIYSANGNLDWIDIPMIIRLKCPFGTRVTQ',
'CGRCGSH-EWL-NIMRNCKFIFWWRPTNAAHIWCARHESPKAD-QIAMTYRML-LDAHIIIVR-',
'T-PMVWRLVWYDHGCDPWMLIV-PIEPCVVKKPQYKDMERFSPDIKCHYLHDKDDGFWGSDKYI',
'LNCPYADLDGL-NPQR-FVVS-RCMRDGFRAVVRVSPDDLS-MWCKAGA-NTTV-DNRH-IVQW'
], protein_alphabet)
align_clean = filter_rows(align, max_gaps=threshold)
# noinspection PyTypeChecker
gap_fraction = np.mean(align.data == '-', axis=1)
# noinspection PyTypeChecker
gap_fraction_clean = np.mean(align_clean.data == '-', axis=1)
self.assertLess(len(align_clean), len(align))
self.assertLessEqual(np.max(gap_fraction_clean), threshold)
self.assertEqual(np.sum(gap_fraction <= threshold), len(align_clean))
def test_returns_copy_even_when_unchanged(self):
from multicov.alignment import Alignment
from multicov.filtering import filter_rows
from multicov.alphabet import protein_alphabet, dna_alphabet
align = Alignment(['IVGGYTCQ', '-VGGTEAQ', 'IGG-KDT-'],
protein_alphabet)
align.add(['ATACAT', 'GATACA', 'AA--GG'], dna_alphabet)
align_clean = filter_rows(align, 0.9)
self.assertEqual(len(align_clean), 3)
self.assertIsNot(align_clean, align)
def test_on_multi_alpha(self):
from multicov.alignment import Alignment
from multicov.filtering import filter_rows
from multicov.alphabet import protein_alphabet, dna_alphabet
align = Alignment(['IVGGYTCQ', '-VGGTEAQ', 'IGG-KDT-'],
protein_alphabet)
align.add(['ATACAT', 'GATACA', 'AA--GG'], dna_alphabet)
align_clean = filter_rows(align, 0.2)
expected = Alignment(['IVGGYTCQ', '-VGGTEAQ'],
protein_alphabet).add(['ATACAT', 'GATACA'],
dna_alphabet)
self.assertEqual(align_clean, expected)
def test_on_empty(self):
from multicov.alignment import Alignment
from multicov.filtering import filter_rows
align1 = Alignment()
align2 = filter_rows(Alignment())
self.assertEqual(align1, align2)