def testSummarizeNoCoverageOneRegionPositionsAtEnd(self):
"""
If the genome has one region with positions with no coverage at
its end, it must be possible to summarize the no coverage region.
"""
reference = AARead('id', 'STRSPFFFFFALFMMM')
genome = AARead('id', 'KTRSLXXXXXALXMXM')
# Not summarized.
self.assertEqual(
'S1K; P5L; no coverage 6-10; no coverage 13; no coverage 15',
getSubstitutionsString(reference, genome))
# Summarized.
self.assertEqual('S1K; P5L; no coverage 6-10, 13, 15',
getSubstitutionsString(reference, genome, True))
def testSummarizeNoCoverageOneRegionTwoPositions(self):
"""
If the genome has one region with two positions with no coverage, it
must be possible to summarize the no coverage region.
"""
reference = AARead('id', 'STRSPFFFFFA')
genome = AARead('id', 'KXRXLXXXXXT')
# Not summarized.
self.assertEqual(
'S1K; no coverage 2; no coverage 4; P5L; no coverage 6-10; A11T',
getSubstitutionsString(reference, genome))
# Summarized.
self.assertEqual('S1K; no coverage 2, 4; P5L; no coverage 6-10; A11T',
getSubstitutionsString(reference, genome, True))
def testSummarizeNoCoverageOneRegionPositionsAtStart(self):
"""
If the genome has one region with two positions with no coverage at
its beginning, it must be possible to summarize the no coverage region.
"""
reference = AARead('id', 'TRSPFFFFFA')
genome = AARead('id', 'XRXLXXXXXT')
# Not summarized.
self.assertEqual(
'no coverage 1; no coverage 3; P4L; no coverage 5-9; A10T',
getSubstitutionsString(reference, genome))
# Summarized.
self.assertEqual('no coverage 1, 3; P4L; no coverage 5-9; A10T',
getSubstitutionsString(reference, genome, True))
def testSummarizeNoCoverageTwoRegionsMultiplePositions(self):
"""
If the genome has two regions with positions with no coverage, it
must be possible to summarize the no coverage regions.
"""
reference = AARead('id', 'STRSPFFFFFALFMMM')
genome = AARead('id', 'KXRXLXXXXXTLXMXM')
# Not summarized.
self.assertEqual(
'S1K; no coverage 2; no coverage 4; P5L; no coverage 6-10; '
'A11T; no coverage 13; no coverage 15',
getSubstitutionsString(reference, genome))
# Summarized.
self.assertEqual(
'S1K; no coverage 2, 4; P5L; no coverage 6-10; A11T; '
'no coverage 13, 15',
getSubstitutionsString(reference, genome, True))
def testTwoStringsOfXs(self):
"""
If the genome has two strings of Xs, they must be summarized correctly.
"""
reference = AARead('id', 'STRSPFFFFFA')
genome = AARead('id', 'KXXXLXXXXXT')
self.assertEqual('S1K; no coverage 2-4; P5L; no coverage 6-10; A11T',
getSubstitutionsString(reference, genome))
def testFinalStringOfXs(self):
"""
If the genome ends with Xs, they must be summarized correctly.
"""
reference = AARead('id', 'TRSP')
genome = AARead('id', 'LXXX')
self.assertEqual('T1L; no coverage 2-4',
getSubstitutionsString(reference, genome))
def testStringOfXs(self):
"""
If the genome has a string of Xs, they must be summarized correctly.
"""
reference = AARead('id', 'STRSP')
genome = AARead('id', 'KXXXL')
self.assertEqual('S1K; no coverage 2-4; P5L',
getSubstitutionsString(reference, genome))
def testInitialStringOfXs(self):
"""
If the genome starts with Xs, they must be summarized correctly.
"""
reference = AARead('id', 'TRSP')
genome = AARead('id', 'XXXL')
self.assertEqual('no coverage 1-3; P4L',
getSubstitutionsString(reference, genome))
def testTwoLettersBothDifferent(self):
"""
If two different two-AA sequences are passed, a string showing the
change at positions 1 and 2 must be retuned.
"""
reference = AARead('id', 'SP')
genome = AARead('id', 'KL')
self.assertEqual('S1K; P2L', getSubstitutionsString(reference, genome))
def testOneLetterGenomeGap(self):
"""
If two different one-AA sequences are passed, with a genome gap,
a string showing the change at position 1 must be retuned.
"""
reference = AARead('id', 'S')
genome = AARead('id', '-')
self.assertEqual('S1-', getSubstitutionsString(reference, genome))
def testOneLetterIdentical(self):
"""
If two identical one-AA sequences are passed, the empty string must
be returned.
"""
reference = AARead('id', 'K')
genome = AARead('id', 'K')
self.assertEqual('', getSubstitutionsString(reference, genome))
def testEmpty(self):
"""
If the empty string is passed for both reference and genome, the empty
string must be returned.
"""
reference = AARead('id', '')
genome = AARead('id', '')
self.assertEqual('', getSubstitutionsString(reference, genome))
def testUnreportedXsIssue21SimpleWOInsert(self):
"""
Small test to trigger the issue in
https://github.com/VirologyCharite/sars2seq/issues/21 but without
an additional insertion.
"""
reference = AARead('id', 'CLABF')
genome = AARead('id', 'CMXXF')
self.assertEqual('L2M; no coverage 3-4',
getSubstitutionsString(reference, genome))
def testUnreportedXsIssue21Simple(self):
"""
Small test to trigger the issue in
https://github.com/VirologyCharite/sars2seq/issues/21
"""
reference = AARead('id', 'C-LABF')
genome = AARead('id', 'CSMXXF')
# Note that the code is currently returning '-2S; L2M; no coverage 3'.
self.assertEqual('-2S; L2M; no coverage 3-4',
getSubstitutionsString(reference, genome))
def testUnreportedXsIssue21(self):
"""
Test with the protein sequences that caused the issue in
https://github.com/VirologyCharite/sars2seq/issues/21
The output should include the fact that site 417 is not covered
in the genome.
"""
reference = AARead(
'id',
'MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTW'
'FHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVI'
'KVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREF'
'VFKNIDGYFKIYSKHTPINLVR---DLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD'
'SSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSN'
'FRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYG'
'VSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKV'
'GGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYR'
'VVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTT'
'DAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYS'
'TGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGA'
'ENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNR'
'ALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLA'
'DAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAA'
'LQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQ'
'ALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRAS'
'ANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDG'
'KAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFK'
'EELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP'
'WYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT*')
genome = AARead(
'id',
'MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTW'
'FHVI--SGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVI'
'KVCEFQFCNDPFLXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXPFLMDLEGKQGNFKNLREF'
'VFKNIDGYFKIYSKHTPII-VREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD'
'SSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSN'
'FRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAXXXXXXXXXXXXXXXXXXXXXXXXXXXXX'
'XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXYKLPDDFTGCVIAWNSNKLDSKV'
'SGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYR'
'VVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTT'
'DAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYS'
'TGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHRRARSVASQSIIAYTMSLGV'
'ENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNXXLQYGSFCTQLKR'
'ALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLA'
'DAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAA'
'LQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNHNAQ'
'ALNTLVKQLSSKFGAISSVLNDIFSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRAS'
'ANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDG'
'KAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFK'
'EELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP'
'WYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT*')
self.assertEqual(
'A67V; H69-; V70-; T95I; no coverage 142-173; N211I; '
'L212-; -215E; -216P; -217E; G339D; no coverage '
'353-422; N440K; G446S; S477N; T478K; E484A; Q493R; '
'G496S; Q498R; N501Y; Y505H; T547K; D614G; H655Y; '
'N679K; P681H; A701V; no coverage 752-753; N764K; '
'D796Y; N856K; Q954H; N969K; L981F',
getSubstitutionsString(reference, genome))