def test20131113Debugging(self):
"""
This is an example I manually examined on 2013-11-13.
"""
hit = (
'GTCGAGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGTGTCCGGCA'
'AGGTTGCCAAGGAGCAGATCGACATCGATAACGCCAAGCACACCAAGTGATGCACTGA'
'CGACGGGTGAGGCCCAGATTCCTACGGCCTGGGCCTCTGTCTGCGTCGGGATGCCATT'
'AGGCCGGTAGGATCGGTCACATGATCGATCCCAAGCTCCTGCGAACGGATCCGGACGC'
'CGTTCGTCGCTCCCAGGCCGCCCGCGGCGAGGACTCCTCGGTTGTGGACGACGTTGTC'
'GCCGCAGATGAGGCTCGTCGTGAGGCTATTGCTGCCCATGAGAACCTGCGTGCAGAAC'
'AGAAGGGACTCGGCAAGCGAATCGCTAAAGCATCCGGTG')
read = (
'GTC-AGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGTGTCCGGCA'
'AGGTTGCCAAGGAGCAGATCGACATCGATAACGCCAAGCACACCAAGTGATGCACTGA'
'CGACGGGTGAGGCCCAGATTCCTACGGCCTGGGCCTCTGTCTGCGTCGGGATGCCATT'
'AGGCCGCTAGGATCGGTCACATGATCGATCCCAAGCTCCTGCGAACGGATCCGGACGC'
'CGTTCGTCGCTCCCAGGCCGCCCGCGGCGAGGACTCCTCGGTTGTGGACGACGTTGTC'
'GCCGCAGATGAGGCTCGTCGTGAGGCTATTGCTGCCCATGAGAACCTGCGTGCAGAAC'
'AGAAGGGACTCGGCAAGCGAATCGCTAAAGCATCCGGTG')
hsp = FakeHSP(subjectStart=2339751, subjectEnd=2339365, readStart=1,
readEnd=386, frame=self.frame, hit=hit, read=read)
normalized = normalizeHSP(hsp, 396, 'blastn')
self.assertEqual({
'subjectStart': 2339364,
'subjectEnd': 2339751,
'readStart': 0,
'readEnd': 386,
'readStartInSubject': 2339354,
'readEndInSubject': 2339751,
}, normalized)
def _dictToAlignments(self, blastDict, read):
"""
Take a dict (made by XMLRecordsReader._convertBlastRecordToDict)
and convert it to a list of alignments.
@param blastDict: A C{dict}, from convertBlastRecordToDict.
@param read: A C{Read} instance, containing the read that BLAST used
to create this record.
@raise ValueError: If the query id in the BLAST dictionary does not
match the id of the read.
@return: A C{list} of L{dark.alignment.Alignment} instances.
"""
if (blastDict['query'] != read.id and
blastDict['query'].split()[0] != read.id):
raise ValueError(
'The reads you have provided do not match the BLAST output: '
'BLAST record query id (%s) does not match the id of the '
'supposedly corresponding read (%s).' %
(blastDict['query'], read.id))
alignments = []
getScore = itemgetter('bits' if self._hspClass is HSP else 'expect')
for blastAlignment in blastDict['alignments']:
alignment = Alignment(blastAlignment['length'],
blastAlignment['title'])
alignments.append(alignment)
for blastHsp in blastAlignment['hsps']:
score = getScore(blastHsp)
normalized = normalizeHSP(blastHsp, len(read),
self.application)
hsp = self._hspClass(
score,
readStart=normalized['readStart'],
readEnd=normalized['readEnd'],
readStartInSubject=normalized['readStartInSubject'],
readEndInSubject=normalized['readEndInSubject'],
readFrame=blastHsp['frame'][0],
subjectStart=normalized['subjectStart'],
subjectEnd=normalized['subjectEnd'],
subjectFrame=blastHsp['frame'][1],
readMatchedSequence=blastHsp['query'],
subjectMatchedSequence=blastHsp['sbjct'],
# Use blastHsp.get on identicalCount and positiveCount
# because they were added in version 2.0.3 and will not
# be present in any of our JSON output generated before
# that. Those values will be None for those JSON files,
# but that's much better than no longer being able to
# read all that data.
identicalCount=blastHsp.get('identicalCount'),
positiveCount=blastHsp.get('positiveCount'))
alignment.addHsp(hsp)
return alignments
def check(self, templateStr):
template = Template(templateStr)
normalized = normalizeHSP(template.hsp(), template.readLen, 'blastn')
self.assertEqual({
'subjectStart': template.hitMatchStart,
'subjectEnd': template.hitMatchStart + template.matchLen,
'readStart': template.readMatchStart,
'readEnd': template.readMatchStart + template.matchLen,
'readStartInSubject': template.readResultStart,
'readEndInSubject': template.readResultStart + template.readLen,
}, normalized)
def check(self, templateStr):
template = Template(templateStr)
normalized = normalizeHSP(template.hsp(), template.readLen, 'blastn')
self.assertEqual(
{
'subjectStart': template.hitMatchStart,
'subjectEnd': template.hitMatchStart + template.matchLen,
'readStart': template.readMatchStart,
'readEnd': template.readMatchStart + template.matchLen,
'readStartInSubject': template.readResultStart,
'readEndInSubject':
template.readResultStart + template.readLen,
}, normalized)
def _dictToAlignments(self, blastDict, read):
"""
Take a dict (made by XMLRecordsReader._convertBlastRecordToDict)
and convert it to a list of alignments.
@param blastDict: A C{dict}, from convertBlastRecordToDict.
@param read: A C{Read} instance, containing the read that BLAST used
to create this record.
@raise ValueError: If the query id in the BLAST dictionary does not
match the id of the read.
@return: A C{list} of L{dark.alignment.Alignment} instances.
"""
if (blastDict['query'] != read.id
and blastDict['query'].split()[0] != read.id):
raise ValueError(
'The reads you have provided do not match the BLAST output: '
'BLAST record query id (%s) does not match the id of the '
'supposedly corresponding read (%s).' %
(blastDict['query'], read.id))
alignments = []
getScore = itemgetter('bits' if self._hspClass is HSP else 'expect')
for blastAlignment in blastDict['alignments']:
alignment = Alignment(blastAlignment['length'],
blastAlignment['title'])
alignments.append(alignment)
for blastHsp in blastAlignment['hsps']:
score = getScore(blastHsp)
normalized = normalizeHSP(blastHsp, len(read),
self.application)
hsp = self._hspClass(
score,
readStart=normalized['readStart'],
readEnd=normalized['readEnd'],
readStartInSubject=normalized['readStartInSubject'],
readEndInSubject=normalized['readEndInSubject'],
readFrame=blastHsp['frame'][0],
subjectStart=normalized['subjectStart'],
subjectEnd=normalized['subjectEnd'],
subjectFrame=blastHsp['frame'][1],
readMatchedSequence=blastHsp['query'],
subjectMatchedSequence=blastHsp['sbjct'])
alignment.addHsp(hsp)
return alignments
def _dictToAlignments(self, blastDict, read):
"""
Take a dict (made by XMLRecordsReader._convertBlastRecordToDict)
and convert it to a list of alignments.
@param blastDict: A C{dict}, from convertBlastRecordToDict.
@param read: A C{Read} instance, containing the read that BLAST used
to create this record.
@raise ValueError: If the query id in the BLAST dictionary does not
match the id of the read.
@return: A C{list} of L{dark.alignment.Alignment} instances.
"""
if (blastDict['query'] != read.id and
blastDict['query'].split()[0] != read.id):
raise ValueError(
'The reads you have provided do not match the BLAST output: '
'BLAST record query id (%s) does not match the id of the '
'supposedly corresponding read (%s).' %
(blastDict['query'], read.id))
alignments = []
getScore = itemgetter('bits' if self._hspClass is HSP else 'expect')
for blastAlignment in blastDict['alignments']:
alignment = Alignment(blastAlignment['length'],
blastAlignment['title'])
alignments.append(alignment)
for blastHsp in blastAlignment['hsps']:
score = getScore(blastHsp)
normalized = normalizeHSP(blastHsp, len(read),
self.application)
hsp = self._hspClass(
score,
readStart=normalized['readStart'],
readEnd=normalized['readEnd'],
readStartInSubject=normalized['readStartInSubject'],
readEndInSubject=normalized['readEndInSubject'],
readFrame=blastHsp['frame'][0],
subjectStart=normalized['subjectStart'],
subjectEnd=normalized['subjectEnd'],
subjectFrame=blastHsp['frame'][1],
readMatchedSequence=blastHsp['query'],
subjectMatchedSequence=blastHsp['sbjct'])
alignment.addHsp(hsp)
return alignments
def testHitExtendsLeft(self):
"""The hit overlaps the read to the left.
ssssss
qqqq
"""
hsp = FakeHSP(subjectStart=3, subjectEnd=6, readStart=1, readEnd=4,
frame=self.frame)
normalized = normalizeHSP(hsp, 4, 'blastn')
self.assertEqual({
'subjectStart': 2,
'subjectEnd': 6,
'readStart': 0,
'readEnd': 4,
'readStartInSubject': 2,
'readEndInSubject': 6,
}, normalized)
def testReadExtendsRight2(self):
"""The read sticks out to the right of the read.
ssss
qqqqqq
"""
hsp = FakeHSP(subjectStart=2, subjectEnd=1, readStart=5, readEnd=6,
frame=self.frame)
normalized = normalizeHSP(hsp, 6, 'blastn')
self.assertEqual({
'subjectStart': 0,
'subjectEnd': 2,
'readStart': 4,
'readEnd': 6,
'readStartInSubject': 0,
'readEndInSubject': 6,
}, normalized)
def testReadExtendsRightAndLeft(self):
"""The read extends to the right and left of the hit.
ssss
qqqqqqq
"""
hsp = FakeHSP(subjectStart=4, subjectEnd=1, readStart=3, readEnd=6,
frame=self.frame)
normalized = normalizeHSP(hsp, 7, 'blastn')
self.assertEqual({
'subjectStart': 0,
'subjectEnd': 4,
'readStart': 2,
'readEnd': 6,
'readStartInSubject': -1,
'readEndInSubject': 6,
}, normalized)
def testIdentical(self):
"""The hit start and end are identical to those of the read.
ssss
qqqq
"""
hsp = FakeHSP(subjectStart=1, subjectEnd=4, readStart=1, readEnd=4,
frame=self.frame)
normalized = normalizeHSP(hsp, 4, 'blastn')
self.assertEqual({
'subjectStart': 0,
'subjectEnd': 4,
'readStart': 0,
'readEnd': 4,
'readStartInSubject': 0,
'readEndInSubject': 4,
}, normalized)
def testHitExtendsRightAndLeft(self):
"""The hit extends to the right and left of the read.
sssssss
qqqq
"""
hsp = FakeHSP(subjectStart=5, subjectEnd=2, readStart=1, readEnd=4,
frame=self.frame)
normalized = normalizeHSP(hsp, 4, 'blastn')
self.assertEqual({
'subjectStart': 1,
'subjectEnd': 5,
'readStart': 0,
'readEnd': 4,
'readStartInSubject': 1,
'readEndInSubject': 5,
}, normalized)
def test20131115Debugging(self):
"""
This is an example I manually examined for BM on 2013-11-15.
"""
read = 'CTCTTGCA-CCTTAGGTACC'
hit = 'CTCTAGCAGCCTTAGGTACC'
hsp = FakeHSP(subjectStart=1776, subjectEnd=1795, readStart=131,
readEnd=149, frame=self.frame, read=read, hit=hit)
normalized = normalizeHSP(hsp, 149, 'blastn')
self.assertEqual({
'subjectStart': 1775,
'subjectEnd': 1795,
'readStart': 130,
'readEnd': 149,
'readStartInSubject': 1775,
'readEndInSubject': 1925,
}, normalized)
def testReadExtendsLeft(self):
"""The read sticks out to the left of the hit.
ssss
qqqqqq
"""
hsp = FakeHSP(subjectStart=4, subjectEnd=1, readStart=1, readEnd=4,
frame=self.frame)
normalized = normalizeHSP(hsp, 6, 'blastn')
self.assertEqual({
'subjectStart': 0,
'subjectEnd': 4,
'readStart': 0,
'readEnd': 4,
'readStartInSubject': -2,
'readEndInSubject': 4,
}, normalized)
def test20131115Debugging(self):
"""
This is an example I manually examined for Barbara on 2013-11-15.
"""
read = 'TTCTTTTTGCATTTGATAGT-TTGCTACAAG'
hit = 'TTCTTTTTGCAATAGTCAGTCTTGCTAAAAG'
hsp = FakeHSP(subjectStart=45, subjectEnd=75, readStart=120,
readEnd=149, frame=self.frame, read=read, hit=hit)
normalized = normalizeHSP(hsp, 149, 'blastn')
self.assertEqual({
'subjectStart': 44,
'subjectEnd': 75,
'readStart': 119,
'readEnd': 149,
'readStartInSubject': -75,
'readEndInSubject': 75,
}, normalized)
def testReadExtendsRight2(self):
"""The read sticks out to the right of the read.
ssss
qqqqqq
"""
hsp = FakeHSP(subjectStart=2,
subjectEnd=1,
readStart=5,
readEnd=6,
frame=self.frame)
normalized = normalizeHSP(hsp, 6, 'blastn')
self.assertEqual(
{
'subjectStart': 0,
'subjectEnd': 2,
'readStart': 4,
'readEnd': 6,
'readStartInSubject': 0,
'readEndInSubject': 6,
}, normalized)
def testHitExtendsRightAndLeft(self):
"""The hit extends to the right and left of the read.
sssssss
qqqq
"""
hsp = FakeHSP(subjectStart=5,
subjectEnd=2,
readStart=1,
readEnd=4,
frame=self.frame)
normalized = normalizeHSP(hsp, 4, 'blastn')
self.assertEqual(
{
'subjectStart': 1,
'subjectEnd': 5,
'readStart': 0,
'readEnd': 4,
'readStartInSubject': 1,
'readEndInSubject': 5,
}, normalized)
def testHitExtendsLeft(self):
"""The hit overlaps the read to the left.
ssssss
qqqq
"""
hsp = FakeHSP(subjectStart=3,
subjectEnd=6,
readStart=1,
readEnd=4,
frame=self.frame)
normalized = normalizeHSP(hsp, 4, 'blastn')
self.assertEqual(
{
'subjectStart': 2,
'subjectEnd': 6,
'readStart': 0,
'readEnd': 4,
'readStartInSubject': 2,
'readEndInSubject': 6,
}, normalized)
def testReadExtendsRightAndLeft(self):
"""The read extends to the right and left of the hit.
ssss
qqqqqqq
"""
hsp = FakeHSP(subjectStart=4,
subjectEnd=1,
readStart=3,
readEnd=6,
frame=self.frame)
normalized = normalizeHSP(hsp, 7, 'blastn')
self.assertEqual(
{
'subjectStart': 0,
'subjectEnd': 4,
'readStart': 2,
'readEnd': 6,
'readStartInSubject': -1,
'readEndInSubject': 6,
}, normalized)
def testIdentical(self):
"""The hit start and end are identical to those of the read.
ssss
qqqq
"""
hsp = FakeHSP(subjectStart=1,
subjectEnd=4,
readStart=1,
readEnd=4,
frame=self.frame)
normalized = normalizeHSP(hsp, 4, 'blastn')
self.assertEqual(
{
'subjectStart': 0,
'subjectEnd': 4,
'readStart': 0,
'readEnd': 4,
'readStartInSubject': 0,
'readEndInSubject': 4,
}, normalized)
def testReadExtendsLeft(self):
"""The read sticks out to the left of the hit.
ssss
qqqqqq
"""
hsp = FakeHSP(subjectStart=4,
subjectEnd=1,
readStart=1,
readEnd=4,
frame=self.frame)
normalized = normalizeHSP(hsp, 6, 'blastn')
self.assertEqual(
{
'subjectStart': 0,
'subjectEnd': 4,
'readStart': 0,
'readEnd': 4,
'readStartInSubject': -2,
'readEndInSubject': 4,
}, normalized)
def test20130721Debugging(self):
"""
This is an example I manually examined on 2013-07-21.
I had to invent hit and read strings though on 2013-11-21 to
introduce 5 gaps in the read due to more rigorous checking in
normalizeHSP.
"""
hit = ('GTCGAGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGT'
'GTCGAGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGT'
'GTCGAGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGT'
'GTCGAGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGT'
'GTCGAGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGT'
'AAAAA')
read = ('GTCGAGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGT'
'GTCGAGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGT'
'GTCGAGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGT'
'GTCGAGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGT'
'GTCGAGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGT'
'-----')
hsp = FakeHSP(subjectStart=9018,
subjectEnd=8764,
readStart=66,
readEnd=315,
frame=self.frame,
hit=hit,
read=read)
normalized = normalizeHSP(hsp, 316, 'blastn')
self.assertEqual(
{
'subjectStart': 8763,
'subjectEnd': 9018,
'readStart': 65,
'readEnd': 315,
'readStartInSubject': 8762,
'readEndInSubject': 9083,
}, normalized)
def test20131115Debugging(self):
"""
This is an example I manually examined for BM on 2013-11-15.
"""
read = 'CTCTTGCA-CCTTAGGTACC'
hit = 'CTCTAGCAGCCTTAGGTACC'
hsp = FakeHSP(subjectStart=1776,
subjectEnd=1795,
readStart=131,
readEnd=149,
frame=self.frame,
read=read,
hit=hit)
normalized = normalizeHSP(hsp, 149, 'blastn')
self.assertEqual(
{
'subjectStart': 1775,
'subjectEnd': 1795,
'readStart': 130,
'readEnd': 149,
'readStartInSubject': 1775,
'readEndInSubject': 1925,
}, normalized)
def test20131113Debugging(self):
"""
This is an example I manually examined on 2013-11-13.
"""
hit = ('GTCGAGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGTGTCCGGCA'
'AGGTTGCCAAGGAGCAGATCGACATCGATAACGCCAAGCACACCAAGTGATGCACTGA'
'CGACGGGTGAGGCCCAGATTCCTACGGCCTGGGCCTCTGTCTGCGTCGGGATGCCATT'
'AGGCCGGTAGGATCGGTCACATGATCGATCCCAAGCTCCTGCGAACGGATCCGGACGC'
'CGTTCGTCGCTCCCAGGCCGCCCGCGGCGAGGACTCCTCGGTTGTGGACGACGTTGTC'
'GCCGCAGATGAGGCTCGTCGTGAGGCTATTGCTGCCCATGAGAACCTGCGTGCAGAAC'
'AGAAGGGACTCGGCAAGCGAATCGCTAAAGCATCCGGTG')
read = ('GTC-AGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGTGTCCGGCA'
'AGGTTGCCAAGGAGCAGATCGACATCGATAACGCCAAGCACACCAAGTGATGCACTGA'
'CGACGGGTGAGGCCCAGATTCCTACGGCCTGGGCCTCTGTCTGCGTCGGGATGCCATT'
'AGGCCGCTAGGATCGGTCACATGATCGATCCCAAGCTCCTGCGAACGGATCCGGACGC'
'CGTTCGTCGCTCCCAGGCCGCCCGCGGCGAGGACTCCTCGGTTGTGGACGACGTTGTC'
'GCCGCAGATGAGGCTCGTCGTGAGGCTATTGCTGCCCATGAGAACCTGCGTGCAGAAC'
'AGAAGGGACTCGGCAAGCGAATCGCTAAAGCATCCGGTG')
hsp = FakeHSP(subjectStart=2339751,
subjectEnd=2339365,
readStart=1,
readEnd=386,
frame=self.frame,
hit=hit,
read=read)
normalized = normalizeHSP(hsp, 396, 'blastn')
self.assertEqual(
{
'subjectStart': 2339364,
'subjectEnd': 2339751,
'readStart': 0,
'readEnd': 386,
'readStartInSubject': 2339354,
'readEndInSubject': 2339751,
}, normalized)
def test20130721Debugging(self):
"""
This is an example I manually examined on 2013-07-21.
I had to invent hit and read strings though on 2013-11-21 to
introduce 5 gaps in the read due to more rigorous checking in
normalizeHSP.
"""
hit = (
'GTCGAGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGT'
'GTCGAGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGT'
'GTCGAGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGT'
'GTCGAGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGT'
'GTCGAGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGT'
'AAAAA')
read = (
'GTCGAGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGT'
'GTCGAGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGT'
'GTCGAGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGT'
'GTCGAGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGT'
'GTCGAGAAGATCAAGATTGGTAAGGAGGCCGTGCAGGACACCGAGACCGT'
'-----')
hsp = FakeHSP(subjectStart=9018, subjectEnd=8764, readStart=66,
readEnd=315, frame=self.frame, hit=hit, read=read)
normalized = normalizeHSP(hsp, 316, 'blastn')
self.assertEqual({
'subjectStart': 8763,
'subjectEnd': 9018,
'readStart': 65,
'readEnd': 315,
'readStartInSubject': 8762,
'readEndInSubject': 9083,
}, normalized)
def test20131115Debugging(self):
"""
This is an example I manually examined for Barbara on 2013-11-15.
"""
read = 'TTCTTTTTGCATTTGATAGT-TTGCTACAAG'
hit = 'TTCTTTTTGCAATAGTCAGTCTTGCTAAAAG'
hsp = FakeHSP(subjectStart=45,
subjectEnd=75,
readStart=120,
readEnd=149,
frame=self.frame,
read=read,
hit=hit)
normalized = normalizeHSP(hsp, 149, 'blastn')
self.assertEqual(
{
'subjectStart': 44,
'subjectEnd': 75,
'readStart': 119,
'readEnd': 149,
'readStartInSubject': -75,
'readEndInSubject': 75,
}, normalized)