def testSimple(self):
"""
A simple example must work as expected.
"""
count = 2
len1 = 10
self.assertEqual('Count is: 2/10 (20.00%)',
countPrint('Count is', count, len1))
def testSimple(self):
"""
A simple example must work as expected.
"""
count = 2
len1 = 10
self.assertEqual('Count is: 2/10 (20.00%)',
countPrint('Count is', count, len1))
def matchToString(aaMatch, read1, read2, indent='', offsets=None):
"""
Format amino acid sequence match as a string.
@param aaMatch: A C{dict} returned by C{compareAaReads}.
@param read1: A C{Read} instance or an instance of one of its subclasses.
@param read2: A C{Read} instance or an instance of one of its subclasses.
@param indent: A C{str} to indent all returned lines with.
@param offsets: If not C{None}, a C{set} of offsets of interest that were
only considered when making C{match}.
@return: A C{str} describing the match.
"""
match = aaMatch['match']
matchCount = match['matchCount']
gapMismatchCount = match['gapMismatchCount']
gapGapMismatchCount = match['gapGapMismatchCount']
nonGapMismatchCount = match['nonGapMismatchCount']
if offsets:
len1 = len2 = len(offsets)
else:
len1, len2 = map(len, (read1, read2))
result = []
append = result.append
append(countPrint('%sMatches' % indent, matchCount, len1, len2))
mismatchCount = (gapMismatchCount + gapGapMismatchCount +
nonGapMismatchCount)
append(countPrint('%sMismatches' % indent, mismatchCount, len1, len2))
append(
countPrint('%s Not involving gaps (i.e., conflicts)' % (indent),
nonGapMismatchCount, len1, len2))
append(
countPrint('%s Involving a gap in one sequence' % indent,
gapMismatchCount, len1, len2))
append(
countPrint('%s Involving a gap in both sequences' % indent,
gapGapMismatchCount, len1, len2))
for read, key in zip((read1, read2), ('read1', 'read2')):
append('%s Id: %s' % (indent, read.id))
length = len(read)
append('%s Length: %d' % (indent, length))
gapCount = len(aaMatch[key]['gapOffsets'])
append(countPrint('%s Gaps' % indent, gapCount, length))
if gapCount:
append('%s Gap locations (1-based): %s' % (indent, ', '.join(
map(lambda offset: str(offset + 1),
sorted(aaMatch[key]['gapOffsets'])))))
extraCount = aaMatch[key]['extraCount']
if extraCount:
append(
countPrint('%s Extra nucleotides at end' % indent,
extraCount, length))
return '\n'.join(result)
def testTwoSequences(self):
"""
An example involving two different lengths must work as expected.
"""
count = 2
len1 = 10
len2 = 8
self.assertEqual(
'Count is: 2/10 (20.00%) of sequence 1,'
' 2/8 (25.00%) of sequence 2',
countPrint('Count is', count, len1, len2))
def testTwoSequences(self):
"""
An example involving two different lengths must work as expected.
"""
count = 2
len1 = 10
len2 = 8
self.assertEqual(
'Count is: 2/10 (20.00%) of sequence 1,'
' 2/8 (25.00%) of sequence 2',
countPrint('Count is', count, len1, len2)
)
def matchToString(dnaMatch,
read1,
read2,
matchAmbiguous=True,
indent='',
offsets=None,
includeGapLocations=True):
"""
Format a DNA match as a string.
@param dnaMatch: A C{dict} returned by C{compareDNAReads}.
@param read1: A C{Read} instance or an instance of one of its subclasses.
@param read2: A C{Read} instance or an instance of one of its subclasses.
@param matchAmbiguous: If C{True}, ambiguous nucleotides that are
possibly correct were counted as actually being correct. Otherwise,
the match was done strictly, insisting that only non-ambiguous
nucleotides could contribute to the matching nucleotide count.
@param indent: A C{str} to indent all returned lines with.
@param offsets: If not C{None}, a C{set} of offsets of interest that were
only considered when making C{match}.
@param includeGapLocations: If C{True} indicate the (1-based) locations of
gaps.
@return: A C{str} describing the match.
"""
match = dnaMatch['match']
identicalMatchCount = match['identicalMatchCount']
ambiguousMatchCount = match['ambiguousMatchCount']
gapMismatchCount = match['gapMismatchCount']
gapGapMismatchCount = match['gapGapMismatchCount']
nonGapMismatchCount = match['nonGapMismatchCount']
if offsets:
len1 = len2 = len(offsets)
else:
len1, len2 = map(len, (read1, read2))
result = []
append = result.append
append(
countPrint('%sExact matches' % indent, identicalMatchCount, len1,
len2))
append(
countPrint('%sAmbiguous matches' % indent, ambiguousMatchCount, len1,
len2))
if ambiguousMatchCount and identicalMatchCount:
anyMatchCount = identicalMatchCount + ambiguousMatchCount
append(
countPrint('%sExact or ambiguous matches' % indent, anyMatchCount,
len1, len2))
mismatchCount = (gapMismatchCount + gapGapMismatchCount +
nonGapMismatchCount)
append(countPrint('%sMismatches' % indent, mismatchCount, len1, len2))
conflicts = 'conflicts' if matchAmbiguous else 'conflicts or ambiguities'
append(
countPrint('%s Not involving gaps (i.e., %s)' % (indent, conflicts),
nonGapMismatchCount, len1, len2))
append(
countPrint('%s Involving a gap in one sequence' % indent,
gapMismatchCount, len1, len2))
append(
countPrint('%s Involving a gap in both sequences' % indent,
gapGapMismatchCount, len1, len2))
for read, key in zip((read1, read2), ('read1', 'read2')):
append('%s Id: %s' % (indent, read.id))
length = len(read)
append('%s Length: %d' % (indent, length))
gapCount = len(dnaMatch[key]['gapOffsets'])
append(countPrint('%s Gaps' % indent, gapCount, length))
if includeGapLocations and gapCount:
append('%s Gap locations (1-based): %s' % (indent, ', '.join(
map(lambda offset: str(offset + 1),
sorted(dnaMatch[key]['gapOffsets'])))))
ambiguousCount = len(dnaMatch[key]['ambiguousOffsets'])
append(countPrint('%s Ambiguous' % indent, ambiguousCount, length))
extraCount = dnaMatch[key]['extraCount']
if extraCount:
append(
countPrint('%s Extra nucleotides at end' % indent,
extraCount, length))
return '\n'.join(result)
def matchToString(dnaMatch, read1, read2, matchAmbiguous=True, indent='',
offsets=None):
"""
Format a DNA match as a string.
@param dnaMatch: A C{dict} returned by C{compareDNAReads}.
@param read1: A C{Read} instance or an instance of one of its subclasses.
@param read2: A C{Read} instance or an instance of one of its subclasses.
@param matchAmbiguous: If C{True}, ambiguous nucleotides that are
possibly correct were counted as actually being correct. Otherwise,
the match was done strictly, insisting that only non-ambiguous
nucleotides could contribute to the matching nucleotide count.
@param indent: A C{str} to indent all returned lines with.
@param offsets: If not C{None}, a C{set} of offsets of interest that were
only considered when making C{match}.
@return: A C{str} describing the match.
"""
match = dnaMatch['match']
identicalMatchCount = match['identicalMatchCount']
ambiguousMatchCount = match['ambiguousMatchCount']
gapMismatchCount = match['gapMismatchCount']
gapGapMismatchCount = match['gapGapMismatchCount']
nonGapMismatchCount = match['nonGapMismatchCount']
if offsets:
len1 = len2 = len(offsets)
else:
len1, len2 = map(len, (read1, read2))
result = []
append = result.append
append(countPrint('%sExact matches' % indent, identicalMatchCount,
len1, len2))
append(countPrint('%sAmbiguous matches' % indent, ambiguousMatchCount,
len1, len2))
if ambiguousMatchCount and identicalMatchCount:
anyMatchCount = identicalMatchCount + ambiguousMatchCount
append(countPrint('%sExact or ambiguous matches' % indent,
anyMatchCount, len1, len2))
mismatchCount = (gapMismatchCount + gapGapMismatchCount +
nonGapMismatchCount)
append(countPrint('%sMismatches' % indent, mismatchCount, len1, len2))
conflicts = 'conflicts' if matchAmbiguous else 'conflicts or ambiguities'
append(countPrint('%s Not involving gaps (i.e., %s)' % (indent,
conflicts), nonGapMismatchCount, len1, len2))
append(countPrint('%s Involving a gap in one sequence' % indent,
gapMismatchCount, len1, len2))
append(countPrint('%s Involving a gap in both sequences' % indent,
gapGapMismatchCount, len1, len2))
for read, key in zip((read1, read2), ('read1', 'read2')):
append('%s Id: %s' % (indent, read.id))
length = len(read)
append('%s Length: %d' % (indent, length))
gapCount = len(dnaMatch[key]['gapOffsets'])
append(countPrint('%s Gaps' % indent, gapCount, length))
if gapCount:
append(
'%s Gap locations (1-based): %s' %
(indent,
', '.join(map(lambda offset: str(offset + 1),
sorted(dnaMatch[key]['gapOffsets'])))))
ambiguousCount = len(dnaMatch[key]['ambiguousOffsets'])
append(countPrint('%s Ambiguous' % indent, ambiguousCount, length))
extraCount = dnaMatch[key]['extraCount']
if extraCount:
append(countPrint('%s Extra nucleotides at end' % indent,
extraCount, length))
return '\n'.join(result)