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)