def readAlignments(self, reads):
"""
Read lines of JSON from self._filename, convert them to read alignments
and yield them.
@param reads: An iterable of L{Read} instances, corresponding to the
reads that were given to DIAMOND.
@raise ValueError: If any of the lines in the file cannot be converted
to JSON.
@return: A generator that yields C{dark.alignments.ReadAlignments}
instances.
"""
if self._fp is None:
self._open(self._filename)
reads = iter(reads)
try:
for lineNumber, line in enumerate(self._fp, start=2):
try:
record = loads(line[:-1])
except ValueError as e:
raise ValueError(
'Could not convert line %d of %r to JSON (%s). '
'Line is %r.' %
(lineNumber, self._filename, e, line[:-1]))
else:
while True:
# Iterate through the input reads until we find the
# one that matches this DIAMOND record.
try:
read = next(reads)
except StopIteration:
raise ValueError(
'Read generator failed to yield a read '
'with id \'%s\' as found in record number %d '
'during parsing of DIAMOND output file %r.' %
(record['query'], lineNumber - 1,
self._filename))
else:
if read.id == record['query']:
alignments = self._dictToAlignments(record,
read)
yield ReadAlignments(read, alignments)
break
else:
# This is an input read that received no
# matches from DIAMOND. So it does not
# appear in the DIAMOND output. Emit an
# empty ReadAlignments for it.
yield ReadAlignments(read, [])
finally:
self._fp.close()
self._fp = None
def testNoAlignments(self):
"""
An read alignments must be able to have no alignments.
"""
read = Read('id', 'ACGT')
readAlignments = ReadAlignments(read)
self.assertEqual(0, len(readAlignments))
def testRead(self):
"""
An read alignments must store its read.
"""
read = Read('id', 'ACGT')
readAlignments = ReadAlignments(read)
self.assertEqual(read, readAlignments.read)
def readAlignments(self):
"""
Read lines of JSON from self._filename, convert them to read alignments
and yield them.
@raise ValueError: If any of the lines in the file cannot be converted
to JSON.
@return: A generator that yields C{dark.alignments.ReadAlignments}
instances.
"""
if self._fp is None:
self._open(self._filename)
try:
for lineNumber, line in enumerate(self._fp, start=2):
try:
record = loads(line[:-1])
except ValueError as e:
raise ValueError(
'Could not convert line %d of %r to JSON (%s). '
'Line is %r.' %
(lineNumber, self._filename, e, line[:-1]))
else:
read = AARead(record['queryId'], record['querySequence'])
alignments = jsonDictToAlignments(record, self._database)
yield ReadAlignments(read, alignments)
finally:
self._fp.close()
self._fp = None
def iter(self):
"""
Extract DIAMOND records and yield C{ReadAlignments} instances.
@return: A generator that yields C{ReadAlignments} instances.
"""
# Note that self._reader is already initialized (in __init__) for
# the first input file. This is less clean than it could be, but it
# makes testing easier, since open() is then only called once for
# each input file.
reads = iter(self.reads)
first = True
for filename in self.filenames:
if first:
# The first file has already been opened, in __init__.
first = False
reader = self._reader
else:
reader = self._getReader(filename, self.scoreClass)
for readAlignments in reader.readAlignments(reads):
yield readAlignments
# Any remaining query reads must have had no subject matches.
for read in reads:
yield ReadAlignments(read, [])
def testAlignments(self):
"""
An read alignments must store its alignments.
"""
read = Read('id', 'ACGT')
alignment1 = Alignment(45, 'title1')
alignment2 = Alignment(55, 'title2')
readAlignments = ReadAlignments(read, [alignment1, alignment2])
self.assertEqual([alignment1, alignment2], readAlignments)
def testOneAlignment(self):
"""
When one alignment is present that alignment must be returned by
bestAlignment.
"""
alignment = Alignment(44, 'Seq 1')
alignment.addHsp(HSP(10))
alignment.addHsp(HSP(9))
alignments = [alignment]
hit = ReadAlignments(Read('id1', 'aaa'), alignments)
best = bestAlignment(hit)
self.assertEqual('Seq 1', best.subjectTitle)
self.assertEqual(44, best.subjectLength)
def readAlignments(self, reads):
"""
Read lines of JSON from self._filename, convert them to read alignments
and yield them.
@param reads: An iterable of L{Read} instances, corresponding to the
reads that were given to BLAST.
@raise ValueError: If any of the lines in the file cannot be converted
to JSON.
@return: A generator that yields C{dark.alignments.ReadAlignments}
instances.
"""
if self._fp is None:
self._open(self._filename)
reads = iter(reads)
try:
for lineNumber, line in enumerate(self._fp, start=2):
try:
record = loads(line[:-1])
except ValueError as e:
raise ValueError(
'Could not convert line %d of %r to JSON (%s). '
'Line is %r.' %
(lineNumber, self._filename, e, line[:-1]))
else:
try:
read = next(reads)
except StopIteration:
raise ValueError(
'Read generator failed to yield read number %d '
'during parsing of BLAST file %r.' %
(lineNumber - 1, self._filename))
else:
alignments = self._dictToAlignments(record, read)
yield ReadAlignments(read, alignments)
finally:
self._fp.close()
self._fp = None
def testThreeAlignments(self):
"""
When three alignments are present, the one with the highest first HSP
must be returned by bestAlignment.
"""
alignment1 = Alignment(33, 'Seq 1')
alignment1.addHsp(HSP(10))
alignment1.addHsp(HSP(9))
alignment2 = Alignment(44, 'Seq 2')
alignment2.addHsp(HSP(30))
alignment2.addHsp(HSP(29))
alignment3 = Alignment(55, 'Seq 3')
alignment3.addHsp(HSP(20))
alignment3.addHsp(HSP(19))
alignments = [alignment1, alignment2, alignment3]
hit = ReadAlignments(Read('id1', 'aaa'), alignments)
best = bestAlignment(hit)
self.assertEqual('Seq 2', best.subjectTitle)
self.assertEqual(44, best.subjectLength)
def readAlignments(self, reads):
"""
Read lines of JSON from self._filename, convert them to read alignments
and yield them.
@param reads: An iterable of L{Read} instances, corresponding to the
reads that were given to DIAMOND.
@raise ValueError: If any of the lines in the file cannot be converted
to JSON.
@return: A generator that yields C{dark.alignments.ReadAlignments}
instances.
"""
if self._fp is None:
self._open(self._filename)
reads = iter(reads)
try:
for lineNumber, line in enumerate(self._fp, start=2):
try:
record = loads(line[:-1])
except ValueError as e:
raise ValueError(
'Could not convert line %d of %r to JSON (%s). '
'Line is %r.' %
(lineNumber, self._filename, e, line[:-1]))
else:
recordTitle = record['query']
while True:
# Iterate through the input reads until we find the
# one that matches this DIAMOND record.
try:
read = next(reads)
except StopIteration:
raise ValueError(
'Read generator failed to yield a read '
'with id \'%s\' as found in record number %d '
'during parsing of DIAMOND output file %r.' %
(recordTitle, lineNumber - 1, self._filename))
else:
# Look for an exact read id / subject title match.
# If that doesn't work, allow for the case where
# the JSON record has a truncated query (i.e.,
# read) id. This covers the situation where a tool
# we use (e.g., bwa mem) unconditionally does this
# truncation in the output it writes.
if (read.id == recordTitle
or read.id.split()[0] == recordTitle):
alignments = self._dictToAlignments(
record, read)
yield ReadAlignments(read, alignments)
break
else:
# This is an input read that had no DIAMOND
# matches. So it does not appear in the
# DIAMOND's output. Yield an empty
# ReadAlignments for it.
yield ReadAlignments(read, [])
finally:
self._fp.close()
self._fp = None
