def testOneLineInOneFileFASTQ(self):
"""
If a protein grouper is given one file with one line, its pathogenNames
dict must be as expected, including for a FASTQ file.
"""
fp = StringIO(
'0.77 46.6 48.1 5 6 74 gi|327|X|I44.6 ubiquitin [Lausannevirus]\n')
pg = ProteinGrouper(format_='fastq')
pg.addFile('sample-filename', fp)
self.assertEqual(
{
'Lausannevirus': {
'sample-filename': {
'proteins': {
'gi|327|X|I44.6 ubiquitin': {
'bestScore': 48.1,
'bluePlotFilename': 'out/0.png',
'coverage': 0.77,
'readsFilename': 'out/0.fastq',
'hspCount': 6,
'index': 0,
'medianScore': 46.6,
'outDir': 'out',
'proteinLength': 74,
'proteinName': 'gi|327|X|I44.6 ubiquitin',
'proteinURL': (
'http://www.ncbi.nlm.nih.gov/nuccore/I44'),
'readCount': 5,
},
},
'uniqueReadCount': None,
},
}
},
pg.pathogenNames)
def testOneLineInOneFileWithDifferentAssetDir(self):
"""
If a protein grouper is given a different assetDir name,
the outDir needs to have that same name, as expected.
"""
fp = StringIO(
'0.77 46.6 48.1 5 6 74 gi|327|X|I44.6 ubiquitin [Lausannevirus]\n')
pg = ProteinGrouper(assetDir='differentname')
pg.addFile('sample-filename', fp)
self.assertEqual(
{
'Lausannevirus': {
'sample-filename': {
'proteins': {
'gi|327|X|I44.6 ubiquitin': {
'bestScore': 48.1,
'bluePlotFilename': 'differentname/0.png',
'coverage': 0.77,
'readsFilename': 'differentname/0.fasta',
'hspCount': 6,
'index': 0,
'medianScore': 46.6,
'outDir': 'differentname',
'proteinLength': 74,
'proteinName': 'gi|327|X|I44.6 ubiquitin',
'proteinURL': (
'http://www.ncbi.nlm.nih.gov/nuccore/I44'),
'readCount': 5,
},
},
'uniqueReadCount': None,
},
}
},
pg.pathogenNames)
def testOneLineInOneFile(self):
"""
If a protein grouper is given one file with one line, its virusTitles
dict must be as expected.
"""
fp = StringIO(
'0.77 46.6 48.1 5 6 74 gi|327|X|I44.6 ubiquitin [Lausannevirus]\n')
pg = ProteinGrouper()
pg.addFile('sample-filename', fp)
self.assertEqual(
{
'Lausannevirus': {
'sample-filename': [
{
'bestScore': 48.1,
'bluePlotFilename': 'out/0.png',
'coverage': 0.77,
'fastaFilename': 'out/0.fasta',
'hspCount': 6,
'index': 0,
'medianScore': 46.6,
'outDir': 'out',
'proteinLength': 74,
'proteinTitle': 'gi|327|X|I44.6 ubiquitin',
'proteinURL': (
'http://www.ncbi.nlm.nih.gov/nuccore/I44'),
'readCount': 5,
},
]
}
},
pg.virusTitles)
def testOneLineInEachOfTwoFilesSamePathogen(self):
"""
If a protein grouper is given two files, each with one line from the
same pathogen, its pathogenNames dict must be as expected.
"""
fp1 = StringIO(
'0.63 41.3 44.2 9 9 12 gi|327410| protein 77 [Lausannevirus]\n'
)
fp2 = StringIO(
'0.77 46.6 48.1 5 6 74 gi|327409| ubiquitin [Lausannevirus]\n'
)
pg = ProteinGrouper()
pg.addFile('sample-filename-1', fp1)
pg.addFile('sample-filename-2', fp2)
self.assertEqual(
{
'Lausannevirus': {
'sample-filename-1': {
'proteins': {
'gi|327410| protein 77': {
'bestScore': 44.2,
'bluePlotFilename': 'out/0.png',
'coverage': 0.63,
'readsFilename': 'out/0.fasta',
'hspCount': 9,
'index': 0,
'medianScore': 41.3,
'outDir': 'out',
'proteinLength': 12,
'proteinName': 'gi|327410| protein 77',
'proteinURL': None,
'readCount': 9,
},
},
'uniqueReadCount': None,
},
'sample-filename-2': {
'proteins': {
'gi|327409| ubiquitin': {
'bestScore': 48.1,
'bluePlotFilename': 'out/0.png',
'coverage': 0.77,
'readsFilename': 'out/0.fasta',
'hspCount': 6,
'index': 0,
'medianScore': 46.6,
'outDir': 'out',
'proteinLength': 74,
'proteinName': 'gi|327409| ubiquitin',
'proteinURL': None,
'readCount': 5,
},
},
'uniqueReadCount': None,
},
},
},
pg.pathogenNames)
def testOneLineInEachOfTwoFilesDifferentPathogens(self):
"""
If a protein grouper is given two files in two different directories,
each with one line from the different pathogens, its pathogenNames dict
must be as expected.
"""
fp1 = StringIO(
'0.63 41.3 44.2 9 9 12 gi|327410| protein 77 [Lausannevirus]\n')
fp2 = StringIO(
'0.77 46.6 48.1 5 6 74 gi|327409| ubiquitin [Hepatitis B virus]\n')
pg = ProteinGrouper()
pg.addFile('dir-1/sample-filename-1', fp1)
pg.addFile('dir-2/sample-filename-2', fp2)
self.assertEqual(
{
'Lausannevirus': {
'dir-1/sample-filename-1': {
'proteins': {
'gi|327410| protein 77': {
'bestScore': 44.2,
'bluePlotFilename': 'dir-1/out/0.png',
'coverage': 0.63,
'readsFilename': 'dir-1/out/0.fasta',
'hspCount': 9,
'index': 0,
'medianScore': 41.3,
'outDir': 'dir-1/out',
'proteinLength': 12,
'proteinName': 'gi|327410| protein 77',
'proteinURL': None,
'readCount': 9,
},
},
'uniqueReadCount': None,
},
},
'Hepatitis B virus': {
'dir-2/sample-filename-2': {
'proteins': {
'gi|327409| ubiquitin': {
'bestScore': 48.1,
'bluePlotFilename': 'dir-2/out/0.png',
'coverage': 0.77,
'readsFilename': 'dir-2/out/0.fasta',
'hspCount': 6,
'index': 0,
'medianScore': 46.6,
'outDir': 'dir-2/out',
'proteinLength': 74,
'proteinName': 'gi|327409| ubiquitin',
'proteinURL': None,
'readCount': 5,
},
},
'uniqueReadCount': None,
},
},
}, pg.pathogenNames)
def testTwoLinesInOneFileDifferentPathogens(self):
"""
If a protein grouper is given one file with two lines from different
pathogens, its pathogenNames dict must be as expected.
"""
fp = StringIO(
'0.63 41.3 44.2 9 9 12 gi|327410| protein 77 [Lausannevirus]\n'
'0.77 46.6 48.1 5 6 74 gi|327409| ubiquitin [Hepatitis B virus]\n'
)
pg = ProteinGrouper()
pg.addFile('sample-filename', fp)
self.assertEqual(
{
'Lausannevirus': {
'sample-filename': {
'proteins': {
'gi|327410| protein 77': {
'bestScore': 44.2,
'bluePlotFilename': 'out/0.png',
'coverage': 0.63,
'readsFilename': 'out/0.fasta',
'hspCount': 9,
'index': 0,
'medianScore': 41.3,
'outDir': 'out',
'proteinLength': 12,
'proteinName': 'gi|327410| protein 77',
'proteinURL': None,
'readCount': 9,
},
},
'uniqueReadCount': None,
},
},
'Hepatitis B virus': {
'sample-filename': {
'proteins': {
'gi|327409| ubiquitin': {
'bestScore': 48.1,
'bluePlotFilename': 'out/1.png',
'coverage': 0.77,
'readsFilename': 'out/1.fasta',
'hspCount': 6,
'index': 1,
'medianScore': 46.6,
'outDir': 'out',
'proteinLength': 74,
'proteinName': 'gi|327409| ubiquitin',
'proteinURL': None,
'readCount': 5,
},
},
'uniqueReadCount': None,
},
},
},
pg.pathogenNames)
def testOneLineInOneFileTitle(self):
"""
If a protein grouper is given one file with one line, its _title method
must return the expected string.
"""
fp = StringIO(
'0.77 46.6 48.1 5 6 74 gi|327|X|I44.6 ubiquitin [Lausannevirus]\n')
pg = ProteinGrouper()
pg.addFile('sample-filename', fp)
self.assertEqual('1 virus found in 1 sample', pg._title())
def testOneLineInOneFileTitle(self):
"""
If a protein grouper is given one file with one line, its _title method
must return the expected string.
"""
fp = StringIO(
'0.77 46.6 48.1 5 6 74 gi|327|X|I44.6 ubiquitin [Lausannevirus]\n')
pg = ProteinGrouper()
pg.addFile('sample-filename', fp)
self.assertEqual('1 virus found in 1 sample', pg._title())
def testOneLineInEachOfTwoFilesDifferentViruses(self):
"""
If a protein grouper is given two files in two different directories,
each with one line from the different viruses, its virusTitles dict
must be as expected.
"""
fp1 = StringIO(
'0.63 41.3 44.2 9 9 12 gi|327410| protein 77 [Lausannevirus]\n'
)
fp2 = StringIO(
'0.77 46.6 48.1 5 6 74 gi|327409| ubiquitin [Hepatitis B virus]\n'
)
pg = ProteinGrouper()
pg.addFile('dir-1/sample-filename-1', fp1)
pg.addFile('dir-2/sample-filename-2', fp2)
self.assertEqual(
{
'Lausannevirus': {
'dir-1/sample-filename-1': [
{
'bestScore': 44.2,
'bluePlotFilename': 'dir-1/out/0.png',
'coverage': 0.63,
'fastaFilename': 'dir-1/out/0.fasta',
'hspCount': 9,
'index': 0,
'medianScore': 41.3,
'outDir': 'dir-1/out',
'proteinLength': 12,
'proteinTitle': 'gi|327410| protein 77',
'proteinURL': None,
'readCount': 9,
},
],
},
'Hepatitis B virus': {
'dir-2/sample-filename-2': [
{
'bestScore': 48.1,
'bluePlotFilename': 'dir-2/out/0.png',
'coverage': 0.77,
'fastaFilename': 'dir-2/out/0.fasta',
'hspCount': 6,
'index': 0,
'medianScore': 46.6,
'outDir': 'dir-2/out',
'proteinLength': 74,
'proteinTitle': 'gi|327409| ubiquitin',
'proteinURL': None,
'readCount': 5,
},
],
},
},
pg.virusTitles)
def testTwoLinesInOneFileDifferentPathogens(self):
"""
If a protein grouper is given one file with two lines from different
pathogens, its pathogenNames dict must be as expected.
"""
fp = StringIO(
'0.63 41.3 44.2 9 9 12 gi|327410| protein 77 [Lausannevirus]\n'
'0.77 46.6 48.1 5 6 74 gi|327409| ubiquitin [Hepatitis B virus]\n')
pg = ProteinGrouper()
pg.addFile('sample-filename', fp)
self.assertEqual(
{
'Lausannevirus': {
'sample-filename': {
'proteins': {
'gi|327410| protein 77': {
'bestScore': 44.2,
'bluePlotFilename': 'out/0.png',
'coverage': 0.63,
'readsFilename': 'out/0.fasta',
'hspCount': 9,
'index': 0,
'medianScore': 41.3,
'outDir': 'out',
'proteinLength': 12,
'proteinName': 'gi|327410| protein 77',
'proteinURL': None,
'readCount': 9,
},
},
'uniqueReadCount': None,
},
},
'Hepatitis B virus': {
'sample-filename': {
'proteins': {
'gi|327409| ubiquitin': {
'bestScore': 48.1,
'bluePlotFilename': 'out/1.png',
'coverage': 0.77,
'readsFilename': 'out/1.fasta',
'hspCount': 6,
'index': 1,
'medianScore': 46.6,
'outDir': 'out',
'proteinLength': 74,
'proteinName': 'gi|327409| ubiquitin',
'proteinURL': None,
'readCount': 5,
},
},
'uniqueReadCount': None,
},
},
}, pg.pathogenNames)
def testTwoLinesInOneFileTitle(self):
"""
If a protein grouper is given one file with two protein lines, each
from a different virus, its _title method must return the expected
string.
"""
fp = StringIO(
'0.77 46.6 48.1 5 6 74 gi|327|X|I44.6 ubiquitin [Lausannevirus]\n'
'0.77 46.6 48.1 5 6 74 gi|327|X|I44.6 ubiquitin [X Virus]\n')
pg = ProteinGrouper()
pg.addFile('sample-filename', fp)
self.assertEqual('2 viruses found in 1 sample', pg._title())
def testOneLineInEachOfTwoFilesDifferentVirusesTitle(self):
"""
If a protein grouper is given two files, each with one line from
different viruses, its _title method must return the expected string.
"""
fp1 = StringIO(
'0.63 41.3 44.2 9 9 12 gi|327410| protein 77 [Lausannevirus]\n')
fp2 = StringIO('0.77 46.6 48.1 5 6 74 gi|327409| ubiquitin [HBV]\n')
pg = ProteinGrouper()
pg.addFile('sample-filename-1', fp1)
pg.addFile('sample-filename-2', fp2)
self.assertEqual('2 viruses found in 2 samples', pg._title())
def testIdenticalReadsRemoved(self):
"""
If two proteins in the same pathogen are matched by the same read, the
de-duplicated FASTA for the pathogen must have only one copy of the
duplicated read.
"""
class Open(object):
def __init__(self, test, manager):
self.test = test
self.manager = manager
self.expectedFilenames = {
'out/0.fasta', 'out/1.fasta',
'out/pathogen-0-sample-0.fasta'
}
def sideEffect(self, filename, *args, **kwargs):
try:
self.expectedFilenames.remove(filename)
except KeyError:
self.test.fail(
'Open called with unexpected filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
else:
if filename == 'out/0.fasta':
return File(['>id1\n', 'ACTG\n'])
elif filename == 'out/1.fasta':
return File(['>id1\n', 'ACTG\n', '>id2\n', 'CAGT\n'])
else:
return self.manager
fp = StringIO(
'0.63 41.3 44.2 9 9 12 gi|327410| protein 77 [Lausannevirus]\n'
'0.77 46.6 48.1 5 6 74 gi|327409| ubiquitin [Lausannevirus]\n')
fastaIO = StringIO()
@contextmanager
def manager():
yield fastaIO
pg = ProteinGrouper()
pg.addFile('filename-1', fp)
pathogenSampleFiles = PathogenSampleFiles(pg)
opener = Open(self, manager())
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = opener.sideEffect
filename = pathogenSampleFiles.add('Lausannevirus', 'filename-1')
self.assertEqual('out/pathogen-0-sample-0.fasta', filename)
self.assertEqual('>id1\nACTG\n>id2\nCAGT\n', fastaIO.getvalue())
# Make sure all expected filenames were seen by the mocked open.
self.assertEqual(set(), opener.expectedFilenames)
def testOpenNotCalledOnRepeatedCall(self):
"""
If a repeated call to pathogenSampleFiles.add is made with the same
arguments, no file should be read because the original result value is
cached.
"""
class Open(object):
def __init__(self, test, manager):
self.test = test
self.manager = manager
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count == 0:
self.test.assertEqual('out/0.fasta', filename)
self.count += 1
return File(['>id1\n', 'ACTG\n'])
elif self.count == 1:
self.test.assertEqual('out/pathogen-0-sample-0.fasta',
filename)
self.count += 1
return self.manager
else:
self.test.fail(
'We are only supposed to be called twice. '
'Filename: %r, Args: %r, Keyword args: %r.' %
(filename, args, kwargs))
fp = StringIO(
'0.63 41.3 44.2 9 9 12 gi|327410| protein 77 [Lausannevirus]\n'
)
fastaIO = StringIO()
@contextmanager
def manager():
yield fastaIO
pg = ProteinGrouper()
pg.addFile('filename-1', fp)
pathogenSampleFiles = PathogenSampleFiles(pg)
sideEffect = Open(self, manager()).sideEffect
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
filename = pathogenSampleFiles.add('Lausannevirus', 'filename-1')
self.assertEqual('out/pathogen-0-sample-0.fasta', filename)
self.assertEqual('>id1\nACTG\n', fastaIO.getvalue())
# Repeated call. The side effect open will fail if open is
# called at this point.
filename = pathogenSampleFiles.add('Lausannevirus', 'filename-1')
self.assertEqual('out/pathogen-0-sample-0.fasta', filename)
def testDuplicatePathogenProteinSample(self):
"""
If a protein grouper is given duplicate information for a
pathogen/protein/sample combination it must raise a ValueError.
"""
fp = StringIO(
'0.77 46.6 48.1 5 6 74 gi|327|X|I44.6 ubiquitin [Lausannevirus]\n')
pg = ProteinGrouper()
pg.addFile('sample', fp)
fp.seek(0)
error = ("^Protein 'gi\|327\|X\|I44.6 ubiquitin' already seen for "
"pathogen 'Lausannevirus' sample 'sample'\.$")
assertRaisesRegex(self, ValueError, error, pg.addFile, 'sample', fp)
def testTwoLinesInOneFileTitle(self):
"""
If a protein grouper is given one file with two protein lines, each
from a different virus, its _title method must return the expected
string.
"""
fp = StringIO(
'0.77 46.6 48.1 5 6 74 gi|327|X|I44.6 ubiquitin [Lausannevirus]\n'
'0.77 46.6 48.1 5 6 74 gi|327|X|I44.6 ubiquitin [X Virus]\n'
)
pg = ProteinGrouper()
pg.addFile('sample-filename', fp)
self.assertEqual('2 viruses found in 1 sample', pg._title())
def testDuplicatePathogenProteinSample(self):
"""
If a protein grouper is given duplicate information for a
pathogen/protein/sample combination it must raise a ValueError.
"""
fp = StringIO(
'0.77 46.6 48.1 5 6 74 gi|327|X|I44.6 ubiquitin [Lausannevirus]\n')
pg = ProteinGrouper()
pg.addFile('sample', fp)
fp.seek(0)
error = ("^Protein 'gi\\|327\\|X\\|I44.6 ubiquitin' already seen for "
"pathogen 'Lausannevirus' sample 'sample'\\.$")
assertRaisesRegex(self, ValueError, error, pg.addFile, 'sample', fp)
def testOpenNotCalledOnRepeatedCall(self):
"""
If a repeated call to pathogenSampleFiles.add is made with the same
arguments, no file should be read because the original result value is
cached.
"""
class Open(object):
def __init__(self, test, manager):
self.test = test
self.manager = manager
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count == 0:
self.test.assertEqual('out/0.fasta', filename)
self.count += 1
return File(['>id1\n', 'ACTG\n'])
elif self.count == 1:
self.test.assertEqual('out/pathogen-0-sample-0.fasta',
filename)
self.count += 1
return self.manager
else:
self.test.fail(
'We are only supposed to be called twice. '
'Filename: %r, Args: %r, Keyword args: %r.' %
(filename, args, kwargs))
fp = StringIO(
'0.63 41.3 44.2 9 9 12 gi|327410| protein 77 [Lausannevirus]\n')
fastaIO = StringIO()
@contextmanager
def manager():
yield fastaIO
pg = ProteinGrouper()
pg.addFile('filename-1', fp)
pathogenSampleFiles = PathogenSampleFiles(pg)
sideEffect = Open(self, manager()).sideEffect
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
filename = pathogenSampleFiles.add('Lausannevirus', 'filename-1')
self.assertEqual('out/pathogen-0-sample-0.fasta', filename)
self.assertEqual('>id1\nACTG\n', fastaIO.getvalue())
# Repeated call. The side effect open will fail if open is
# called at this point.
filename = pathogenSampleFiles.add('Lausannevirus', 'filename-1')
self.assertEqual('out/pathogen-0-sample-0.fasta', filename)
def testIdenticalReadsRemoved(self):
"""
If two proteins in the same pathogen are matched by the same read, the
de-duplicated FASTA for the pathogen must have only one copy of the
duplicated read.
"""
class Open(object):
def __init__(self, test, manager):
self.test = test
self.manager = manager
self.expectedFilenames = {'out/0.fasta', 'out/1.fasta',
'out/pathogen-0-sample-0.fasta'}
def sideEffect(self, filename, *args, **kwargs):
try:
self.expectedFilenames.remove(filename)
except KeyError:
self.test.fail(
'Open called with unexpected filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
else:
if filename == 'out/0.fasta':
return File(['>id1\n', 'ACTG\n'])
elif filename == 'out/1.fasta':
return File(['>id1\n', 'ACTG\n', '>id2\n', 'CAGT\n'])
else:
return self.manager
fp = StringIO(
'0.63 41.3 44.2 9 9 12 gi|327410| protein 77 [Lausannevirus]\n'
'0.77 46.6 48.1 5 6 74 gi|327409| ubiquitin [Lausannevirus]\n'
)
fastaIO = StringIO()
@contextmanager
def manager():
yield fastaIO
pg = ProteinGrouper()
pg.addFile('filename-1', fp)
pathogenSampleFiles = PathogenSampleFiles(pg)
opener = Open(self, manager())
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = opener.sideEffect
filename = pathogenSampleFiles.add('Lausannevirus', 'filename-1')
self.assertEqual('out/pathogen-0-sample-0.fasta', filename)
self.assertEqual('>id1\nACTG\n>id2\nCAGT\n', fastaIO.getvalue())
# Make sure all expected filenames were seen by the mocked open.
self.assertEqual(set(), opener.expectedFilenames)
def testReadLengthsAdded(self):
"""
If saveReadLengths is True for a ProteinGrouper, read lengths must be
saved for each protein.
"""
class Open(object):
def __init__(self, test, manager):
self.test = test
self.manager = manager
self.expectedFilenames = {
'out/0.fasta', 'out/1.fasta',
'out/pathogen-0-sample-0.fasta'
}
def sideEffect(self, filename, *args, **kwargs):
if filename in self.expectedFilenames:
if filename == 'out/0.fasta':
return File(['>id1\n', 'ACTG\n'])
elif filename == 'out/1.fasta':
return File(['>id2\n', 'AC\n', '>id3\n', 'CAGTTTT\n'])
else:
return self.manager
else:
self.test.fail(
'Open called with unexpected filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
fp = StringIO(
'0.63 41.3 44.2 9 9 12 gi|327410| protein 77 [Lausannevirus]\n'
'0.77 46.6 48.1 5 6 74 gi|327409| ubiquitin [Lausannevirus]\n')
fastaIO = StringIO()
@contextmanager
def manager():
yield fastaIO
opener = Open(self, manager())
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = opener.sideEffect
pg = ProteinGrouper(saveReadLengths=True)
pg.addFile('filename-1', fp)
pathogenSampleFiles = PathogenSampleFiles(pg)
pathogenSampleFiles.add('Lausannevirus', 'filename-1')
# Read lengths must be saved correctly.
proteins = pg.pathogenNames['Lausannevirus']['filename-1']['proteins']
self.assertEqual((4, ),
proteins['gi|327410| protein 77']['readLengths'])
self.assertEqual((2, 7),
proteins['gi|327409| ubiquitin']['readLengths'])
def testReadLengthsAdded(self):
"""
If saveReadLengths is True for a ProteinGrouper, read lengths must be
saved for each protein.
"""
class Open(object):
def __init__(self, test, manager):
self.test = test
self.manager = manager
self.expectedFilenames = {'out/0.fasta', 'out/1.fasta',
'out/pathogen-0-sample-0.fasta'}
def sideEffect(self, filename, *args, **kwargs):
if filename in self.expectedFilenames:
if filename == 'out/0.fasta':
return File(['>id1\n', 'ACTG\n'])
elif filename == 'out/1.fasta':
return File(['>id2\n', 'AC\n', '>id3\n', 'CAGTTTT\n'])
else:
return self.manager
else:
self.test.fail(
'Open called with unexpected filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
fp = StringIO(
'0.63 41.3 44.2 9 9 12 gi|327410| protein 77 [Lausannevirus]\n'
'0.77 46.6 48.1 5 6 74 gi|327409| ubiquitin [Lausannevirus]\n'
)
fastaIO = StringIO()
@contextmanager
def manager():
yield fastaIO
opener = Open(self, manager())
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = opener.sideEffect
pg = ProteinGrouper(saveReadLengths=True)
pg.addFile('filename-1', fp)
pathogenSampleFiles = PathogenSampleFiles(pg)
pathogenSampleFiles.add('Lausannevirus', 'filename-1')
# Read lengths must be saved correctly.
proteins = pg.pathogenNames['Lausannevirus']['filename-1']['proteins']
self.assertEqual((4,),
proteins['gi|327410| protein 77']['readLengths'])
self.assertEqual((2, 7),
proteins['gi|327409| ubiquitin']['readLengths'])
def testOneLineInEachOfTwoFilesDifferentVirusesTitle(self):
"""
If a protein grouper is given two files, each with one line from
different viruses, its _title method must return the expected string.
"""
fp1 = StringIO(
'0.63 41.3 44.2 9 9 12 gi|327410| protein 77 [Lausannevirus]\n'
)
fp2 = StringIO(
'0.77 46.6 48.1 5 6 74 gi|327409| ubiquitin [HBV]\n'
)
pg = ProteinGrouper()
pg.addFile('sample-filename-1', fp1)
pg.addFile('sample-filename-2', fp2)
self.assertEqual('2 viruses found in 2 samples', pg._title())
def testOneLineInOneFileToStr(self):
"""
If a protein grouper is given one file with one line, its toStr method
must produce the expected result.
"""
fp = StringIO('0.77 46.6 48.1 5 6 74 gi|32|X|I4 protein X [HBV]\n')
pg = ProteinGrouper()
pg.addFile('sample-filename', fp)
self.assertEqual(
'1 virus found in 1 sample\n'
'\n'
'HBV (in 1 sample)\n'
' sample-filename (1 protein, 5 reads)\n'
' 0.77\t46.60\t48.10\t 5\t 6\t 0\tgi|32|X|I4 protein X\n',
pg.toStr())
def testOneLineInEachOfTwoFilesSamePathogenTitle(self):
"""
If a protein grouper is given two files, each with one line from the
same pathogen, its _title method must return the expected string.
"""
fp1 = StringIO(
'0.63 41.3 44.2 9 9 12 gi|327410| protein 77 [Lausannevirus]\n')
fp2 = StringIO(
'0.77 46.6 48.1 5 6 74 gi|327409| ubiquitin [Lausannevirus]\n')
pg = ProteinGrouper()
pg.addFile('sample-filename-1', fp1)
pg.addFile('sample-filename-2', fp2)
self.assertEqual(
'Overall, proteins from 1 pathogen were found in 2 samples.',
pg._title())
def testOneLineInOneFileToStr(self):
"""
If a protein grouper is given one file with one line, its toStr method
must produce the expected result.
"""
fp = StringIO(
'0.77 46.6 48.1 5 6 74 gi|32|X|I4 protein X [HBV]\n')
pg = ProteinGrouper()
pg.addFile('sample-filename', fp)
self.assertEqual(
'1 virus found in 1 sample\n'
'\n'
'HBV (in 1 sample)\n'
' sample-filename (1 protein, 5 reads)\n'
' 0.77\t46.60\t48.10\t 5\t 6\t 0\tgi|32|X|I4 protein X\n',
pg.toStr())
def testTwoLinesInOneFileSameVirus(self):
"""
If a protein grouper is given one file with two lines from the same
virus, its virusTitles dict must be as expected.
"""
fp = StringIO(
'0.63 41.3 44.2 9 9 12 gi|327410| protein 77 [Lausannevirus]\n'
'0.77 46.6 48.1 5 6 74 gi|327409| ubiquitin [Lausannevirus]\n'
)
pg = ProteinGrouper()
pg.addFile('sample-filename', fp)
self.assertEqual(
{
'Lausannevirus': {
'sample-filename': [
{
'bestScore': 44.2,
'bluePlotFilename': 'out/0.png',
'coverage': 0.63,
'fastaFilename': 'out/0.fasta',
'hspCount': 9,
'index': 0,
'medianScore': 41.3,
'outDir': 'out',
'proteinLength': 12,
'proteinTitle': 'gi|327410| protein 77',
'proteinURL': None,
'readCount': 9,
},
{
'bestScore': 48.1,
'bluePlotFilename': 'out/1.png',
'coverage': 0.77,
'fastaFilename': 'out/1.fasta',
'hspCount': 6,
'index': 1,
'medianScore': 46.6,
'outDir': 'out',
'proteinLength': 74,
'proteinTitle': 'gi|327409| ubiquitin',
'proteinURL': None,
'readCount': 5,
},
],
},
},
pg.virusTitles)
def testOneLineInEachOfTwoFilesSameVirus(self):
"""
If a protein grouper is given two files, each with one line from the
same virus, its virusTitles dict must be as expected.
"""
fp1 = StringIO(
'0.63 41.3 44.2 9 9 12 gi|327410| protein 77 [Lausannevirus]\n')
fp2 = StringIO(
'0.77 46.6 48.1 5 6 74 gi|327409| ubiquitin [Lausannevirus]\n')
pg = ProteinGrouper()
pg.addFile('sample-filename-1', fp1)
pg.addFile('sample-filename-2', fp2)
self.assertEqual(
{
'Lausannevirus': {
'sample-filename-1': [
{
'bestScore': 44.2,
'bluePlotFilename': 'out/0.png',
'coverage': 0.63,
'fastaFilename': 'out/0.fasta',
'hspCount': 9,
'index': 0,
'medianScore': 41.3,
'proteinLength': 12,
'proteinTitle': 'gi|327410| protein 77',
'proteinURL': None,
'readCount': 9,
},
],
'sample-filename-2': [
{
'bestScore': 48.1,
'bluePlotFilename': 'out/0.png',
'coverage': 0.77,
'fastaFilename': 'out/0.fasta',
'hspCount': 6,
'index': 0,
'medianScore': 46.6,
'proteinLength': 74,
'proteinTitle': 'gi|327409| ubiquitin',
'proteinURL': None,
'readCount': 5,
},
],
},
}, pg.virusTitles)
def testOneLineInEachOfTwoFilesSamePathogenTitle(self):
"""
If a protein grouper is given two files, each with one line from the
same pathogen, its _title method must return the expected string.
"""
fp1 = StringIO(
'0.63 41.3 44.2 9 9 12 gi|327410| protein 77 [Lausannevirus]\n'
)
fp2 = StringIO(
'0.77 46.6 48.1 5 6 74 gi|327409| ubiquitin [Lausannevirus]\n'
)
pg = ProteinGrouper()
pg.addFile('sample-filename-1', fp1)
pg.addFile('sample-filename-2', fp2)
self.assertEqual(
'Overall, proteins from 1 pathogen were found in 2 samples.',
pg._title())
def testOneLineInOneFileFASTQ(self):
"""
If a protein grouper is given one file with one line, its pathogenNames
dict must be as expected, including for a FASTQ file.
"""
fp = StringIO(
'0.77 46.6 48.1 5 6 74 gi|327|X|I44.6 ubiquitin [Lausannevirus]\n')
pg = ProteinGrouper(format_='fastq')
pg.addFile('sample-filename', fp)
self.assertEqual(
{
'Lausannevirus': {
'sample-filename': {
'proteins': {
'gi|327|X|I44.6 ubiquitin': {
'bestScore':
48.1,
'bluePlotFilename':
'out/0.png',
'coverage':
0.77,
'readsFilename':
'out/0.fastq',
'hspCount':
6,
'index':
0,
'medianScore':
46.6,
'outDir':
'out',
'proteinLength':
74,
'proteinName':
'gi|327|X|I44.6 ubiquitin',
'proteinURL':
('http://www.ncbi.nlm.nih.gov/nuccore/I44'),
'readCount':
5,
},
},
'uniqueReadCount': None,
},
}
}, pg.pathogenNames)
def testOneLineInOneFileWithDifferentAssetDir(self):
"""
If a protein grouper is given a different assetDir name,
the outDir needs to have that same name, as expected.
"""
fp = StringIO(
'0.77 46.6 48.1 5 6 74 gi|327|X|I44.6 ubiquitin [Lausannevirus]\n')
pg = ProteinGrouper(assetDir='differentname')
pg.addFile('sample-filename', fp)
self.assertEqual(
{
'Lausannevirus': {
'sample-filename': {
'proteins': {
'gi|327|X|I44.6 ubiquitin': {
'bestScore':
48.1,
'bluePlotFilename':
'differentname/0.png',
'coverage':
0.77,
'readsFilename':
'differentname/0.fasta',
'hspCount':
6,
'index':
0,
'medianScore':
46.6,
'outDir':
'differentname',
'proteinLength':
74,
'proteinName':
'gi|327|X|I44.6 ubiquitin',
'proteinURL':
('http://www.ncbi.nlm.nih.gov/nuccore/I44'),
'readCount':
5,
},
},
'uniqueReadCount': None,
},
}
}, pg.pathogenNames)
def testOneLineInOneFile(self):
"""
If a protein grouper is given one file with one line, its virusTitles
dict must be as expected.
"""
fp = StringIO(
'0.77 46.6 48.1 5 6 74 gi|327|X|I44.6 ubiquitin [Lausannevirus]\n')
pg = ProteinGrouper()
pg.addFile('sample-filename', fp)
self.assertEqual(
{
'Lausannevirus': {
'sample-filename': [
{
'bestScore':
48.1,
'bluePlotFilename':
'out/0.png',
'coverage':
0.77,
'fastaFilename':
'out/0.fasta',
'hspCount':
6,
'index':
0,
'medianScore':
46.6,
'proteinLength':
74,
'proteinTitle':
'gi|327|X|I44.6 ubiquitin',
'proteinURL':
('http://www.ncbi.nlm.nih.gov/nuccore/I44'),
'readCount':
5,
},
]
}
}, pg.virusTitles)
def testMaxProteinFraction(self):
"""
The maxProteinFraction method must return the correct values.
"""
class SideEffect(object):
def __init__(self, test):
self.test = test
self.count = 0
def sideEffect(self, filename, **kwargs):
if self.count == 0:
self.test.assertEqual('proteins.fasta', filename)
self.count += 1
return File(['>protein 1 [pathogen 1]\n',
'ACTG\n',
'>protein 2 [pathogen 1]\n',
'AA\n',
'>protein 3 [pathogen 1]\n',
'AA\n',
'>protein 4 [pathogen 1]\n',
'AA\n',
'>no pathogen name here\n',
'AA\n',
'>protein 5 [pathogen 2]\n',
'AA\n'])
else:
self.test.fail('We are only supposed to be called once!')
sideEffect = SideEffect(self)
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = sideEffect.sideEffect
pg = ProteinGrouper(proteinFastaFilenames=['proteins.fasta'])
self.assertEqual(1, sideEffect.count)
fp = StringIO(
'0.77 46.6 48.1 5 6 74 gi|32|X|I4 protein 1 [pathogen 1]\n'
'0.77 46.6 48.1 5 6 74 gi|32|X|I4 protein 5 [pathogen 2]\n'
)
pg.addFile('sample-1', fp)
fp = StringIO(
'0.77 46.6 48.1 5 6 74 gi|32|X|I4 protein 2 [pathogen 1]\n'
'0.77 46.6 48.1 5 6 74 gi|32|X|I4 protein 3 [pathogen 1]\n'
)
pg.addFile('sample-1', fp)
fp = StringIO(
'0.77 46.6 48.1 5 6 74 gi|32|X|I4 protein 1 [pathogen 1]\n'
'0.77 46.6 48.1 5 6 74 gi|32|X|I4 protein 2 [pathogen 1]\n'
)
pg.addFile('sample-2', fp)
self.assertEqual(0.75, pg.maxProteinFraction('pathogen 1'))
self.assertEqual(1.0, pg.maxProteinFraction('pathogen 2'))
# encountered in https://github.com/acorg/dark-matter/issues/453
proteinFastaFilenames = list(chain.from_iterable(
args.proteinFastaFilename))
else:
proteinFastaFilenames = None
grouper = ProteinGrouper(assetDir=args.assetDir,
sampleName=args.sampleName,
sampleNameRegex=args.sampleNameRegex,
format_=args.format,
proteinFastaFilenames=proteinFastaFilenames,
saveReadLengths=args.showReadLengths)
if args.filenames:
filenames = args.filenames
else:
filenames = (line[:-1] for line in sys.stdin)
for filename in filenames:
with open(filename) as fp:
grouper.addFile(filename, fp)
if args.html:
print(grouper.toHTML(args.pathogenPanelFilename,
minProteinFraction=args.minProteinFraction,
pathogenType=args.pathogenType,
sampleIndexFilename=args.sampleIndexFilename,
pathogenIndexFilename=args.pathogenIndexFilename))
else:
print(grouper.toStr())
# use it and you also can't be hit by the subtle problem
# encountered in https://github.com/acorg/dark-matter/issues/453
proteinFastaFilenames = list(chain.from_iterable(
args.proteinFastaFilename))
else:
proteinFastaFilenames = None
grouper = ProteinGrouper(assetDir=args.assetDir,
sampleNameRegex=args.sampleNameRegex,
format_=args.format,
proteinFastaFilenames=proteinFastaFilenames,
saveReadLengths=args.showReadLengths)
if args.filenames:
filenames = args.filenames
else:
filenames = (line[:-1] for line in sys.stdin)
for filename in filenames:
with open(filename) as fp:
grouper.addFile(filename, fp)
if args.html:
print(grouper.toHTML(args.pathogenPanelFilename,
minProteinFraction=args.minProteinFraction,
pathogenType=args.pathogenType,
sampleIndexFilename=args.sampleIndexFilename,
pathogenIndexFilename=args.pathogenIndexFilename))
else:
print(grouper.toStr())
def testProteinsSavedCorrectly(self):
"""
Information about proteins must be saved correctly in the
ProteinGrouper for a given pathogen/sample combination.
"""
class Open(object):
def __init__(self, test, manager):
self.test = test
self.manager = manager
self.expectedFilenames = {
'out/0.fasta', 'out/1.fasta',
'out/pathogen-0-sample-0.fasta'
}
def sideEffect(self, filename, *args, **kwargs):
if filename in self.expectedFilenames:
if filename == 'out/0.fasta':
return File(['>id1\n', 'ACTG\n'])
elif filename == 'out/1.fasta':
return File(['>id2\n', 'AC\n', '>id3\n', 'CAGTTTT\n'])
else:
return self.manager
else:
self.test.fail(
'Open called with unexpected filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
fp = StringIO(
'0.63 41.3 44.2 9 9 12 gi|327410| protein 77 [Lausannevirus]\n'
'0.77 46.6 48.1 5 6 74 gi|327409| ubiquitin [Lausannevirus]\n')
fastaIO = StringIO()
@contextmanager
def manager():
yield fastaIO
opener = Open(self, manager())
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = opener.sideEffect
pg = ProteinGrouper()
pg.addFile('filename-1', fp)
pathogenSampleFiles = PathogenSampleFiles(pg)
pathogenSampleFiles.add('Lausannevirus', 'filename-1')
self.assertEqual(
{
'proteins': {
'gi|327409| ubiquitin': {
'bestScore': 48.1,
'bluePlotFilename': 'out/1.png',
'coverage': 0.77,
'hspCount': 6,
'index': 1,
'medianScore': 46.6,
'outDir': 'out',
'proteinLength': 74,
'proteinName': 'gi|327409| ubiquitin',
'proteinURL': None,
'readCount': 5,
'readsFilename': 'out/1.fasta',
},
'gi|327410| protein 77': {
'bestScore': 44.2,
'bluePlotFilename': 'out/0.png',
'coverage': 0.63,
'hspCount': 9,
'index': 0,
'medianScore': 41.3,
'outDir': 'out',
'proteinLength': 12,
'proteinName': 'gi|327410| protein 77',
'proteinURL': None,
'readCount': 9,
'readsFilename': 'out/0.fasta',
}
},
'uniqueReadCount': 3,
}, pg.pathogenNames['Lausannevirus']['filename-1'])
def testProteinsSavedCorrectly(self):
"""
Information about proteins must be saved correctly in the
ProteinGrouper for a given pathogen/sample combination.
"""
class Open(object):
def __init__(self, test, manager):
self.test = test
self.manager = manager
self.expectedFilenames = {'out/0.fasta', 'out/1.fasta',
'out/pathogen-0-sample-0.fasta'}
def sideEffect(self, filename, *args, **kwargs):
if filename in self.expectedFilenames:
if filename == 'out/0.fasta':
return File(['>id1\n', 'ACTG\n'])
elif filename == 'out/1.fasta':
return File(['>id2\n', 'AC\n', '>id3\n', 'CAGTTTT\n'])
else:
return self.manager
else:
self.test.fail(
'Open called with unexpected filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
fp = StringIO(
'0.63 41.3 44.2 9 9 12 gi|327410| protein 77 [Lausannevirus]\n'
'0.77 46.6 48.1 5 6 74 gi|327409| ubiquitin [Lausannevirus]\n'
)
fastaIO = StringIO()
@contextmanager
def manager():
yield fastaIO
opener = Open(self, manager())
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = opener.sideEffect
pg = ProteinGrouper()
pg.addFile('filename-1', fp)
pathogenSampleFiles = PathogenSampleFiles(pg)
pathogenSampleFiles.add('Lausannevirus', 'filename-1')
self.assertEqual(
{
'proteins': {
'gi|327409| ubiquitin': {
'bestScore': 48.1,
'bluePlotFilename': 'out/1.png',
'coverage': 0.77,
'hspCount': 6,
'index': 1,
'medianScore': 46.6,
'outDir': 'out',
'proteinLength': 74,
'proteinName': 'gi|327409| ubiquitin',
'proteinURL': None,
'readCount': 5,
'readsFilename': 'out/1.fasta',
},
'gi|327410| protein 77': {
'bestScore': 44.2,
'bluePlotFilename': 'out/0.png',
'coverage': 0.63,
'hspCount': 9,
'index': 0,
'medianScore': 41.3,
'outDir': 'out',
'proteinLength': 12,
'proteinName': 'gi|327410| protein 77',
'proteinURL': None,
'readCount': 9,
'readsFilename': 'out/0.fasta',
}
},
'uniqueReadCount': 3,
},
pg.pathogenNames['Lausannevirus']['filename-1'])