本文整理汇总了Python中dark.proteins.ProteinGrouper.addFile方法的典型用法代码示例。如果您正苦于以下问题：Python ProteinGrouper.addFile方法的具体用法？Python ProteinGrouper.addFile怎么用？Python ProteinGrouper.addFile使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类dark.proteins.ProteinGrouper的用法示例。
在下文中一共展示了ProteinGrouper.addFile方法的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: testOneLineInOneFile
# 需要导入模块: from dark.proteins import ProteinGrouper [as 别名]
# 或者: from dark.proteins.ProteinGrouper import addFile [as 别名]
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)示例2: testOneLineInOneFileFASTQ
# 需要导入模块: from dark.proteins import ProteinGrouper [as 别名]
# 或者: from dark.proteins.ProteinGrouper import addFile [as 别名]
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)示例3: testOneLineInOneFileWithDifferentAssetDir
# 需要导入模块: from dark.proteins import ProteinGrouper [as 别名]
# 或者: from dark.proteins.ProteinGrouper import addFile [as 别名]
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)示例4: testOneLineInEachOfTwoFilesSamePathogen
# 需要导入模块: from dark.proteins import ProteinGrouper [as 别名]
# 或者: from dark.proteins.ProteinGrouper import addFile [as 别名]
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)示例5: testTwoLinesInOneFileDifferentPathogens
# 需要导入模块: from dark.proteins import ProteinGrouper [as 别名]
# 或者: from dark.proteins.ProteinGrouper import addFile [as 别名]
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)示例6: testOneLineInOneFileTitle
# 需要导入模块: from dark.proteins import ProteinGrouper [as 别名]
# 或者: from dark.proteins.ProteinGrouper import addFile [as 别名]
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())示例7: testOneLineInEachOfTwoFilesDifferentViruses
# 需要导入模块: from dark.proteins import ProteinGrouper [as 别名]
# 或者: from dark.proteins.ProteinGrouper import addFile [as 别名]
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)示例8: testOpenNotCalledOnRepeatedCall
# 需要导入模块: from dark.proteins import ProteinGrouper [as 别名]
# 或者: from dark.proteins.ProteinGrouper import addFile [as 别名]
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)示例9: testDuplicatePathogenProteinSample
# 需要导入模块: from dark.proteins import ProteinGrouper [as 别名]
# 或者: from dark.proteins.ProteinGrouper import addFile [as 别名]
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)示例10: testTwoLinesInOneFileTitle
# 需要导入模块: from dark.proteins import ProteinGrouper [as 别名]
# 或者: from dark.proteins.ProteinGrouper import addFile [as 别名]
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())示例11: testIdenticalReadsRemoved
# 需要导入模块: from dark.proteins import ProteinGrouper [as 别名]
# 或者: from dark.proteins.ProteinGrouper import addFile [as 别名]
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)示例12: testReadLengthsAdded
# 需要导入模块: from dark.proteins import ProteinGrouper [as 别名]
# 或者: from dark.proteins.ProteinGrouper import addFile [as 别名]
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'])示例13: testOneLineInEachOfTwoFilesDifferentVirusesTitle
# 需要导入模块: from dark.proteins import ProteinGrouper [as 别名]
# 或者: from dark.proteins.ProteinGrouper import addFile [as 别名]
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())示例14: testOneLineInOneFileToStr
# 需要导入模块: from dark.proteins import ProteinGrouper [as 别名]
# 或者: from dark.proteins.ProteinGrouper import addFile [as 别名]
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())示例15: testTwoLinesInOneFileSameVirus
# 需要导入模块: from dark.proteins import ProteinGrouper [as 别名]
# 或者: from dark.proteins.ProteinGrouper import addFile [as 别名]
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)