def test_failure(self):
""" Harvester should raise exception if clumpp generation sees weird line structure.
"""
tmpDirParent = makeTempDirParent()
tmpDirs = []
for example in td.clumppLineStructure:
tmpDirs.append(
os.path.abspath(
makeTempDir('clumppLineStructure_%s' % example.name)))
results = os.path.join(tmpDirs[-1], 'results')
out = os.path.join(tmpDirs[-1], 'out')
if not os.path.exists(out):
os.mkdir(out)
populateExample(example, tmpDirs[-1])
files = glob(os.path.join(results, '*_f'))
for f in files:
data = hc.Data()
data.records = {} # key is K, value is an array
run, errorString = hc.readFile(f, data)
self.assertTrue(run is not None)
data.records.setdefault(run.k, []).append(run)
data.sortedKs = data.records.keys()
data.sortedKs.sort()
self.assertRaises(hc.ClumppLineStructure, hc.clumppPopFile,
results, out, data)
[self.addCleanup(removeDir, d) for d in tmpDirs]
self.addCleanup(removeDirIfEmpty, tmpDirParent)
def main():
usage = (
'usage: %(prog)s --dir=path/to/dir/ --out=path/to/dir/ [options]\n\n'
'%(prog)s takes a STRUCTURE results directory (--dir) and an\n'
'output directory (--out will be created if it does not exist) '
'and then\n'
'depending on the other options selected harvests data from the '
'results\n'
'directory and performs the selected analyses')
data = hc.Data()
parser = ArgumentParser(usage=usage,
version='%(prog)s ' + '%s core %s' %
(__version__, hc.__version__))
initializeArguments(parser)
args = parser.parse_args()
checkArguments(parser, args)
harvestFiles(data, args)
hc.calculateMeansAndSds(data)
if args.clumpp:
try:
hc.clumppGeneration(args.resultsDir, args.outDir, data)
except hc.ClumppRegEx as e:
clumppRegExFailure(e.filename, e.regexs, e.lineno, e.line, e.data)
except hc.ClumppPriorPopInfo as e:
clumppPriorPopInfoFailure(e.filename, data)
try:
hc.clumppPopFile(args.resultsDir, args.outDir, data)
except hc.ClumppLineStructure as e:
clumppLineStructureFailure(e.filename, e.regex, e.lineno, e.line,
e.data)
evannoMethod(data, args)
hc.writeRawOutputToFile(os.path.join(args.outDir, 'summary.txt'), data)
def test_failure(self):
""" Harvester should raise exception if the input contains unexpected values.
"""
tmpDirParent = makeTempDirParent()
tmpDirs = []
for example in td.readFileUnexpectedValue:
tmpDirs.append(
os.path.abspath(
makeTempDir('readFileUnexpected_%s' % example.name)))
results = os.path.join(tmpDirs[-1], 'results')
out = os.path.join(tmpDirs[-1], 'out')
if not os.path.exists(out):
os.mkdir(out)
populateExample(example, tmpDirs[-1])
files = glob(os.path.join(results, '*_f'))
for f in files:
data = hc.Data()
data.records = {} # key is K, value is an array
self.assertRaises(hc.UnexpectedValue, hc.readFile, f, data)
[self.addCleanup(removeDir, d) for d in tmpDirs]
self.addCleanup(removeDirIfEmpty, tmpDirParent)
def main():
usage = (
'usage: %prog --dir=path/to/dir/ --out=path/to/dir/ [options]\n\n'
'%prog takes a STRUCTURE results directory (--dir) and an\n'
'output directory (--out will be created if it does not exist) and then\n'
'depending on the other options selected harvests data from the results\n'
'directory and performs the selected analyses')
data = hc.Data()
parser = OptionParser(usage=usage,
version='%prog ' + __version__ + ' core ' +
hc.__version__)
initOptions(parser)
(options, args) = parser.parse_args()
checkOptions(parser, options)
harvestFiles(data, options)
hc.calculateMeansAndSds(data)
if options.clumpp:
hc.clumppGeneration(options.resultsDir, options.outDir, data,
failHandler)
hc.clumppPopFile(options.resultsDir, options.outDir, data, failHandler)
evannoMethod(data, options)
hc.writeRawOutputToFile(os.path.join(options.outDir, 'summary.txt'), data)