def renameStdTrack(genome, oldTn, newTn):
oldPath = createOrigPath(genome, oldTn)
assert os.path.exists(oldPath), 'ERROR: TN did not exist in stdTracks: ' + oldPath
print '(renaming track in stdTracks..)'
newPath = createOrigPath(genome, newTn)
if not ONLY_SIMULATION:
assert not os.path.exists(newPath), 'ERROR: Target path already exists: ' + newPath
ensurePathExists(newPath)
print 'Moving from %s to %s' % (oldPath, newPath)
shutil.move(oldPath, newPath)
else:
print 'Would move %s to %s' % (oldPath, newPath)
def _writeTestFile(self, case):
fn = createOrigPath(self.GENOME, self.TRACK_NAME_PREFIX + case.trackName, 'testfile' + case.suffix)
ensurePathExists(fn)
testfile = open(fn, 'w')
testfile.write('\n'.join(case.headerLines + case.lines))
testfile.close()
return fn
def _commonSetup(self):
from gtrackcore_memmap.test.input.core.TestGenomeElementSource import TestGenomeElementSource
testGESource = TestGenomeElementSource()
testGESource.setUp()
origDir = createOrigPath(self.GENOME, self.TRACK_NAME_PREFIX)
self._removeDir(origDir, self.TRACK_NAME_PREFIX)
return testGESource
def yielder(self):
#literatureTN = GenomeInfo.getPropertyTrackName(self._genome, 'literature')
#literatureTNBase = literatureTN[:-1]
basePath = createOrigPath(self._genome, self._trackNameFilter)
for root, dirs, files in os.walk(basePath,topdown=True):
dirsToRemove = []
if root==basePath:
dirsToRemove.append('Trash')
dirsToRemove.append('Trashcan')
trackName = extractTrackNameFromOrigPath(root)
#if self._avoidLiterature and trackName == literatureTNBase:
#dirsToRemove.append(literatureTN[-1])
for oneDir in dirs:
if oneDir[0] in ['.','_','#']:
dirsToRemove.append(oneDir)
for rmDir in dirsToRemove:
if rmDir in dirs:
dirs.remove(rmDir)
#if sum(1 for f in files if f[0] not in ['.','_','#']) == 0:
# continue
#if any([part[0]=='.' for part in trackName]):
# continue
filterLen = len(self._trackNameFilter)
if (self._trackNameFilter != trackName[:filterLen]):
continue
yield trackName
def _allGESources(self, trackName):
baseDir = createOrigPath(self._genome, trackName)
self._status = 'Trying os.listdir on: ' + baseDir
for relFn in sorted(os.listdir( baseDir )):
fn = os.sep.join([baseDir, relFn])
self._status = 'Checking file: ' + fn
if os.path.isdir(fn):
continue
fnPart = os.path.split(fn)[-1]
if fnPart[0] in ['.','_','#'] or fnPart[-1] in ['~','#']: #to avoid hidden files..
continue
self._status = 'Trying to create geSource from fn: ' + fn
yield GenomeElementSource(fn, self._genome, forPreProcessor=True)
def importFile(fileName, genome, trackName):
"""fileName genome trackName"""
trackName = _convertTrackName(trackName)
from gtrackcore_memmap.util.CommonFunctions import createOrigPath, ensurePathExists
origFn = createOrigPath(genome, trackName, os.path.basename(fileName))
if os.path.exists(origFn):
shutil.rmtree(os.path.dirname(origFn))
ensurePathExists(origFn)
shutil.copy(fileName, origFn)
os.chmod(origFn, 0664)
from gtrackcore_memmap.preprocess.PreProcessTracksJob import PreProcessAllTracksJob
PreProcessAllTracksJob(genome, trackName).process()
def _removeAllTrackData(self, trackName, removeOrigData=True):
self._removeDir(createDirPath(trackName, self.GENOME, allowOverlaps=False), trackName)
self._removeDir(createDirPath(trackName, self.GENOME, allowOverlaps=True), trackName)
if removeOrigData:
self._removeDir(createOrigPath(self.GENOME, trackName), trackName)
