def process(self):
"""
Run the conversion script if the output needs updating.
"""
# Note: _needs_update() does the logging.
if not self._needs_update():
return
if not os.path.exists(self.script):
raise ValueError(
"Processing script {0.script} does not exist".format(self))
if not (stat.S_IXUSR & os.stat(self.script)[stat.ST_MODE]):
raise ValueError(
Fore.RED +
"Processing script {0.script} not executable".format(self) +
Fore.RESET)
utils.makedirs(os.path.dirname(self.processed))
cmds = [
self.script,
self.original,
self.processed
]
retval = subprocess.check_call(cmds)
if self._needs_update():
raise ValueError(
Fore.RED + 'The following command did not update '
'{1}:\n\n{0}\n'.format(' \\\n'.join(cmds), self.processed) +
Fore.RESET
)
def process(self):
"""
Run the conversion script if the output needs updating.
"""
# Note: _needs_update() does the logging.
if not self._needs_update():
return
if not os.path.exists(self.script):
raise ValueError(
"Processing script {0.script} does not exist".format(self))
if not (stat.S_IXUSR & os.stat(self.script)[stat.ST_MODE]):
raise ValueError(
Fore.RED +
"Processing script {0.script} not executable".format(self) +
Fore.RESET)
utils.makedirs(os.path.dirname(self.processed))
cmds = [self.script, self.original, self.processed]
retval = subprocess.check_call(cmds)
if self._needs_update():
raise ValueError(
Fore.RED + 'The following command did not update '
'{1}:\n\n{0}\n'.format(' \\\n'.join(cmds), self.processed) +
Fore.RESET)
def liftover(self, from_assembly, to_assembly, newfile):
"""
Lifts over the processed file to a new file, but only if needed.
Uses a hidden sentinel file to indicate whether it's been lifted over.
Parameters
----------
from_assembly : str
Existing data are in this assembly's coordinates
to_assembly : str
Lift over existing data to this assembly's coordinates
newfile : str
Target filename of the lifted-over data
"""
if not from_assembly == self.genome:
log(
"{0} not from assembly {1}. Skipping liftover from {1} to {2} "
"and simply copying the file as-is to {3}"
.format(self.label, from_assembly, to_assembly, newfile)
)
shutil.copy(self.processed, newfile)
if not self._needs_liftover(from_assembly, to_assembly, newfile):
log("{0} is already lifted over and up-to-date. Skipping."
.format(newfile))
return
tmp = tempfile.NamedTemporaryFile(delete=False).name
log("Lift over {0} to {1}".format(self.processed, tmp))
liftover.liftover(
from_assembly, to_assembly, self.processed, tmp, self.type_)
utils.makedirs(os.path.dirname(newfile))
log("Moving {0} to {1}".format(tmp, newfile))
shutil.move(tmp, newfile)
if self.type_.lower() == 'bam':
shutil.move(tmp + '.bai', newfile + '.bai')
# CrossMap.py seems to `chmod go-rw` on lifted-over file. So we copy
# permissions from the original one.
shutil.copymode(self.processed, newfile)
# Write the sentinel file to indicate genome we lifted over to.
sentinel = self._liftover_sentinel(from_assembly, to_assembly, newfile)
with open(sentinel, 'w') as fout:
pass
def liftover(self, from_assembly, to_assembly, newfile):
"""
Lifts over the processed file to a new file, but only if needed.
Uses a hidden sentinel file to indicate whether it's been lifted over.
Parameters
----------
from_assembly : str
Existing data are in this assembly's coordinates
to_assembly : str
Lift over existing data to this assembly's coordinates
newfile : str
Target filename of the lifted-over data
"""
if not from_assembly == self.genome:
log("{0} not from assembly {1}. Skipping liftover from {1} to {2} "
"and simply copying the file as-is to {3}".format(
self.label, from_assembly, to_assembly, newfile))
shutil.copy(self.processed, newfile)
if not self._needs_liftover(from_assembly, to_assembly, newfile):
log("{0} is already lifted over and up-to-date. Skipping.".format(
newfile))
return
tmp = tempfile.NamedTemporaryFile(delete=False).name
log("Lift over {0} to {1}".format(self.processed, tmp))
liftover.liftover(from_assembly, to_assembly, self.processed, tmp,
self.type_)
utils.makedirs(os.path.dirname(newfile))
log("Moving {0} to {1}".format(tmp, newfile))
shutil.move(tmp, newfile)
# CrossMap.py seems to `chmod go-rw` on lifted-over file. So we copy
# permissions from the original one.
shutil.copymode(self.processed, newfile)
# Write the sentinel file to indicate genome we lifted over to.
sentinel = self._liftover_sentinel(from_assembly, to_assembly, newfile)
with open(sentinel, 'w') as fout:
pass