"""
This file is part of Picopore.
Picopore is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
Picopore is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with Picopore. If not, see <http://www.gnu.org/licenses/>.
"""
import os
from time import sleep
from watchdog.observers import Observer
from watchdog.events import PatternMatchingEventHandler
from picopore.multiprocess import Multiprocessor
from picopore.runner import PicoporeCompressionRunner
from picopore.compress import chooseCompressFunc
from picopore.parse_args import parseArgs, checkSure
from picopore.util import log
class ReadsFolder(object):
def __init__(self, runner):
self.runner = runner
self.event_handler = PatternMatchingEventHandler(patterns=["*.fast5"],
ignore_patterns=[],
ignore_directories=True)
self.event_handler.on_created = self.on_created
self.event_handler.on_moved = self.on_moved
self.observer = Observer()
self.observedPaths = []
for path in self.runner.input:
if os.path.isdir(path):
self.observer.schedule(self.event_handler, path, recursive=True)
self.observedPaths.append(path)
log("Monitoring {} in real time. Press Ctrl+C to exit.".format(", ".join(self.observedPaths)))
def start(self):
self.observer.start()
self.runner.run(postprocess=False)
def add_file(self, path):
self.runner.process([path])
def on_created(self, event):
if self.runner.skip_root and os.path.dirname(event.src_path) in self.observedPaths:
return 0
elif self.runner.prefix is not None and os.path.basename(event.src_path).startswith(self.runner.prefix):
return 0
else:
self.add_file(event.src_path)
return 0
def on_moved(self, event):
if self.runner.skip_root and os.path.dirname(event.src_path) in self.observedPaths and os.path.dirname(event.dest_path) not in self.observedPaths:
self.add_file(event.dest_path)
def stop(self):
log("Processing in-progress files. Press Ctrl-C again to abort.")
try:
self.runner.stop()
except KeyboardInterrupt:
log("Aborted.")
pass
self.observer.stop()
self.observer.join()
class PicoporeRealtimeRunner(PicoporeCompressionRunner):
def __init__(self, args):
super(PicoporeRealtimeRunner, self).__init__(args)
_, name = chooseCompressFunc(self.revert, self.mode, self.fastq, self.summary, self.manual, realtime=True)
log(name + "...",end='')
if self.y:
log()
elif checkSure():
self.y = True
else:
exit(1)
self.readsFolder = ReadsFolder(self)
def execute(self):
self.readsFolder.start()
try:
while True:
sleep(5)
except KeyboardInterrupt:
log("\nExiting Picopore.")
self.readsFolder.stop()
return 0
__description = """"picopore-realtime monitors a directory for new reads and compresses them in real time"""
def main():
args = parseArgs(description=__description, prog='picopore-realtime')
runner = PicoporeRealtimeRunner(args)
return runner.execute()
if __name__ == "__main__":
exit(main())
