def calculateTaskForMissingWindowsForSequence(seriesSourceNumber, taskDescription, debug=False):
config.initLogging()
logging.warning("Processing task %s" % taskDescription)
print(taskDescription)
#def __init__(self, windowWidth=40, logfile=None, debugDoneWriteResults=False, computationTag="rna-fold-window-40-0", seriesSourceNumber=db.Sour
(taxId, protId, seqIds, requestedShuffleIds, lastWindowStart, windowStep, windowRef, shuffleType) = parseTaskDescription(taskDescription)
windowWidth = db.getWindowWidthForComputationTag( seriesSourceNumber )
firstWindowStart = 0
if seriesSourceNumber in (db.Sources.RNAfoldEnergy_SlidingWindow40_v2, db.Sources.RNAfoldEnergy_SlidingWindow30_v2, db.Sources.RNAfoldEnergy_SlidingWindow50_v2, db.Sources.RNAfoldEnergy_SlidingWindow40_v2_native_temp, db.Sources.TEST_StepFunction_BeginReferenced, db.Sources.TEST_StepFunction_EndReferenced, db.Sources.GC_content_SlidingWindow40, db.Sources.Purine_content_SlidingWindow40, db.Sources.StopCodon_content_SlidingWindow30, db.Sources.StopCodon_content_SlidingWindow50, db.Sources.StopCodon_content_SlidingWindow50 ):
f = CalculateSlidingWindowRandomizedComparisonSeries(windowWidth, seriesSourceNumber=seriesSourceNumber)
else:
raise Exception("Got invalid sourceSeries: {}".format(seriesSourceNumber))
try:
#def calculateMissingWindowsForSequence(self, taxId, protId, seqIds, requestedShuffleIds, firstWindow, lastWindowStart, windowStep, reference="begin"):
ret = f.calculateMissingWindowsForSequence(taxId, protId, seqIds, requestedShuffleIds, firstWindowStart, lastWindowStart, windowStep, windowRef, shuffleType, debug=debug)
except Exception as e:
logging.error("calculateMissingWindowsForSequence() caught exception")
logging.error(e)
logging.error(taskDescription)
raise
if useProfiling and rl(): # display performance timers
pre = timerForPreFolding.stats()[0]
fold = timerForFolding.stats()[0]
post = timerForPostFolding.stats()[0]
logging.warning("Performance timers: Pre: %.4gs; Folding: %.4gs; Post: %.4gs; Total: %.4gs" % (pre, fold, post, pre+fold+post))
return taskDescription
def main():
args = initParser()
config = initConfig(args.settings_file)
db = initDatabase(config)
initLogging(config)
if exists(args.filename):
log_entry = LogEntry(args.filename)
db.insert_entry(log_entry)
return 0
else:
logging.error("%s does not exist. Exiting..." % args.filename)
return 1
from collections import Counter
from itertools import compress
import logging
import traceback
import config
import mysql_rnafold as db
from data_helpers import CDSHelper, countSpeciesCDS, getSpeciesName, SpeciesCDSSource, numItemsInQueue
import _distributed
import dask
from store_new_shuffles import storeNewShuffles
from calculate_sliding_window_series import calculateTaskForMissingWindowsForSequence
import notify_pushover
scheduler = _distributed.open()
config.initLogging()
def parseList(conversion=str):
def convert(values):
return list(map(conversion, values.split(",")))
return convert
argsParser = argparse.ArgumentParser()
argsParser.add_argument("--species", type=parseList(int), required=True)
argsParser.add_argument("--computation-tag", default="rna-fold-window-40-0")
argsParser.add_argument("--random-fraction", type=int, default=1)
argsParser.add_argument("--window-step", type=int, default=10)
argsParser.add_argument("--from-shuffle", type=int, default=-1)