def run():
print '--> mission Break Their Will'
if not ship.enableDefense():
return False
if not overview.switchTo('lcs'):
return False
if not overview.lockTarget('repair_station'):
return False
if not general.openMissionDetails():
return False
if not drones.launchSentry():
return False
if not drones.engage():
return False
if not general.missionObjectiveComplete():
return False
if not drones.back():
return False
print '<-- mission Break Their Will\n'
return True
def run():
print "--> mission Intercept the Pirate Smugglers"
result = None
begin = time.time()
while not result and time.time() - begin < 5:
time.sleep(0.2)
result = findAtFull("close")
if result:
mouse.leftClickAtP(result)
if not ship.enableDefense():
return False
if not drones.launchSmall():
return False
if not general.openMissionDetails():
return False
ship.enableAfterburn()
overview.seekAndDestory()
if not general.missionObjectiveComplete():
return False
if not drones.back():
return False
print "<-- mission Intercept the Pirate Smugglers\n"
return True
def Start(self):
self.queue.put(lambda: self.FlexAID.root.withdraw())
cmd.window('hide')
self.queue.put(lambda: cmd.window('show'))
cmd.refresh_wizard()
# Display the ligand from the PDB file
if self.DisplayLigand():
self.FlexAID.DisplayMessage("Error while trying to display the ligand from PDB file", 1)
self.Quit_Wizard(self.ErrorCode)
return
# Color the Atoms based on their type
if self.ColorByType():
self.FlexAID.DisplayMessage("Error while coloring the ligand atoms by type", 1)
self.Quit_Wizard(self.ErrorCode)
return
# Mask everythign except modifyable object (ligand)
self.exc = [self.LigDisplay]
General.mask_Objects(self.exc)
self.selection_mode = cmd.get("mouse_selection_mode")
cmd.set("mouse_selection_mode", 0) # set selection mode to atomic
# remove any possible selection before selecting atoms
cmd.deselect()
self.ErrorCode += 1
def run():
print '--> mission What Comes Around Goes Around'
if not ship.enableDefense():
return False
if not drones.launchSmall():
return False
result = None
begin = time.time()
while not result and time.time() - begin < 5:
time.sleep(0.2)
result = findAtFull('close')
if result:
mouse.leftClickAtP(result)
if not general.openMissionDetails():
return False
if not general.missionObjectiveComplete():
return False
if not drones.back():
return False
print '<-- mission What Comes Around Goes Around\n'
return True
def Quit_Wizard(self, rv):
try:
cmd.delete(self.LigDisplay)
cmd.delete(self.AtomDisplay)
cmd.deselect()
if rv != 1:
General.unmask_Objects(self.exc)
cmd.set('mouse_selection_mode', self.selection_mode)
#cmd.config_mouse('three_button_editing', 1)
if rv > 0:
self.FlexAID.WizardError = True
self.FlexAID.ActiveWizard = None
cmd.set_wizard()
cmd.set_view(self.View)
cmd.refresh()
self.top.SATRunning(False)
self.queue.put(lambda: self.top.AnchorRunning(False))
self.queue.put(lambda: self.FlexAID.root.deiconify())
self.queue.put(lambda: self.FlexAID.root.update())
except:
pass
def run(): print '--> mission The Guristas Spies' if not ship.enableDefense(): return False if not overview.activateAccelerationGate(): return False if not drones.launchSmall(): return False if not general.openMissionDetails(): return False overview.seekAndDestory() if not general.missionObjectiveComplete(): return False if not drones.back(): return False print '<-- mission The Guristas Spies\n' return True
def run():
print '--> mission The Space Telescope'
if not ship.enableDefense():
return False
if not overview.activateAccelerationGate():
return False
if not overview.switchTo('lcs'):
return False
if not overview.lockTarget('guristas_space', 15):
return False
if not drones.launchSmall():
return False
ship.fireOnce()
drones.engage()
if not general.openMissionDetails():
return False
if not general.missionObjectiveComplete():
return False
if not drones.back():
return False
print '<-- mission The Space Telescope\n'
return True
def run():
print '--> mission Deadly Arrival'
if not ship.enableDefense():
return False
if not overview.switchTo('lco'):
return False
if not overview.lockTarget('ruined_structure'):
return False
if not ship.approach():
return False
if not ship.enableAfterburn():
return False
if not general.openMissionDetails():
return False
if not general.missionObjectiveComplete():
return False
print '<-- mission Deadly Arrival\n'
return True
def run(): print '--> mission New Frontiers - Asnendanne (7 of 7)' if not ship.enableDefense(): return False if not general.openMissionDetails(): return False ship.enableAfterburn() if not overview.activateAccelerationGate(): return False print 'pocket 1' if not drones.launchSmall(): return False overview.seekAndDestory() if not general.missionObjectiveComplete(): return False if not drones.back(): return False print '<-- mission New Frontiers - Asnendanne (7 of 7)\n' return True
def run():
print '--> mission Retribution'
if not ship.enableDefense():
return False
if not overview.activateAccelerationGate():
return False
if not overview.switchTo('lcs'):
return False
if not overview.lockTarget('guristas_outpost', 5):
return False
if not general.openMissionDetails():
return False
if not drones.launchSentry():
return False
ship.fireOnce()
drones.engage()
if not general.missionObjectiveComplete():
return False
if not drones.back():
return False
print '<-- mission Retribution\n'
return True
def run():
print '--> mission Unauthorized Military Presence'
if not ship.enableDefense():
return False
if not general.openMissionDetails():
return False
ship.enableAfterburn()
if not overview.activateAccelerationGate():
return False
if not overview.switchTo('battle'):
return False
if not overview.lockTarget('guristas_personnel'):
return False
if not ship.enableAfterburn():
return False
if not ship.approachFor(240):
return False
if not overview.lockTarget('guristas_personnel', 20):
return False
if not drones.launchSmall():
return False
if not ship.fireOnce():
return False
if not drones.engage():
return False
# mission item is in wreck
while not findAtMissionDetails('v'):
# collect
overview.pickWreck()
if not general.missionObjectiveComplete():
return False
# sometimes we already has millitans
# but the mission is not complete until all enemy dies
overview.seekAndDestory()
# just in case
overview.pickTarget('guristas_personnel')
if not drones.back():
return False
print '<-- mission Unauthorized Military Presence\n'
return True
def run():
print '--> mission Eliminate the Pirate Campers'
if not ship.enableDefense():
return False
if not drones.launchSentry():
return False
if not overview.switchTo('battle'):
return False
begin = time.time()
result = None
while not result and time.time() - begin < 5:
result = findAtFull('close')
if result:
mouse.leftClickAtP(result)
# kill small
count = 0
while count < 4:
result = overview.lockTarget('s', 1)
if result:
count += 1
begin = time.time()
while time.time() - begin < 120:
overview.lockTarget('s', 1)
ship.fireOnce()
drones.engage()
if not drones.back():
return False
# seek and destory
if not general.openMissionDetails():
return False
ship.enableAfterburn()
if not drones.launchSmall():
return False
overview.seekAndDestory()
if not general.missionObjectiveComplete():
return False
if not drones.back():
return False
print '<-- mission Eliminate the Pirate Campers\n'
return True
def start_with_computer(enabled):
"""If enabled, create shortcut to start application with computer.
If disabled, then delete the shortcut."""
if not enabled:
if os.path.lexists(autostart_path):
FileUtilities.delete(autostart_path)
return
if os.path.lexists(autostart_path):
return
import shutil
General.makedirs(os.path.dirname(autostart_path))
shutil.copy(launcher_path, autostart_path)
os.chmod(autostart_path, 0755)
if General.sudo_mode():
General.chownself(autostart_path)
def activateAccelerationGate():
switchTo('pilot')
general.enterStarMap()
print '--> activate acceleration gate\n'
mouse.leftDownAtP(panel.center(panel.Full))
mouse.move(500, 200)
mouse.leftUp()
result = findTarget('acceleration_gate')
if not result:
return False
mouse.leftClickAtP(result)
key.pressEx(sc.Activate)
print 'wait to activate gate'
while not findAtDashboard('warp_drive_active'):
result = findAtFull('close')
if not result:
result = findAtFull('ok')
if result:
mouse.leftClickAtP(result)
mouse.moveTo(result[0], result[1] - 200)
handleDangerousAction();
key.pressEx(sc.Activate)
time.sleep(1)
print 'wait until reach location'
while findAtDashboard('warp_drive_active'):
time.sleep(0.5)
result = findAtFull('close')
if not result:
result = findAtFull('ok')
if result:
mouse.leftClickAtP(result)
mouse.moveTo(result[0], result[1] - 200)
time.sleep(1)
while findAtDashboard('warp_drive_active'):
time.sleep(0.5)
print '<-- activate acceleration gate\n'
general.exitStarMap()
return True
def getAvgMov(track, **kwargs): SPEED_CONVERSION_FACTOR = kwargs["speedConversionFactor"] avgMov = [] diff = [] frameDistanceBetweenFrames = [] positionalDistanceBetweenFrames = [] for index in range(0, len(track.x) - 1): #the number of frames by which two adjacent elements in track are separated frameDistanceBetweenFrames = track.t[index + 1] - track.t[index] #the absolute positional distance between adjacent tracked frames positionalDistanceBetweenFrames = gen.getDistance(track.x[index], track.x[index + 1], track.y[index], track.y[index + 1]) #the distance traveled per frame between adjacent tracked frames diff.append(positionalDistanceBetweenFrames / frameDistanceBetweenFrames) return gen.nanMean(diff) * SPEED_CONVERSION_FACTOR
def __init__(self, action_element):
"""Initialize file search"""
self.regex = action_element.getAttribute('regex')
assert(isinstance(self.regex, (str, unicode, types.NoneType)))
self.nregex = action_element.getAttribute('nregex')
assert(isinstance(self.nregex, (str, unicode, types.NoneType)))
self.wholeregex = action_element.getAttribute('wholeregex')
assert(isinstance(self.wholeregex, (str, unicode, types.NoneType)))
self.nwholeregex = action_element.getAttribute('nwholeregex')
assert(isinstance(self.nwholeregex, (str, unicode, types.NoneType)))
self.search = action_element.getAttribute('search')
self.object_type = action_element.getAttribute('type')
self.path = os.path.expanduser(FileUtilities.expandvars(
action_element.getAttribute('path')))
if 'nt' == os.name and self.path:
# convert forward slash to backslash for compatibility with getsize()
# and for display. Do not convert an empty path, or it will become
# the current directory (.).
self.path = os.path.normpath(self.path)
self.ds = {}
if 'deep' == self.search:
self.ds['regex'] = self.regex
self.ds['nregex'] = self.nregex
self.ds['cache'] = General.boolstr_to_bool(
action_element.getAttribute('cache'))
self.ds['command'] = action_element.getAttribute('command')
self.ds['path'] = self.path
if not any([self.object_type, self.regex, self.nregex, self.wholeregex, self.nwholeregex]):
# If the filter is not needed, bypass it for speed.
self.get_paths = self._get_paths
def run():
print '--> mission New Frontiers - Raw Materials (6 of 7)'
if not station.openInventory():
return False
if not station.loadItem('mission_cargo'):
return False
if not station.closeInventory():
return False
if not station.undock():
return False
pilot.autopilot()
if not general.setMissionWaypoint():
return False
if not station.startConversation(agent):
return False
if not station.completeMission():
return False
if not station.undock():
return False
pilot.autopilot()
print '<-- mission New Frontiers - Raw Materials (6 of 7)\n'
return True
def Save_SessionFile(self, SaveFile):
if len(SaveFile) > 0:
SaveFile = os.path.normpath(SaveFile)
if General.validate_String(SaveFile, '.nrgfs', True, True, False):
self.DisplayMessage(" ERROR: Could not save the file because you entered an invalid name.", 2)
return
if self.ValidateSaveProject(SaveFile, 'Session'):
self.DisplayMessage(" ERROR: The file can only be saved at its default location", 2)
return
try:
out = open(SaveFile, 'wb')
pickle.dump(self.SessionPath, out)
for Tab in self.listTabs:
pickle.dump(Tab.Vars, out)
out.close()
self.SaveSessionFile = SaveFile
self.DisplayMessage(" The session '" + os.path.split(SaveFile)[1] + "' was saved successfully.", 2)
except pickle.PicklingError:
self.DisplayMessage(" ERROR: Could not properly save the session: " + str(sys.exc_info()), 2)
except:
self.DisplayMessage(" Unexpected error: " + str(sys.exc_info()), 2)
def run():
print '--> mission Technological Secrets 2'
# this is a transport mission
if not (station.openInventory() \
and station.loadItem('dna_sample') \
and station.closeInventory()):
return False
if not station.undock():
return False
pilot.autopilot()
if not general.setMissionWaypoint():
return False
if not station.startConversation(agent):
return False
if not station.completeMission():
return False
if not station.undock():
return False
pilot.autopilot()
print '<-- mission Technological Secrets 2\n'
return True
def __init__(self, action_element):
"""Initialize file search"""
self.regex = action_element.getAttribute('regex')
assert(isinstance(self.regex, (str, unicode, types.NoneType)))
self.nregex = action_element.getAttribute('nregex')
assert(isinstance(self.nregex, (str, unicode, types.NoneType)))
self.search = action_element.getAttribute('search')
self.object_type = action_element.getAttribute('type')
self.path = os.path.expanduser(os.path.expandvars(
action_element.getAttribute('path')))
if 'nt' == os.name and self.path:
# convert forward slash to backslash for compatibility with getsize()
# and for display. Do not convert an empty path, or it will become
# the current directory (.).
self.path = os.path.normpath(self.path)
self.ds = {}
if 'deep' == self.search:
self.ds['regex'] = self.regex
self.ds['nregex'] = self.nregex
self.ds['cache'] = General.boolstr_to_bool(
action_element.getAttribute('cache'))
self.ds['command'] = action_element.getAttribute('command')
self.ds['path'] = self.path
if self.object_type:
if 'f' == self.object_type:
self.object_filter = os.path.isfile
elif 'd' == self.object_type:
self.object_filter = os.path.isdir
else:
raise RuntimeError('unsupported type %s in %s' % \
(self.object_type, self.action_element))
else:
# faster to bypass
self.get_paths = self._get_paths
def getVelocity(track, **kwargs): SPEED_CONVERSION_FACTOR = kwargs["speedConversionFactor"] age = getAge(track) xTravel = track.x[-1] - track.x[0] yTravel = track.y[-1] - track.y[0] return (gen.pythagorean(xTravel, yTravel) / age) * SPEED_CONVERSION_FACTOR
def Btn_Create_Clicked(self):
name = self.ProjName.get().strip()
if name != '':
if General.validate_String(name, '', False, True, False):
print(' ERROR: The name \'' + name + '\' is invalid. Try again.')
return
Project_Dir = os.path.join(self.ActualDirPath,name)
if not os.path.isdir(Project_Dir):
try:
os.makedirs(Project_Dir)
except OSError:
print(' ERROR: Could not create the project: \'' + name + '\' under that directory.')
return
self.Update_ProjectFile(Project_Dir, name)
self.top.Project_Dir = Project_Dir
self.top.ProjectName = name
self.Quit()
self.After_Quit()
print(' Successfully created the project: \'' + name + '\'')
print(' The project was loaded by default.')
else:
print(' The project: \'' + name + '\' already exists.')
def getMP(track, **kwargs): travel = [] xDiffs = gen.getDifferenceArray(track.x) yDiffs = gen.getDifferenceArray(track.y) for x, y in zip(xDiffs, yDiffs): travel.append(gen.pythagorean(x, y)) totalTravel = np.sum(travel) xDistance = track.x[-1] - track.x[0] yDistance = track.y[-1] - track.y[0] if totalTravel == 0: return 0 return gen.pythagorean(xDistance, yDistance) / totalTravel
def __flush(self):
"""Write information to disk"""
if not self.purged:
self.__purge()
if not os.path.exists(Common.options_dir):
General.makedirs(Common.options_dir)
mkfile = not os.path.exists(Common.options_file)
_file = open(Common.options_file, 'wb')
try:
self.config.write(_file)
except IOError, e:
print e
from errno import ENOSPC
if e.errno == ENOSPC:
print "Error: disk is full writing configuration '%s'" % Common.options_file
else:
raise
def get_proc_swaps():
"""Return the output of 'swapon -s'"""
# Usually 'swapon -s' is identical to '/proc/swaps'
# Here is one exception: https://bugs.launchpad.net/ubuntu/+source/bleachbit/+bug/1092792
(rc, stdout, _) = General.run_external(["swapon", "-s"])
if 0 == rc:
return stdout
print 'debug: "swapoff -s" failed so falling back to /proc/swaps'
return open("/proc/swaps").read()
def Enter(self):
if General.validate_String(self.SmilesName.get(), '', False, False, True):
self.top.DisplayMessage(" ERROR: Could not process the smiles string because you entered an invalid name.", 2)
return
#Test : CCC[C@@H](O)CC\C=C\C=C\C#CC#C\C=C\CO
self.inputWindow.destroy()
self.top.SmilesRunning(False, True)
def Add_List(self, Items, BGColors):
for n in range(0, len(Items)):
for i in range(0, self.nCol):
self.Columns[self.ColNames[i]]['List'].insert(END, General.repeat(' ', self.Columns[self.ColNames[i]]['Spacer']) + str(Items[n][i]))
if BGColors[n][i] != None:
self.Columns[self.ColNames[i]]['List'].itemconfig(self.Columns[self.ColNames[i]]['List'].size()-1,
bg=BGColors[n][i])
def is_process_running_wmic(name):
"""Return boolean whether process (like firefox.exe) is running
Works on Windows XP Professional but not on XP Home
"""
clean_name = re.sub("[^A-Za-z\.]", "_", name).lower()
args = ["wmic", "path", "win32_process", "where", "caption='%s'" % clean_name, "get", "Caption"]
(_, stdout, _) = General.run_external(args)
return stdout.lower().find(clean_name) > -1
def Add(self, Item, BGColor):
for i in range(0, self.nCol):
try:
self.Columns[self.ColNames[i]]['List'].insert(END, General.repeat(' ', self.Columns[self.ColNames[i]]['Spacer']) + str(Item[i]))
if BGColor[i] != None:
self.Columns[self.ColNames[i]]['List'].itemconfig(self.Columns[self.ColNames[i]]['List'].size()-1, bg=BGColor[i])
except:
pass
def is_process_running_wmic(name):
"""Return boolean whether process (like firefox.exe) is running
Works on Windows XP Professional but not on XP Home
"""
clean_name = re.sub('[^A-Za-z\.]', '_', name).lower()
args = ['wmic', 'path', 'win32_process', 'where', "caption='%s'" % clean_name, 'get', 'Caption']
(_, stdout, _) = General.run_external(args)
return stdout.lower().find(clean_name) > -1
if loginServer == False:
sendmsg("DataX","LOGIN la78zg294dap7swpe6wx ")
loginServer = True
if nick.lower() == "datax":
ircmsg = ircmsg.split(" :",1)[1]
if "ECHO PENDING " in ircmsg:
sendmsg("datax","ECHO " + ircmsg.split("ECHO PENDING")[1])
elif "JOIN " in ircmsg:
joinchan(ircmsg.split(" ")[-1])
elif "SEND" in ircmsg and "PRIVMSG" in ircmsg:
sendmsg(ircmsg.split(" :")[0].split(" ")[-1]," " + ircmsg.split(":")[1])
#Get titles of items if in special channels
urlData = General.urlInfo(data_channels,channel,ircmsg)
if urlData != None:
sendmsg(channel,urlData)
#Copy of auto op
for i in auto_ops:
data = i.split(',')
if data[0].lower() == nick.lower() or data[0].lower() == hostmask.lower():
if data[1].lower() == channel or data[1] == "all":
if data[2] == "kick":
kickuser(channel,nick,"Sorry you are autokicked")
#Anti iovoidbot inforce :D
if ircmsg.find("?!enforce +b") != -1 and ircmsg.find("unaffiliated/bowserinator") != -1:
sendmsg(channel,"?!unenforce +b *!*@unaffiliated/bowserinator")
kickuser(channel,"IovoidBot","Damn you iovoid")
def checkParam( self, typ, time2go, duration ):
if not typ or time2go < 0 or duration < 0 or not General.checkActionType( typ ):
return False
return True
def Btn_StartGetCleft_Clicked(self):
if self.top.ValidateProcessRunning():
return
if self.Validate_Fields():
self.DisplayMessage(" ERROR: Not all fields are validated.", 2)
return
try:
TmpFile = os.path.join(self.top.GetCleftProject_Dir, 'tmp.pdb')
if self.PyMOL:
if cmd.count_atoms(self.defaultOption.get()) == 0:
self.DisplayMessage(
" ERROR: No atoms found for object/selection '" +
self.defaultOption.get() + "'", 2)
return
cmd.save(TmpFile, self.defaultOption.get(), 1)
except:
self.DisplayMessage(
" ERROR: Could not save the object/selection '" +
self.defaultOption.get() + "'", 2)
return
if self.ResiduValue.get() != '':
# with HETATM groups
if General.store_Residues(self.listResidues, TmpFile, 1) == -1:
self.DisplayMessage(
" ERROR: Could not retrieve list of residues for object/selection '"
+ self.defaultOption.get() + "'", 2)
return
if self.listResidues.count(self.ResiduValue.get()) == 0:
self.DisplayMessage(
" ERROR: The residue entered could not be found in the object/selection '"
+ self.defaultOption.get() + "'", 2)
self.EntryResidu.config(bg=self.top.Color_Red)
return
self.EntryResidu.config(bg=self.top.Color_White)
self.DisplayMessage(
" Analyzing clefts for object/selection '" +
self.defaultOption.get() + "'...", 0)
#TmpFile = '/Users/francisgaudreault/1stp.pdb'
Command_Line = '"' + self.top.GetCleftExecutable + '" -p "' + TmpFile + '"' + self.Get_Arguments(
)
# Clear temporary clefts
self.Btn_Clear_Clicked()
self.top.ProcessError = False
self.top.ProcessRunning = True
self.GetCleftRunning(True)
# Run GetCleft
StartRun = Start(self, self.queue, Command_Line)
def remove_gap_columns(id2seq, refSeq=None, refStr=None, minGapRatio=1.0):
"""
Remove alignment columns with too many gaps
minGapRatio -- Remove columns with gap ratio greater than minGapRatio [0-1]
Return {
'id2seq': {id1:aligned_seq1, id2:aligned_seq2, ...},
'refSeq': refSeq, # if refSeq != None
'refStr': refStr # if refStr != None
}
"""
keys = list(id2seq.keys())
alignment_list = []
for key in keys:
alignment_list.append(id2seq[key].replace('~', '-').replace(
':', '-').replace('.', '-').upper().replace('U', 'T'))
align_columns = collect_columns(alignment_list)
Len = len(id2seq[keys[0]])
if refStr is None:
refBpmap = {}
else:
refBpmap = Structure.dot2bpmap(refStr)
columns_to_remove = []
for i in range(Len):
if i in columns_to_remove:
continue
#print( i, align_columns[i].count('-'), len(align_columns[i]) )
if align_columns[i].count('-') / len(align_columns[i]) >= minGapRatio:
columns_to_remove.append(i)
if i + 1 in refBpmap:
columns_to_remove.append(refBpmap[i + 1] - 1)
columns_to_remove.sort()
#print(columns_to_remove)
clean_id2seq = {}
for key in id2seq:
clean_id2seq[key] = ""
cur_seq = id2seq[key]
for i in range(Len):
if not General.bi_search(i, columns_to_remove):
clean_id2seq[key] += cur_seq[i]
return_value = {'id2seq': clean_id2seq}
if refSeq:
_refSeq = ""
for i in range(Len):
if not General.bi_search(i, columns_to_remove):
_refSeq += refSeq[i]
return_value['refSeq'] = _refSeq
if refStr:
_refStr = ""
for i in range(Len):
if not General.bi_search(i, columns_to_remove):
_refStr += refStr[i]
_Len = len(_refStr)
#_refStr = Structure.ct2dot(Structure.dot2ct(_refStr), _Len)
return_value['refStr'] = _refStr
return return_value
def call_covariation(query_seq,
query_dot,
model_name,
seqdbFn,
workdir=None,
nohmm=False,
cmsearchE=1,
cpu=20,
use_LSF=True,
LSF_parameters={},
progress=True,
clean=False):
"""
Call covariation has two steps:
1. Search homology sequence from sequence databse;
2. Call covaring base pairs
query_seq -- Query sequence
query_dot -- Query dot-bracket structure
model_name -- CM model name and R-scape output file name
seqdbFn -- File name of sequence database
workdir -- Working directory, if not provide a random directory will generate.
nohmm -- cmsearch parameter
cmsearchE -- cmsearch E-value
cpu -- Threads for cmcalibrate and cmsearch
use_LSF -- Submit to LSF if True
LSF_parameters -- { 'queue': 'Z-ZQF', 'cpu': 20, 'job_name': 'cmsearch', 'logFn': '/dev/null', 'errFn': '/dev/null' }
progress -- Print the progress
clean -- Clean the directory after running
Return a list of covaring base pairs:
[ (left, right), ... ]
"""
import os, General, Colors, shutil
if workdir is None:
randID = random.randint(1000000, 9000000)
dirname = f"call_covariation_{randID}"
workdir = os.path.join(os.environ['HOME'], dirname)
if not os.path.exists(workdir):
os.mkdir(workdir)
new_seqdbFn = os.path.join(workdir, "seqDB.fa")
sto_file = os.path.join(workdir, "input.sto")
cm_file = os.path.join(workdir, "model.cm")
output_sto = os.path.join(workdir, "output.sto")
output_txt = os.path.join(workdir, "output.txt")
R_scape_dir = os.path.join(workdir, "R-scape")
### Step 0. Prepare combined Fasta file
if progress:
print(Colors.f(f"The work directory is: {workdir}", fc='green'))
print(Colors.f("Step 0. Prepare combined Fasta file", fc='green'))
General.write_fasta({'input': query_seq}, new_seqdbFn)
os.system(f'cat {seqdbFn} >> {new_seqdbFn}')
### Step 1. Build stockholm file
if progress:
print(Colors.f("Step 1. Build stockholm file", fc='green'))
dot2sto({'input': [query_seq, query_dot]}, model_name, sto_file, mode='w')
### Step 2. Build cm file from sto file
if progress:
print(Colors.f("Step 2. Build cm file from sto file", fc='green'))
cmbuild(sto_file, cm_file, verbose=False, showCMD=progress)
### Step 3. Calibrate file
if progress:
print(Colors.f("Step 3. Calibrate file", fc='green'))
job = cmcalibrate(cm_file,
cpu=cpu,
verbose=False,
showCMD=progress,
use_LSF=use_LSF,
LSF_parameters={})
job.wait()
### Step 4. Search with CM
if progress:
print(Colors.f("Step 4. Search with CM", fc='green'))
job = cmsearch(cm_file,
new_seqdbFn,
output_txt,
output_sto,
cpu=cpu,
toponly=True,
nohmm=nohmm,
nohmmonly=True,
outputE=20,
acceptE=cmsearchE,
cut_ga=False,
rfam=False,
glocal=False,
verbose=False,
showCMD=progress,
use_LSF=use_LSF,
LSF_parameters={})
job.wait()
#### Step 5. R-scape Runing
if progress:
print(Colors.f("Step 5. R-scape Runing", fc='green'))
R_scape(output_sto,
R_scape_dir,
outname=model_name,
maxIdentity=0.985,
minIndentity=0.500,
F=0.5,
gapthresh=0.5,
two_set_test=True,
fold=False,
acceptE=0.05,
nseqmin=5,
verbose=False,
showCMD=progress)
#### Step 6. Read R-scape result
rscape_file = os.path.join(R_scape_dir, f'{model_name}.cov')
covary_bps = []
if os.path.exists(rscape_file):
rscape_list = read_RScape_result(rscape_file)
id2seq, refStr, refAnnot = General.load_stockholm(output_sto)[0]
input_id = [key for key in id2seq if key.startswith('input')][0]
posDict = get_alignedPos2cleanPos_dict(id2seq[input_id])
for bp in rscape_list:
covary_bps.append((posDict[bp[0]], posDict[bp[1]]))
l, r = covary_bps[-1]
bp_base = query_seq[l - 1] + query_seq[r - 1]
if bp_base.replace('U', 'T') not in ('AT', 'TA', 'GC', 'CG', 'GT',
'TG'):
print(f"Warning: {bp_base} is not a RNA base pair")
if clean:
shutil.rmtree(workdir)
return covary_bps
def calc_covBP_from_sto(stoFn,
querySeq=None,
query_id_pattern=None,
full_seq=None,
allpair=False,
min_seqs=8,
min_score=0.4):
"""
Calculate the RNAalignfold_stack score for all base pairs in stockholm
Please note that the refseq in stockholm file should be consistent with querySeq you provide
stoFn -- Stockholm file
querySeq -- Query sequence, the reference sequence (#=GC RF) will aligned with querySeq
If no querySeq provided, the ID match query_id_pattern will used as query sequence
query_id_pattern -- The query ID mattern, if querySeq is provided, will be ignored
full_seq -- If full_seq is provide and querySeq=None, the sequence index by query_id_pattern will
be search in full_seq, the left and right index will be re-indexed
allpair -- Calculate all base pairs, not only pairs in structure
min_seqs -- Minimum sequences in the alignments
min_score -- Minimum score to record
Return [ [left, right, score],.... ]
"""
import Structure, re
id2seq_dict, refStr, refSeq = General.load_stockholm(stoFn)[0]
if len(id2seq_dict) < min_seqs:
return []
columns = collect_columns([value for key, value in id2seq_dict.items()])
alignLen = len(refSeq)
if allpair:
ct = []
for i in range(alignLen):
for j in range(i + 1, alignLen):
ct.append([i, j])
else:
ct = Structure.dot2ct(refStr)
covary_bps = []
for b1, b2 in ct:
rnaalignscore2 = calc_RNAalignfold_stack(columns, b1, b2)
if rnaalignscore2 > min_score:
covary_bps.append([b1, b2, round(rnaalignscore2, 3)])
refSeq = refSeq.replace('~', '-').replace(':', '-').replace(
'.', '-').upper().replace('U', 'T')
if querySeq:
refSeq_realigned, query_aligned = Structure.multi_alignment(
[refSeq.replace('-', ''),
querySeq.upper().replace('U', 'T')])
### 构建一个字典：从refSeq的坐标指向querySeq的坐标
refseq2query = {}
pos_ref, pos_refrealign = 0, 0
query_pos = 0
while pos_ref < len(refSeq):
while pos_ref < len(refSeq) and refSeq[pos_ref] == '-':
pos_ref += 1
if pos_ref == len(refSeq): break
while refSeq_realigned[pos_refrealign] == '-':
if query_aligned[pos_refrealign] != '-':
query_pos += 1
pos_refrealign += 1
#if pos_refrealign==len(query_aligned): break
refseq2query[pos_ref + 1] = query_pos + 1
pos_ref += 1
pos_refrealign += 1
query_pos += 1
i = 0
while i < len(covary_bps):
if covary_bps[i][0] in refseq2query and covary_bps[i][
1] in refseq2query:
covary_bps[i][0] = refseq2query[covary_bps[i][0]]
covary_bps[i][1] = refseq2query[covary_bps[i][1]]
i += 1
else:
del covary_bps[i]
elif query_id_pattern:
tid_list = [
name for name in id2seq_dict.keys()
if re.match(query_id_pattern, name)
]
assert len(tid_list) == 1, f"Error: {len(tid_list)} tid match pattern"
query_tid = tid_list[0]
clean_query_seq = id2seq_dict[query_tid].replace('~', '').replace(
':', '').replace('.', '').replace('-',
'').upper().replace('U', 'T')
if full_seq:
full_seq = full_seq.replace('U', 'T')
start_pos = full_seq.find(clean_query_seq)
if start_pos == -1:
raise RuntimeError('queryseq not in full_seq')
if full_seq.find(clean_query_seq, start_pos + 1) != -1:
raise RuntimeError('queryseq are find in multiple position')
else:
start_pos = 0
aligned_query_seq = id2seq_dict[query_tid].upper().replace('U', 'T')
alignedPos2cleanPos = get_alignedPos2cleanPos_dict(
id2seq_dict[query_tid])
i = 0
while i < len(covary_bps):
l, r = covary_bps[i][:2]
if alignedPos2cleanPos[l] and alignedPos2cleanPos[r]:
nl = alignedPos2cleanPos[l] + start_pos
nr = alignedPos2cleanPos[r] + start_pos
covary_bps[i][0] = nl
covary_bps[i][1] = nr
if full_seq:
assert aligned_query_seq[l - 1] == full_seq[
nl - 1], "Exception: seq not same with full_seq"
assert aligned_query_seq[r - 1] == full_seq[
nr - 1], "Exception: seq not same with full_seq"
i += 1
else:
del covary_bps[i]
else:
raise RuntimeError('querySeq or query_id_pattern must be specified')
return covary_bps
bp[i + 1] = {}
for t in tags_p:
w2_t = t
V[i + 1][t] = {}
bp[i + 1][t] = {}
l = {}
for r in tags_curr:
l[r] = {}
for tT in tags_p2:
w1_t = tT
score = (V[i][tT][t]) + getScore(w1,w2,word,w4,w5,w1_t,w2_t)
for r in tags_curr:
l[r][tT] = score[features_m[r]]
for r in tags_curr:
V[i + 1][t][r] = max(list(l[r].values()))
bp[i + 1][t][r] = General.argmax(l[r])
tags_p2 = tags_p
tags_p = tags_curr
V.pop(0)
bp.pop(0)
endMatrix = map(lambda x: x.values(), V[row_l-1].values())
maxEnd = list(map(max, endMatrix))
maxV = max(maxEnd)
maxTIndex = maxEnd.index(maxV)
maxT = list(V[row_l-1].keys())[maxTIndex]
maxR = General.argmax(V[row_l-1][maxT])
y = [0 for i in range(0, row_l)]
y[row_l-1] = maxR
y[row_l-2] = maxT
for i in reversed(range(0, row_l-2)):
y[i] = bp[i + 2][y[i + 1]][y[i + 2]]
def cmsearch(CMFile,
seqdbFn,
outTXT,
outSto,
cpu=0,
toponly=False,
nohmm=False,
nohmmonly=False,
outputE=20,
acceptE=1,
cut_ga=False,
rfam=False,
glocal=False,
verbose=True,
showCMD=True,
use_LSF=False,
LSF_parameters={}):
"""
Search CM model from sequence database
CMFile -- CM file
seqdbFn -- File name of sequence database
outTXT -- Output txt file
outSto -- Output Stockholm file
cpu -- How many threads to use
toponly -- Only search the top(forward) strand
nohmm -- skip all HMM filter stages, use only CM (slow)
nohmmonly -- never run HMM-only mode, not even for models with 0 basepairs
outputE -- report sequences <= this E-value threshold in output [10.0] (x>0)
acceptE -- consider sequences <= this E-value threshold as significant [0.01]
cut_ga -- use CM's GA gathering cutoffs as reporting thresholds
rfam -- set heuristic filters at Rfam-level (fast)
glocal -- configure CM for glocal alignment [default: local]
verbose -- Show command and log information
showCMD -- Print the command
use_LSF -- Submit to LSF if True
LSF_parameters -- { 'queue': 'Z-ZQF', 'cpu': 20, 'job_name': 'cmsearch', 'logFn': '/dev/null', 'errFn': '/dev/null' }
Require: cmsearch
"""
import General
import shutil
cmsearch_exe = General.require_exec("cmsearch", exception=True)
cmd = f"{cmsearch_exe} --notextw "
if cpu > 0:
cmd += f"--cpu {cpu} "
if toponly:
cmd += "--toponly "
if nohmm:
cmd += "--nohmm "
if nohmmonly:
cmd += "--nohmmonly "
if cut_ga:
cmd += "--cut_ga "
if rfam:
cmd += "--rfam "
if glocal:
cmd += "-g "
cmd += f"-E {outputE} --incE {acceptE} -o {outTXT} -A {outSto} {CMFile} {seqdbFn}"
if not verbose:
cmd += " > /dev/null"
if showCMD:
import Colors
print(Colors.f(cmd, fc='yellow'))
if use_LSF:
import Cluster
job = Cluster.new_job(command=cmd,
queue=LSF_parameters.get('queue', 'Z-ZQF'),
cpu=LSF_parameters.get('cpu', 20),
job_name=LSF_parameters.get(
'job_name', 'cmsearch'),
logFn=LSF_parameters.get('logFn', '/dev/null'),
errFn=LSF_parameters.get('errFn', '/dev/null'))
#print(job.get_submit_command())
job.submit()
return job
else:
os.system(cmd)
def __init__(self, root, top, menuindex, Project_Dir, Install_Dir,
NRGsuite_Dir, OSid, PyMOL, Name, WINDOWWIDTH, WINDOWHEIGHT,
RootPrefs):
self.Name = Name
self.OSid = OSid
self.PyMOL = PyMOL
self.NRGsuite_Dir = NRGsuite_Dir
self.Install_Dir = Install_Dir
self.Project_Dir = Project_Dir
self.Folders = [self.NRGsuite_Dir]
if self.Project_Dir:
self.Folders.append(self.Project_Dir)
self.Set_Folders()
self.Validate_Folders()
self.Prefs = RootPrefs
self.Color_Green = '#CCFFCC'
self.Color_Grey = '#EDEDED'
self.Color_Gray = '#EDEDED'
self.Color_Blue = '#6699FF'
self.Color_Red = '#FF9999'
self.Color_White = '#FFFFFF'
self.Color_Black = '#000000'
self.root = root
self.root.title(self.Name)
self.top = top
self.menuindex = menuindex
if self.menuindex != -1:
self.top.menuBar.component('NRGsuite-menu').entryconfig(
self.menuindex, state='disabled')
self.WINDOWWIDTH = WINDOWWIDTH
self.WINDOWHEIGHT = WINDOWHEIGHT
#self.root.geometry() # Interface DIMENSIONS
#self.root.maxsize(WINDOWWIDTH,WINDOWHEIGHT)
self.root.minsize(self.WINDOWWIDTH, self.WINDOWHEIGHT)
self.root.protocol('WM_DELETE_WINDOW', self.Quit)
General.CenterWindow(self.root, self.WINDOWWIDTH, self.WINDOWHEIGHT)
#==================================================================================
# SET the default fonts of the interface
#==================================================================================
FontType = self.Prefs.GetFontType()
FontSize = self.Prefs.GetFontSize()
self.font_Title = tkFont.Font(family=FontType,
size=FontSize,
weight=tkFont.BOLD)
self.font_Title_H = tkFont.Font(family=FontType,
size=FontSize + 1,
weight=tkFont.BOLD)
self.font_Text = tkFont.Font(family=FontType, size=FontSize)
self.font_Text_H = tkFont.Font(family=FontType, size=FontSize + 1)
self.font_Text_I = tkFont.Font(family=FontType,
size=FontSize,
slant=tkFont.ITALIC)
self.font_Text_U = tkFont.Font(family=FontType,
size=FontSize,
underline=True)
self.ChildWindow = None
self.ActiveFrame = None
self.Run = None
self.ProcessError = False
self.ProcessRunning = False
self.ProcessParsing = False
self.ProcessDone = False
self.ParseState = 10
self.SimulateState = -1
self.fMain = Frame(self.root)
self.fMain.pack(expand=True)
self.Def_Vars()
self.Init_Vars()
self.Frame_Main()
self.Build_Tabs()
self.MakeMenuBar()
self.After_Init()
self.Clean()
def Build_Rfam_seed(input_sto,
input_seq,
seqDBFastaFn,
workdir,
toponly=True,
iteration=3,
blastFilter=None,
use_LSF=True,
cores=5,
verbose=True):
"""
This function build a rfam seed according to https://docs.rfam.org/en/latest/building-families.html
Repeat this process "iteration" times:
Seed -[cmbuild]-> CM -[cmcalibrate]-> CM -[cmsearch]-> Stockholm -[Filter]-> Fasta -[cmalign]-> Stockholm -[cmbuild]-> CM
input_sto -- Seed stockholm file, contains single sequence and structure, output file of Covariation.dot2sto
input_seq -- The sequence in input_sto
seqDBFastaFn -- The target sequences, contains all homologous sequences
workdir -- Work directory, all immediate files will be contained
toponly -- Only search the positive strand
iteration -- How many times to repeat the cmsearch processes
blastFilter -- If set, will use blast result to filter the cmsearch target. The cmsearch coordinate will
be compared with blast result. The purpose is to prevent the cmsearch give too much weight
on structure and ignore the sequence
{ 'full_seq': "ACTG...", # The full length sequence contain input_seq
'blastdb':"/path/to/blastdb",
'flanking': 20, # Max distance between the cmsearch result and blast result
'blast_identity': 0.4, # Blast cutoff
'min_match': 5, # Minimun target
'ignore_seq': ['input'] # Which results to ignore
}
use_LSF -- bsub or run in local
cores -- How many cores to use
verbose -- If print the information in the screen
Return:
Return a stockholm file with final alignment
"""
import Alignment, Colors
if blastFilter:
input_start = blastFilter['full_seq'].find(input_seq)
assert input_start != -1, f"input_seq not in full_seq, consider maintain consistent letter case and U/T"
input_end = input_start + len(input_seq)
start = max(input_start - blastFilter.get('flanking', 20), 0)
end = min(input_end + blastFilter.get('flanking', 20),
len(blastFilter['full_seq']))
hits = Alignment.blast_sequence_V2(
blastFilter['full_seq'][start:end],
blastFilter['blastdb'],
verbose=verbose,
task='blastn',
maxhit=5000,
perc_identity=blastFilter['blast_identity'])
target_valid_range = {}
for hit in hits:
if hit.hit_acc not in target_valid_range:
target_valid_range[hit.hit_acc] = (hit.hit_from, hit.hit_to)
if len(target_valid_range) < blastFilter.get('min_match', 5):
if verbose:
print(Colors.f("Failed: Too little blast target", 'red'))
return False
else:
if verbose:
print(f"Blast: {len(target_valid_range)} results found")
for it_num in range(iteration):
if verbose: print(f"===========>>> Iteration {it_num} <<<===========")
### Define files
if it_num == 0:
input_sto = input_sto
else:
input_sto = os.path.join(workdir, f'cmalign_output_{it_num-1}.sto')
input_cm = os.path.join(workdir, f'cmsearch_input_{it_num}.cm')
cmsearch_output_txt = os.path.join(workdir,
f'cmsearch_output_{it_num}.txt')
cmsearch_output_sto = os.path.join(workdir,
f'cmsearch_output_{it_num}.sto')
cmalign_input_fa = os.path.join(workdir, f'cmalign_input_{it_num}.fa')
cmalign_output_sto = os.path.join(workdir,
f'cmalign_output_{it_num}.sto')
### Build CM model
cmbuild(input_sto, input_cm)
h = cmcalibrate(input_cm,
use_LSF=use_LSF,
LSF_parameters={'cpu': cores})
if use_LSF: h.wait()
### cmsearch
tmp_fa, tmp_annot = General.load_fasta(seqDBFastaFn,
load_annotation=True)
tmp_fa['input'] = input_seq
General.write_fasta(tmp_fa, os.path.join(workdir, 'tmp_ref.fa'),
tmp_annot)
del tmp_fa
h = cmsearch(input_cm, os.path.join(workdir, 'tmp_ref.fa'), \
cmsearch_output_txt, cmsearch_output_sto, cpu=cores, toponly=toponly, nohmm=False, nohmmonly=False, \
outputE=20, acceptE=1, cut_ga=False, rfam=False, glocal=False, verbose=True, showCMD=True, use_LSF=use_LSF,
LSF_parameters={'cpu': cores})
if use_LSF: h.wait()
os.remove(os.path.join(workdir, 'tmp_ref.fa'))
### Read cmsearch result
id2seq_dict, refStr, refSeq = General.load_stockholm(
cmsearch_output_sto)[0]
refID = [key for key in id2seq_dict if key.startswith('input')][0]
refSeq = id2seq_dict[refID]
### Filter results not in blast hits
if blastFilter:
for key in list(id2seq_dict.keys()):
if '/' in key:
true_id, start_end = key.rsplit('/', 1)
start, end = start_end.split('-')
start = int(start)
end = int(end)
if true_id in target_valid_range:
valid_start, valid_end = target_valid_range[true_id]
if (end < valid_start or start > valid_end):
del id2seq_dict[key]
elif true_id in blastFilter.get('ignore_seq', ['input']):
if verbose: print("Ignored:", true_id)
else:
if verbose:
print("Killed:", Colors.f(true_id, fc='red'))
del id2seq_dict[key]
else:
if verbose: print("Killed:", Colors.f(true_id, fc='green'))
del id2seq_dict[key]
### Remove highly similar sequences
uniq_seq = collapse_sequences(id2seq_dict,
refSeq,
max_identity=0.98,
min_match_identity=0.2,
max_indel_ratio=0.5)
### Remove sequences with too many base pairs broken
clean_id2seq = remove_bpbreak_sequences(uniq_seq,
refStr,
maxBpBreakRatio=0.2,
maxBpDeletRatio=0.5,
maxBpBreakCount=99,
maxBpDeletion=99)
### Remove sequences with nucleotides other than AUCG
for key in list(clean_id2seq.keys()):
v = clean_id2seq[key].replace('~', '-').replace(':', '-').replace(
'.', '-').upper().replace('U', 'T')
if len(v) != v.count('A') + v.count('T') + v.count('C') + v.count(
'G') + v.count('-'):
del clean_id2seq[key]
pure_fasta = {
k: v.replace('~', '').replace(':', '').replace('.', '').replace(
'-', '').upper().replace('U', 'T')
for k, v in clean_id2seq.items()
}
### Remove highly similar sequences
collapsed_pure_fasta = Alignment.cd_hit_est(pure_fasta,
identity=0.98,
verbose=True)
clean_id2seq = {k: clean_id2seq[k] for k in collapsed_pure_fasta}
if len(clean_id2seq) == 0:
#### No homologous sequence to call covariation in the sequence db
if verbose:
print(Colors.f("Failed: No homologous sequences left", 'red'))
return False
### Remove alignment columns with too many gaps
returnvalues = remove_gap_columns(clean_id2seq,
refSeq=refSeq,
refStr=refStr,
minGapRatio=1.0)
### cmalign
GS_DE = read_sto_DE(cmsearch_output_sto) # read description
small_seqdb = {
k: v.replace('-', '')
for k, v in returnvalues['id2seq'].items()
}
small_seqdb['input'] = input_seq
General.write_fasta(small_seqdb,
os.path.join(workdir, 'cmalign_input.fa'), GS_DE)
h = cmalign(input_cm,
os.path.join(workdir, 'cmalign_input.fa'),
cmalign_output_sto,
cpu=cores,
glocal=False,
outformat='Stockholm',
mxsize=1028.0,
verbose=True,
showCMD=True,
use_LSF=use_LSF,
LSF_parameters={'cpu': cores})
if use_LSF: h.wait()
return cmalign_output_sto
import General, Structure, Visual, SARS2, Covariation
wuhan_id = 'NC_045512.2'
#shape = General.load_shape('/Share2/home/zhangqf7/lipan/SARS2/icSHAPE/2020-06-01-process/virus.shape')[wuhan_id]
shape = General.load_shape(
'/Share/home/zhangqf8/sunlei/data/SARS2/20200529-SARS2-huh7/SARS2-huh7/Processing/8.calcSHAPE/virus-w50.shape'
)[wuhan_id]
seq = General.load_fasta(
'/Share2/home/zhangqf7/lipan/SARS2/sequence/SARS2.fa')[wuhan_id]
dot = General.load_dot(
'/Share2/home/zhangqf7/lipan/SARS2/2nd_structures/Rfam/structures.dot')
utr_5 = [1, 299]
utr_3 = [29536, 29870]
seq5 = seq[utr_5[0] - 1:utr_5[1]]
shape5 = shape[utr_5[0] - 1:utr_5[1]]
seq3 = seq[utr_3[0] - 1:utr_3[1]]
shape3 = shape[utr_3[0] - 1:utr_3[1]]
dot['RF03120_UTR5'][0] == seq5
dot['RF03125_UTR3'][0] == seq3
######## 预测二级结构
prob3, pfs3 = Structure.partition(seq3,
shape_list=shape3,
si=-0.4,
sm=1.5,
md=300,
def main():
start_time = time.time()
f = open('Kakilog.log', 'a+', encoding='utf-8')
now = datetime.now()
print("Log started: ", now, file=f)
# read config file
config = configparser.ConfigParser()
try:
config.read('config.ini', encoding='utf-8')
except:
config.read('config.ini', encoding='utf-8-sig')
title = 'KakiRaid'
if int(config['DEFAULT']['AdjustWindow']) == 1:
General.adjust_window(title, [0, 0])
elif int(config['DEFAULT']['AdjustWindow']) == 2:
General.adjust_window(title, [245, 123])
window = General.get_window_coordinate(title) # x, y, w, h
window.append(start_time) # index 4
auto_legend_count = int(config['DEFAULT']['AutoLegendCount'])
if int(config['DEFAULT']['ModeSelection']) == 0:
count = 0
max_count = int(config['DEFAULT']['MainLoopCount'])
current_floor = 0
stat = dict()
stat['Total_Resources'] = 0
stat['Total_Monster'] = 0
stat['Total_Loot_Curse'] = 0
stat['Total_Loot_Other'] = 0
stat['Total_Camp'] = 0
stat['Total_Ruin'] = 0
window.append(stat) # index 5
window.append(config) # index 6
window.append(f)
keys = [
window[6]['Baidu_API']['API_ID'],
window[6]['Baidu_API']['API_KEY'],
window[6]['Baidu_API']['SECRET_KEY']
]
while count < max_count:
print('\n', file=f)
f.flush()
temp_start_time = time.time()
if count != 0:
if current_floor > 500:
time.sleep(130)
elif current_floor > 400:
time.sleep(120)
elif current_floor > 300:
time.sleep(95)
elif current_floor > 200:
time.sleep(85)
else:
time.sleep(75)
General.failure_detect(window)
curse_page_result = General.curse_page_detect(window)
if not curse_page_result:
stuck_result = General.stuck_detect(window)
curse_page_result = General.curse_page_detect(
window, 400) # 400 as count to bypass repeated detect
while stuck_result != 0 and not curse_page_result:
if stuck_result == 1:
# To add support for network turbulence and portal stuck?
print('Progress stuck at unknown, quitting program..',
file=f)
f.close()
General.send_email('Kaki script stuck, quit program.')
sys.exit()
elif stuck_result == 2:
print(
'Progress stuck at relic augmentation, try resolving..',
file=f)
pyautogui.click(x=window[0] + (320 - 245),
y=window[1] + (213 - 123),
duration=0.1)
stuck_result = General.stuck_detect(window)
if stuck_result == 1:
General.toggle_auto_path_finding(window)
stuck_result = General.stuck_detect(window)
else:
stuck_result = 0
else:
curse_images = General.get_curse_image(window)
curses = General.parse_curse_image(curse_images, keys)
General.select_curse(window, curses)
General.resource_completion_detect(window)
General.map_management(window)
elapsed_time = time.time() - temp_start_time
count += 1
print("Curse " + str(count) + " selected!", file=f)
print('time elapsed: ' + str(elapsed_time) + ' seconds.', file=f)
time.sleep(10)
if current_floor == 0:
current_floor = General.floor_detection(window)
else:
current_floor += 5
print('Current Floor: ' + str(current_floor) + '\n', file=f)
f.close()
General.send_email('Kaki script quit with time out')
print('Quit with time out')
elif int(config['DEFAULT']['ModeSelection']) == 1:
General.auto_legend(window, auto_legend_count)
elif int(config['DEFAULT']['ModeSelection']) == 2:
grind_count = int(config['Void_Island']['Count'])
if grind_count == 0:
grind_count = 9999
while grind_count > 0:
General.void_island_grind(window)
print('Void Island Completed', file=f)
f.flush()
grind_count -= 1
