def getStatusBarHPAttribute(self):
percentHealth = float(self.getHP())/self.getMaxHP()
if (percentHealth <= 0.333):
return Colors.getPairNumber('RED', 'BLACK')
elif (percentHealth <= 0.666):
return Colors.getPairNumber('YELLOW', 'BLACK')
else:
return Colors.getPairNumber('GREEN', 'BLACK')
def updateColor(self, fgColor, bgColor):
self.attribute = Colors.getPairNumber(fgColor, bgColor)
self.fgColor = fgColor
self.bgColor = bgColor
self.zDepthAttribute = self.attribute
if (fgColor == bgColor): #Same color! Uh oh!
if (bgColor != 'BLACK'):
self.zDepthAttribute = Colors.getPairNumber(self.fgColor, 'BLACK')
else:
self.zDepthAttribute = Colors.getPairNumber(self.fgColor, 'WHITE')
def check_first_and_last_line(self):
num_lines = sum(1 for line in self.fd)
self.fd.seek(0)
self.end_val = num_lines
rows, self.bar_length = popen('stty size', 'r').read().split()
self.bar_length = int(self.bar_length) - len(' 00\rPercent: 100 {1}%')
print Colors.change_color(
' Nombre de lignes au total: %s' % num_lines, 'OKGREEN')
def check_first_and_last_line(self):
num_lines = sum(1 for line in self.fd)
self.fd.seek(0)
self.end_val = num_lines
rows, self.bar_length = popen('stty size', 'r').read().split()
self.bar_length = int(self.bar_length) - len(' 00\rPercent: 100 {1}%')
print Colors.change_color(
' Nombre de lignes au total: %s' % num_lines, 'OKGREEN')
def annotate_covariation(ref_aligned_seq,
input_aligned_seq,
ref_aligned_dot,
anno_loop=False):
"""
ref_aligned_seq -- Reference aligned sequence
input_aligned_seq -- An input aligned sequence to annotate
ref_aligned_dot -- Reference aligned dotbracket structure
anno_loop -- Will annotate loop mutations
Use color to annotate mutate bases in stem loop
"""
import Colors
assert len(ref_aligned_seq) == len(input_aligned_seq) == len(
ref_aligned_dot)
ref_aligned_seq = ref_aligned_seq.replace('U', 'T')
input_aligned_seq = input_aligned_seq.replace('U', 'T')
anno_align_seq = list(input_aligned_seq)
pair_bps = ['AT', 'TA', 'CG', 'GC', 'TG', 'GT']
bp_list = dot2ct(ref_aligned_dot)
for bp in bp_list:
raw_bp = ref_aligned_seq[bp[0] - 1] + ref_aligned_seq[bp[1] - 1]
new_bp = input_aligned_seq[bp[0] - 1] + input_aligned_seq[bp[1] - 1]
assert raw_bp in pair_bps
if new_bp in pair_bps:
if raw_bp != new_bp:
anno_align_seq[bp[0] - 1] = Colors.f(
anno_align_seq[bp[0] - 1], fc="cyan"
) #'\x1b[1;36;40m' + anno_align_seq[ bp[0]-1 ] + '\x1b[0m'
anno_align_seq[bp[1] - 1] = Colors.f(
anno_align_seq[bp[1] - 1], fc="cyan"
) #'\x1b[1;36;40m' + anno_align_seq[ bp[1]-1 ] + '\x1b[0m'
else:
anno_align_seq[bp[0] - 1] = Colors.f(
anno_align_seq[bp[0] - 1], fc="red"
) #'\x1b[1;31;40m' + anno_align_seq[ bp[0]-1 ] + '\x1b[0m'
anno_align_seq[bp[1] - 1] = Colors.f(
anno_align_seq[bp[1] - 1], fc="red"
) #'\x1b[1;31;40m' + anno_align_seq[ bp[1]-1 ] + '\x1b[0m'
if anno_loop:
for i in range(len(anno_align_seq)):
if ref_aligned_dot[
i] == '.' and input_aligned_seq[i] != ref_aligned_seq[i]:
anno_align_seq[i] = Colors.f(
anno_align_seq[i], fc="yellow"
) #'\x1b[1;33;40m' + anno_align_seq[ i ] + '\x1b[0m'
return "".join(anno_align_seq)
def checkfile_shell(self, path):
check_zip = \
"file %s | sed 's/^.*gzip.*/gzip/'" % path
check_ascii = \
"file %s | sed 's/^.*ASCII.*/ASCII/'" % path
check_sas = \
"file %s | sed 's/^.*SAS.*/SAS/'" % path
check_empty = \
"file %s | sed 's/^.*empty.*/EMPTY/'" % path
if self.check_path(path) is False:
return False
if self.execute.cmd(check_zip) == 'gzip':
print Colors.change_color(' File Type: gzip', 'OKGREEN')
self.fd = gzip.open(path, 'rb')
elif (self.execute.cmd(check_ascii) == "ASCII"
or self.execute.cmd(check_sas) == "SAS"):
print Colors.change_color(' File Type: ASCII', 'OKGREEN')
self.fd = open(path, 'r')
elif (self.execute.cmd(check_empty) == 'EMPTY'):
print Colors.change_color('\n This File is Empty.', 'FAIL')
return False
else:
print Colors.change_color('\n Unrecognized file type ', 'FAIL')
return False
return True
def checkfile_shell(self, path):
check_zip = \
"file %s | sed 's/^.*gzip.*/gzip/'" % path
check_ascii = \
"file %s | sed 's/^.*ASCII.*/ASCII/'" % path
check_sas = \
"file %s | sed 's/^.*SAS.*/SAS/'" % path
check_empty = \
"file %s | sed 's/^.*empty.*/EMPTY/'" % path
if self.check_path(path) is False:
return False
if self.execute.cmd(check_zip) == 'gzip':
print Colors.change_color(' File Type: gzip', 'OKGREEN')
self.fd = gzip.open(path, 'rb')
elif (self.execute.cmd(check_ascii) == "ASCII" or
self.execute.cmd(check_sas) == "SAS"):
print Colors.change_color(' File Type: ASCII', 'OKGREEN')
self.fd = open(path, 'r')
elif (self.execute.cmd(check_empty) == 'EMPTY'):
print Colors.change_color('\n This File is Empty.', 'FAIL')
return False
else:
print Colors.change_color('\n Unrecognized file type ', 'FAIL')
return False
return True
def __init__(self, dataSet):
self.dataSet = dataSet
self.cardType = CardType.createType(self.generateList('type'), self.model)
self.cardTypes = CardTypes.createTypes(self.generateList('types'), self.model)
self.cmc = Cmc.createCmc(self.generateList('cmc'), self.model)
self.colorIdentity = ColorIdentity.createColorIdentity(self.generateList('colorIdentity'), self.model)
self.colors = Colors.createColors(self.generateList('colors'), self.model)
self.hand = Hand.createHand(self.generateList('hand'), self.model)
self.imageName = ImageName.createImageName(self.generateList('imageName'), self.model)
self.layouts = Layouts.createLayouts(self.generateList('layout'), self.model)
self.legalities = Legalities.createLegalities(self.generateList('legalities'), self.model)
self.life = Life.createLife(self.generateList('life'), self.model)
self.loyalty = Loyalty.createLoyalty(self.generateList('loyalty'), self.model)
self.manaCost = ManaCost.createManaCost(self.generateList('manaCost'), self.model)
self.name = Name.createName(self.generateList('name'), self.model)
self.names = Names.createNames(self.generateList('names'), self.model)
self.power = Power.createPower(self.generateList('power'), self.model)
self.printings = Printings.createPrintings(self.generateList('printings'), self.model)
self.rulings = Rulings.createRulings(self.generateList('rulings'), self.model)
self.source = Source.createSource(self.generateList('source'), self.model)
self.starter = Starter.createStarter(self.generateList('starter'), self.model)
self.cardSubTypes = CardSubTypes.createSubTypes(self.generateList('subtypes'), self.model)
self.cardSuperTypes = CardSuperTypes.createSuperTypes(self.generateList('supertypes'), self.model)
self.text = Text.createText(self.generateList('text'), self.model)
self.toughness = Toughness.createToughness(self.generateList('toughness'), self.model)
def create_labels(self):
"""Create the labels for the socket."""
Element.create_labels(self)
self._bg_color = Colors.get_color(self.get_color())
# create the layout
layout = gtk.DrawingArea().create_pango_layout('')
layout.set_markup(
Utils.parse_template(PORT_MARKUP_TMPL, port=self, font=PORT_FONT))
self.w, self.h = layout.get_pixel_size()
self.W = 2 * PORT_LABEL_PADDING + self.w
self.H = 2 * PORT_LABEL_PADDING + self.h * (3 if self.get_type()
== 'bus' else 1)
self.H += self.H % 2
# create the pixmap
pixmap = self.get_parent().get_parent().new_pixmap(self.w, self.h)
gc = pixmap.new_gc()
gc.set_foreground(self._bg_color)
pixmap.draw_rectangle(gc, True, 0, 0, self.w, self.h)
pixmap.draw_layout(gc, 0, 0, layout)
# create vertical and horizontal pixmaps
self.horizontal_label = pixmap
if self.is_vertical():
self.vertical_label = self.get_parent().get_parent().new_pixmap(
self.h, self.w)
Utils.rotate_pixmap(gc, self.horizontal_label, self.vertical_label)
def create_shapes(self):
"""Precalculate relative coordinates."""
Element.create_shapes(self)
self._sink_rot = None
self._source_rot = None
self._sink_coor = None
self._source_coor = None
#get the source coordinate
try:
connector_length = self.get_source().get_connector_length()
except:
return
self.x1, self.y1 = Utils.get_rotated_coordinate((connector_length, 0), self.get_source().get_rotation())
#get the sink coordinate
connector_length = self.get_sink().get_connector_length() + CONNECTOR_ARROW_HEIGHT
self.x2, self.y2 = Utils.get_rotated_coordinate((-connector_length, 0), self.get_sink().get_rotation())
#build the arrow
self.arrow = [(0, 0),
Utils.get_rotated_coordinate((-CONNECTOR_ARROW_HEIGHT, -CONNECTOR_ARROW_BASE/2), self.get_sink().get_rotation()),
Utils.get_rotated_coordinate((-CONNECTOR_ARROW_HEIGHT, CONNECTOR_ARROW_BASE/2), self.get_sink().get_rotation()),
]
source_domain = self.get_source().get_domain()
sink_domain = self.get_sink().get_domain()
self.line_attributes[0] = 2 if source_domain != sink_domain else 0
self.line_attributes[1] = gtk.gdk.LINE_DOUBLE_DASH \
if not source_domain == sink_domain == GR_MESSAGE_DOMAIN \
else gtk.gdk.LINE_ON_OFF_DASH
get_domain_color = lambda d: Colors.get_color((
self.get_parent().get_parent().get_domain(d) or {}
).get('color') or Colors.DEFAULT_DOMAIN_COLOR_CODE)
self._color = get_domain_color(source_domain)
self._bg_color = get_domain_color(sink_domain)
self._arrow_color = self._bg_color if self.is_valid() else Colors.CONNECTION_ERROR_COLOR
self._update_after_move()
def waitForStatusLineUpdateConfirmation(self, inputHandler = None):
if (inputHandler == None):
inputHandler = InputHandler.SingletonKeyboardInputHander(self.screen)
promptMessage = 'PRESS A KEY'
promptMessageLength = len(promptMessage)
y = self.getTerminalHeight() - 1
x = self.getTerminalWidth() - self.maxSideBarLen - 1
promptMessageAttr = Colors.BLINK | Colors.getPairNumber('BLACK', 'YELLOW')
self.screen.addnstr(y, x, promptMessage, promptMessageAttr)
self.draw()
curses.flash() #Visual bell
keyPressed = inputHandler.waitForKey()
Logger.put(' key found: %s' % (str(keyPressed)))
self.resetStatusLinesAppended()
#erase the prompt message
self.screen.addnstr(y, x, ' ' * promptMessageLength, promptMessageAttr)
self.draw()
def launchGame(screenParam):
global screen
screen = screenParam
Colors.init()
curses.curs_set(1)
screen.keypad(1)
screen.nodelay(1)
doIntro(screenParam)
#val = k.getKey()
#screen.addstr(2, 1, "%d" % (val))
w = World.World(screen, 80, 30)
w.doEventLoop()
def __init__(self,
entity_property: EntityProperty,
property_value: float = None,
parent: EntityGroup = None,
children: List[EntityGroup] = None) -> None:
self._entity_property = entity_property
self._property_value = property_value
# all entities in the group
self._entities = []
# #todo new update, if works, delete later
if parent is not None:
self._parent: EntityGroup = parent
# self._has_parent = True
self._has_parent: bool = parent is not None
if children is not None:
self._children: List[EntityGroup] = children
self._has_children: bool = True
else:
self._children: List[EntityGroup] = []
self._has_children: bool = False
# default blue line
self._color_line: str = Colors.RGBColor([0, 128, 255]).to_hex().hex
def generateXml(self, contourDB, contourFile, mapfile):
config = Config.get()
regionClusters = Utils.read_features(
config.get("MapData", "clusters_with_region_id"))
regionIds = sorted(
set(
int(region['cluster_id'])
for region in regionClusters.values()))
regionIds = map(str, regionIds)
countryBorders = Utils.read_features(
config.get("GeneratedFiles", "country_borders"))
colorFactory = Colors.ColorSelector(countryBorders,
Config.getColorWheel())
colors = colorFactory.optimalColoring()
ms = MapStyler(config, colors)
imgfile = config.get("MapOutput", "img_src_name")
ms.addCustomFonts(config.get("MapResources", "fontDir"))
ms.makeMap(contourFile, config.get("MapData", "countries_geojson"),
regionIds, contourDB)
ms.saveMapXml(config.get("MapData", "countries_geojson"), mapfile)
ms.saveImage(mapfile, imgfile + ".png")
ms.saveImage(mapfile, imgfile + ".svg")
def cmalign(CMFile,
seqdbFn,
outFn,
cpu=0,
glocal=False,
outformat='Stockholm',
mxsize=1028.0,
verbose=True,
showCMD=True,
use_LSF=False,
LSF_parameters={}):
"""
Search CM model from sequence database
CMFile -- CM file
seqdbFn -- File name of sequence database
outFn -- Output file
cpu -- How many threads to use
glocal -- Configure CM for global alignment [default: local]
outformat -- Output alignment in format <s> [Stockholm]
Stockholm, Pfam, AFA (aligned FASTA), A2M, Clustal, PHYLIP
mxsize -- Set maximum allowable DP matrix size to <x> Mb [1028.0] (x>0.)
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': 'cmalign', 'logFn': '/dev/null', 'errFn': '/dev/null' }
Require: cmalign
"""
import General
import shutil
cmalign_exe = General.require_exec("cmalign", exception=True)
cmd = f"{cmalign_exe} "
if cpu > 0:
cmd += f"--cpu {cpu} "
if glocal:
cmd += "-g "
cmd += f"--outformat {outformat} --mxsize {mxsize} -o {outFn} {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):
CreatureWithInventory.__init__(self)
self.description = 'outlaw'
self.representation = 'T'
self.speed = 220
self.attribute = Colors.getPairNumber("RED", "BLACK")
"Outlaws cannot see in the dark well."
self.minimumLightToSeeThreshold = self.minimumLightToSeeThreshold + 1
def __init__(self):
CreatureWithInventory.__init__(self)
self.description = 'deputy'
self.representation = '@'
self.speed = 200
self.attribute = Colors.getPairNumber("WHITE", "BLACK")
w = BaseItems.Revolver()
self.addToInventory(w)
self.setWeapon(w)
def showtext(self, text, fontsize):
self.clearscreen()
font = pygame.font.Font(None, fontsize)
fontWidth = font.size(text)[0]
fontHeight = font.size(text)[1]
midX = self.windowsize[0] / 2 - fontWidth / 2
midY = self.windowsize[1] / 2 - fontHeight / 2
screentext = font.render(text, True, Colors.randomcolor_rgb())
self.screen.blit(screentext, (midX, midY))
self.updatescreen()
def __init__(self, semObject, className, modelPath=None):
# Use the AToM3 Tkinter root window
self.className = className
root = self.rootInitilization(semObject, modelPath)
if (not root): return
self.root = root
self.mainHandler = MainHandler.MainHandler(self)
root.bind("<Key>", self.mainHandler.onKey)
root.bind("<Shift-Key>", self.mainHandler.onShiftKey)
root.bind("<Control-Key>", self.mainHandler.onControlKey)
zoom = 1.0
self.menuBar = Tools.MenuBar(root, self,
self.mainHandler) #goes to top by itself
self.statusBar = Tools.StatusBar(root, "", zoom, 0,
0) #goes to bottom by itself
self.colorSelector = Colors.ColorSelector(
root, self.mainHandler) #goes to bottom by itself
self.toolFrame = Tkinter.Frame(root, relief=Tkinter.RAISED, bd=1)
self.toolSelector = Tools.ToolSelector(self.toolFrame,
self.mainHandler, Tkinter.TOP)
self.outlineFillOptionSelector = Tools.OutlineFillOptionSelector(
self.toolFrame, self.mainHandler, Tkinter.TOP)
self.lineWidthSelector = Tools.LineWidthSelector(
self.toolFrame, self.mainHandler, Tkinter.TOP)
self.toolFrame.pack(side=Tkinter.LEFT)
self.workspace = Workspace(self, self.CANVAS_SIZE_TUPLE[2],
self.CANVAS_SIZE_TUPLE[3],
self.CANVAS_SIZE_TUPLE[2],
self.CANVAS_SIZE_TUPLE[3], self.mainHandler,
zoom) #goes to the right by itself
self.workspace.setZoom(zoom, 0, 0)
self.canvas = self.workspace.getCanvas()
self.scripting = Scripting()
## self.GFs = self.open()
self.GFs = []
self.extendedInitilization(semObject)
self.clipboardList = []
self.undoStack = []
self.mainHandler.start()
self.compositionVisitor = GFVisitors.CompositionVisitor(self)
self.colorVisitor = GFVisitors.ColorVisitor()
self.widthVisitor = GFVisitors.WidthVisitor()
self.optionVisitor = GFVisitors.OptionVisitor(self)
# Carefully try to load the GF model (may fail for random reasons)
try:
self.GFs = self.open()
except:
raise
def __init__(self, screen, width = None, height = None):
self.screen = screen
self.width = width
self.height = height
self.statusLinesHeight = 5
self.maxSideBarLen = 11
self.time = 0
self.eventHeap = []
self.shouldPause = False
self.lightSources = []
self.defaultOverlay = Overlay.Overlay(self)
self.overlay = self.defaultOverlay
self.setDrawMode(World.DRAW_DETAIL_PHYSICAL)
self.setViewMode(World.VIEW_VIEWER_INFORMATION)
#self.world is referenced by x first, then y
self.world = []
if (self.width == None):
self.width = self.screen.getmaxyx()[1]
if (self.height == None):
self.height = self.screen.getmaxyx()[0] - 5
#self.makeForestMap()
self.loadMapFromFile('testMap.txt')
playerA = BaseCreatures.Deputy()
playerB = BaseCreatures.Sheriff()
playerA.makePlayerControlled()
playerB.makePlayerControlled()
self.team = TeamViewer(self, [playerA, playerB])
self.currentViewer = self.team.getTeamMember(0)
for i in range(0, len(self.team.getTeamList())):
self.placeItem(self.team.getTeamMember(i), i, 0)
#initialize some static data if not already initialized
if (World.cannotSeeAttribute == None):
World.cannotSeeAttribute = Colors.getPairNumber('WHITE', 'BLACK')
for k in World.zHeightLookupTable.keys():
result = WorldState.WorldRepresentation.convertString(World.zHeightLookupTable[k])
if (k < 0):
World.zHeightLookupTable[k] = result
else:
World.zHeightLookupTable[k] = result
self.statusLinesAttribute = 0
self.statusLines = []
self.statusOffset = 11-6
self.statusLinesAppended = 0
def __init__(self):
CreatureWithInventory.__init__(self)
self.description = 'thieving bandito'
self.representation = 'B'
self.speed = 180
self.attribute = Colors.getPairNumber("YELLOW", "BLACK")
w = BaseItems.Revolver()
self.addToInventory(w)
self.setWeapon(w)
"Banditos can see in the dark pretty well."
self.minimumLightToSeeThreshold = self.minimumLightToSeeThreshold - 1
def askQuestion(question, lChoices):
"""
Ask a question to the user, and return his answer.
"""
mess = "\n%s\n%s" % (colorQ(question), '\n'.join([
" [%s] %s" % (colorC(i + 1), lChoices[i]) for i in range(len(lChoices))
]))
mess += "\n [%s] Quit\nChoice: %s" % (colorC('Q'),
txt.buildColor(fgColor="Red"))
choice = raw_input(mess)
sys.stdout.write(txt.reset())
sys.stdout.flush()
if choice.lower() == 'q':
sys.exit(0)
if choice not in map(str, range(1, len(lChoices) + 1)):
print "Your choice \"%s\" doesn't exist." % choice
return askQuestion(question, lChoices)
return int(choice) - 1
def R_scape(StoFn,
outDir,
outname=None,
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=True):
"""
StoFn -- Stockholm file
outDir -- Output the file to this directory
outname -- File prefix
maxIdentity -- require seqs to have < <x> id [1.0] (0<x<=1.0)
minIndentity -- require seqs to have >= <x> id (0<=x<1.0)
F -- filter out seqs <x*seq_cons residues (0<x<=1.0)
gapthresh -- keep columns with < <x> fraction of gaps [0.75] (0<=x<=1)
two_set_test -- two-set test: basepairs / all other pairs. Requires a given structure
fold -- obtain the structure with maximum covariation
acceptE -- Eval: max expected number of covNBPs allowed [0.05] (x>=0)
nseqmin -- minimum number of sequences in the alignment (n>0)
verbose -- Show command and log information
showCMD -- Print the command
Require: R-scape
"""
import General
import shutil
R_scape_exe = General.require_exec("R-scape", exception=True)
if not os.path.exists(outDir):
os.mkdir(outDir)
cmd = f"{R_scape_exe} --outmsa --r2rall --outtree --roc --voutput --outnull --consensus "
cmd += f"--outdir {outDir} -I {maxIdentity} -i {minIndentity} -F {F} --gapthresh {gapthresh} -E {acceptE} --nseqmin {nseqmin} "
if outname:
cmd += f"--outname {outname} "
if two_set_test:
cmd += "-s "
if fold:
cmd += "--fold "
cmd += f" {StoFn} "
if not verbose:
cmd += "> /dev/null"
if showCMD:
import Colors
print(Colors.f(cmd, fc='yellow'))
os.system(cmd)
def showRNAStructure(transFeature, sequence, bias=0):
cds_start = transFeature['cds_start']
cds_end = transFeature['cds_end']
UTR5 = sequence[:cds_start-1]
Start_codon = sequence[cds_start-1:cds_start+2]
CDS = sequence[ cds_start+2:cds_end-3+bias ]
Stop_codon = sequence[ cds_end-3+bias:cds_end+bias ]
UTR3 = sequence[cds_end+bias:]
if len(CDS)%3 != 0:
print >>sys.stderr, "Warning: The length of the CDS is not an integer multiple of 3"
formatCDS = ""
i = 0; j = 0
while i<len(CDS):
if j % 2 == 0:
formatCDS += Colors.f(CDS[i:i+3], fc='black', bc='yellow', ft='normal')
else:
formatCDS += Colors.f(CDS[i:i+3], fc='black', bc='lightyellow', ft='normal')
i += 3
j += 1
UTR5 = Colors.f(UTR5, fc='green', bc='default', ft='normal')
Start_codon = Colors.f(Start_codon, fc='lightred', bc='default', ft='bold')
Stop_codon = Colors.f(Stop_codon, fc='lightred', bc='default', ft='bold')
UTR3 = Colors.f(UTR3, fc='green', bc='default', ft='normal')
return UTR5+Start_codon+formatCDS+Stop_codon+UTR3
def run(self):
config = Config.get()
colorWheel = Config.getColorWheel()
countryBorders = Utils.read_features(
config.get("GeneratedFiles", "country_borders"))
colorFactory = Colors.ColorSelector(countryBorders, colorWheel)
colors = colorFactory.optimalColoring()
ms = MapStyler(config, colors)
ms = MapStyler(config, colorWheel)
ms.saveImage(config.get("MapOutput", "map_file_density"),
config.get("MapOutput", "img_src_name") + ".png")
ms.saveImage(config.get("MapOutput", "map_file_density"),
config.get("MapOutput", "img_src_name") + ".svg")
def you_lost():
exit_game = False
temp_color = Colors.rand_col()
while not exit_game:
gameWindow.fill(temp_color)
text_screen("press x to restart" , Colors.black , 350 , 300)
pygame.display.update()
for event in pygame.event.get():
if event.type == pygame.QUIT:
exit_game = True
if event.type == pygame.KEYDOWN:
if event.key == pygame.K_x:
game_loop()
def question_safe(self, question):
while True:
try:
try_input = raw_input(question)
if (len(try_input) > 0):
return try_input
else:
Message = "\n No Input Detected"
exit(Colors.change_color(Message, 'FAIL'))
except EOFError:
self.quit_gracefully()
except KeyboardInterrupt:
self.quit_gracefully()
def question_safe(self, question):
while True:
try:
try_input = raw_input(question)
if (len(try_input) > 0):
return try_input
else:
Message = "\n No Input Detected"
exit(Colors.change_color(Message, 'FAIL'))
except EOFError:
self.quit_gracefully()
except KeyboardInterrupt:
self.quit_gracefully()
def __processinput(self, inputvalue):
line = Line.Line()
choices = inputvalue.split(" ")
if len(choices) != self.nbcolor:
print "Il faut ", self.nbcolor , " couleurs"
return False
for colorname in choices:
color = Colors.getcolorfromname(colorname)
if color == 0:
print "la couleur ", colorname, " n'existe pas"
return False
line.addcolor(color)
self.line = line
return True
def __processinput(self, inputvalue):
line = Line.Line()
choices = inputvalue.split(" ")
if len(choices) != self.nbcolor:
print "Il faut ", self.nbcolor, " couleurs"
return False
for colorname in choices:
color = Colors.getcolorfromname(colorname)
if color == 0:
print "la couleur ", colorname, " n'existe pas"
return False
line.addcolor(color)
self.line = line
return True
def cmcalibrate(CMFn,
cpu=0,
verbose=True,
showCMD=True,
use_LSF=False,
LSF_parameters={}):
"""
Calibrate the CM model
CMFn -- CM file
cpu -- How many CPU to use
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': 'cmcalibrate', 'logFn': '/dev/null', 'errFn': '/dev/null' }
Return:
Return job object if use_LSF==True
Return None if use_LSF==False
Require: cmcalibrate
"""
import General
import shutil
cmcalibrate_exe = General.require_exec("cmcalibrate", exception=True)
cmd = f"{cmcalibrate_exe} "
if cpu > 0:
cmd += f"--cpu {cpu} "
cmd += CMFn
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', 'cmcalibrate'),
logFn=LSF_parameters.get('logFn', '/dev/null'),
errFn=LSF_parameters.get('errFn', '/dev/null'))
job.get_submit_command()
job.submit()
return job
else:
os.system(cmd)
def welcome():
exit_game = False
temp_color = Colors.rand_col()
while not exit_game:
gameWindow.fill(temp_color)
text_screen("Press space to start" , Colors.black , 350 , 300)
pygame.display.update()
for event in pygame.event.get():
if event.type == pygame.QUIT:
exit_game = True
pygame.quit()
quit()
if event.type == pygame.KEYDOWN:
if event.key == pygame.K_SPACE:
return 0
def __init__(self, parent=None, tab_title='Batch.io', isStatic=False):
super(AssetListWidget, self).__init__(parent)
self.setGeometry(0, 0, 240, 0)
self.assetWidgets = {}
self.tab_dict = {}
self.isDroppable = True
self.titleLbl = QLabel(tab_title)
self.tab_title = tab_title
self.animWaitingColor = False
self.log = None
self.colors = Colors()
self.isStatic = isStatic
self.initUI()
def _setup(self, host, task):
"""
Implementation specific setup for outputting to the CLI.
:Parameters:
- `host`: name of the host
- `task`: name of the task
"""
import Colors
import sys
self._c = Colors.Colors()
self._sys = sys
self._sys.stdout.write('%s:\n' % (self._c.format_string(host, 'blue')))
self._sys.stdout.write(
'%s Starting Task[%s]\n' %
(self.timestamp, self._c.format_string(task, 'white')))
def create_shapes(self):
"""Precalculate relative coordinates."""
Element.create_shapes(self)
self._sink_rot = None
self._source_rot = None
self._sink_coor = None
self._source_coor = None
#get the source coordinate
try:
connector_length = self.get_source().get_connector_length()
except:
return
self.x1, self.y1 = Utils.get_rotated_coordinate(
(connector_length, 0),
self.get_source().get_rotation())
#get the sink coordinate
connector_length = self.get_sink().get_connector_length(
) + CONNECTOR_ARROW_HEIGHT
self.x2, self.y2 = Utils.get_rotated_coordinate(
(-connector_length, 0),
self.get_sink().get_rotation())
#build the arrow
self.arrow = [
(0, 0),
Utils.get_rotated_coordinate(
(-CONNECTOR_ARROW_HEIGHT, -CONNECTOR_ARROW_BASE / 2),
self.get_sink().get_rotation()),
Utils.get_rotated_coordinate(
(-CONNECTOR_ARROW_HEIGHT, CONNECTOR_ARROW_BASE / 2),
self.get_sink().get_rotation()),
]
source_domain = self.get_source().get_domain()
sink_domain = self.get_sink().get_domain()
self.line_attributes[0] = 2 if source_domain != sink_domain else 0
self.line_attributes[1] = gtk.gdk.LINE_DOUBLE_DASH \
if not source_domain == sink_domain == GR_MESSAGE_DOMAIN \
else gtk.gdk.LINE_ON_OFF_DASH
get_domain_color = lambda d: Colors.get_color(
(self.get_parent().get_parent().get_domain(d) or {}).get(
'color') or Colors.DEFAULT_DOMAIN_COLOR_CODE)
self._color = get_domain_color(source_domain)
self._bg_color = get_domain_color(sink_domain)
self._arrow_color = self._bg_color if self.is_valid(
) else Colors.CONNECTION_ERROR_COLOR
self._update_after_move()
def __init__(self, parent=None):
super(AssetWidget, self).__init__(parent)
self.isDraggable = False
self.isDroppable = False
self.isAssetWidget = True
self.isTrigger = False
self.isHeader = False
self.asset_width = 210
self.asset_height = 50
self.button_size = self.asset_height / 2
self.hasProgressBar = False
self.hasContextMenu = False
self.isInterative = True
self.colors = Colors()
self.asset_btn_list = []
self.type = None
self.initUI()
def _color_command_heatmap(base_score,
gradient_list,
min_score=0,
max_score=1):
import numpy as np
if base_score == 'NULL':
return "0.51 0.51 0.51 setrgbcolor"
else:
v = np.clip(float(base_score), min_score, max_score)
ind = int(
(v - min_score) / (max_score - min_score) * len(gradient_list))
#print(ind)
ind = int(np.clip(ind, 0, len(gradient_list) - 1))
color = gradient_list[ind]
#print(color)
r, g, b = Colors._hex_to_RGB(color)
r, g, b = r / 255, g / 255, b / 255
#print(r,g,b)
return f"{r:.2f} {g:.2f} {b:.2f} setrgbcolor"
def _create_labels(self):
"""Create the labels for the socket."""
self._bg_color = Colors.get_color(self.get_color())
#create the layout
layout = gtk.DrawingArea().create_pango_layout('')
layout.set_markup(Utils.parse_template(PORT_MARKUP_TMPL, port=self))
self.w, self.h = layout.get_pixel_size()
self.W, self.H = 2*PORT_LABEL_PADDING+self.w, 2*PORT_LABEL_PADDING+self.h
#create the pixmap
pixmap = self.get_parent().get_parent().new_pixmap(self.w, self.h)
gc = pixmap.new_gc()
gc.set_foreground(self._bg_color)
pixmap.draw_rectangle(gc, True, 0, 0, self.w, self.h)
pixmap.draw_layout(gc, 0, 0, layout)
#create the images
self.horizontal_label = image = pixmap.get_image(0, 0, self.w, self.h)
if self.is_vertical():
self.vertical_label = vimage = gtk.gdk.Image(gtk.gdk.IMAGE_NORMAL, pixmap.get_visual(), self.h, self.w)
for i in range(self.w):
for j in range(self.h): vimage.put_pixel(j, self.w-i-1, image.get_pixel(i, j))
def create_labels(self):
"""Create the labels for the socket."""
Element.create_labels(self)
self._bg_color = Colors.get_color(self.get_color())
#create the layout
layout = gtk.DrawingArea().create_pango_layout('')
layout.set_markup(Utils.parse_template(PORT_MARKUP_TMPL, port=self))
self.w, self.h = layout.get_pixel_size()
self.W, self.H = 2*PORT_LABEL_PADDING+self.w, 2*PORT_LABEL_PADDING+self.h
#create the pixmap
pixmap = self.get_parent().get_parent().new_pixmap(self.w, self.h)
gc = pixmap.new_gc()
gc.set_foreground(self._bg_color)
pixmap.draw_rectangle(gc, True, 0, 0, self.w, self.h)
pixmap.draw_layout(gc, 0, 0, layout)
#create vertical and horizontal pixmaps
self.horizontal_label = pixmap
if self.is_vertical():
self.vertical_label = self.get_parent().get_parent().new_pixmap(self.h, self.w)
Utils.rotate_pixmap(gc, self.horizontal_label, self.vertical_label)
def __init__(self):
super(Background, self).__init__(
(getGameDimension()[0], getGameDimension()[1]))
# the rect is the score table of this game
pygame.draw.rect(self,
Colors().FloralWhite,
(0, 0, getGameDimension()[2], getGameDimension()[3]))
backgroundImg = pygame.image.load(
'./assets/images/field/soccer-field.png')
backgroundImg2 = pygame.image.load(
'./assets/images/background/WechatIMG174.png')
backgroundImg3 = pygame.image.load(
'./assets/images/background/WechatIMG173.png')
resizedbackgroundImg2 = pygame.transform.scale(backgroundImg2,
(1100, 60))
resizedbackgroundImg3 = pygame.transform.scale(backgroundImg3,
(300, 60))
self.blit(backgroundImg, (0, getGameDimension()[3]))
self.blit(resizedbackgroundImg2, (0, 0))
self.blit(resizedbackgroundImg3, (800, 0))
def ssecFromPDB(pdb, clean=True, verbose=False):
"""
pdb -- A PDB id or PDB file, for example, 5CD1, /tmp/5CD1.cif
If you provide a PDB ID, it will download pdf file automaticly
clean -- Clean the directory
verbose -- Print the command to the screen
Return:
{ 'm1_chain_L5': {'bseq': 'ACTAGTCAGCTAGC', 'sstr': '....((((..))))...'}, ... }
"""
import tempfile, shutil, os, Colors
import json, General
tmpdir = tempfile.mkdtemp(prefix="PDB_", dir='/tmp/')
tmp_result_json = os.path.join(tmpdir, "result.json")
if len(pdb)==4:
import Bio
from Bio.PDB import PDBList
pdbl = PDBList(verbose=False)
pdbFn = pdbl.retrieve_pdb_file(pdb, pdir=tmpdir, overwrite=True)
else:
pdbFn = pdb
cmd = f'x3dna-dssr -i={pdbFn} -o={tmp_result_json} --json 2>/dev/null'
if verbose:
print( Colors.f(cmd, 'yellow') )
os.system(cmd)
x3dna_result = json.load(open(tmp_result_json))
ssec = {}
for key in x3dna_result['dbn']:
if key != 'all_chains':
ssec[key] = { 'bseq':x3dna_result['dbn'][key]['bseq'], 'sstr':x3dna_result['dbn'][key]['sstr'] }
if clean:
shutil.rmtree(tmpdir)
return ssec
def printWin(w):
''' TODO: For Testing
for r in range(len(w)):
print(' '.join(str(n) for n in w[r]))
'''
ret = ''
colors = Colors.getColors()[::-1]
length = len(colors)
for r in range(len(w)):
for c in range(len(w[r])):
if w[r][c] == 0: ret += colors[0] + ' '
if w[r][c] == 1: ret += colors[1] + '. '
if w[r][c] == 2: ret += colors[2] + '- '
if w[r][c] == 3: ret += colors[3] + '~ '
if w[r][c] == 4: ret += colors[4] + '+ '
if w[r][c] == 5: ret += colors[5] + '* '
if w[r][c] == 6: ret += colors[6] + '# '
if w[r][c] == 7: ret += colors[7] + '% '
if w[r][c] == 8: ret += colors[8] + '$ '
if w[r][c] == 9: ret += colors[9] + '& '
ret += '\n'
print(ret)
def __init__(self):
Item.LocationAwareItem.__init__(self)
self.x = None
self.y = None
self.world = None
self.speed = 100
self.description = 'uninherited-from creature'
self.representation = 't'
self.foreGroundColorName = 'YELLOW'
self.attribute = Colors.BOLD | Colors.getPairNumber(self.foreGroundColorName, "BLACK")
self.inputHandler = InputHandler.SingletonKeyboardInputHander(ToastWrangler.screen)
Logger.put(str(self.inputHandler))
self.minimumLightToSeeThreshold = 3
self.seeDistance = 99
self.fov = None
self.light = None
self.moveActionDistance = 3
self.moveDistanceThisTurn = 0
self.didAttack = False
self.maxHP = 10
self.hp = 10
self.horizontalAttackDistance = 1
self.verticalAttackDistance = 1
self.attackDamage = 1
self.toggleLightCost = 1
self.team = 0
self.originalThink = self.doThink
def cmbuild(inStoFn, outCMFn, verbose=False, showCMD=True):
"""
Build a cm file from stockholm file
inStoFn -- Input stockholm file
outCMFn -- Output CM file
verbose -- Show command and log information
showCMD -- Print the command
Require: cmbuild
"""
import General
import shutil
cmbuild_exe = General.require_exec("cmbuild", exception=True)
cmd = f"{cmbuild_exe} -F "
if not verbose:
cmd += '-o /dev/null '
cmd += f"{outCMFn} {inStoFn}"
if showCMD:
import Colors
print( Colors.f(cmd, fc='yellow') )
os.system(cmd)
def create_dock_windows(self):
self.dockManager = TkUtil.DockManager.DockManager(
left=self.leftDockArea, right=self.rightDockArea)
self.colorsDock = Colors.Dock(self.master, self.dockManager)
self.colorsDock.dock_right()
self.dockWindows.append(self.colorsDock)
self.colorsDock.bind("<<ForegroundChange>>", lambda *args:
self.editor.text.config(
foreground=self.colorsDock.foreground))
self.colorsDock.bind("<<BackgroundChange>>", lambda *args:
self.editor.text.config(
background=self.colorsDock.background))
self.displayDock = Display.Dock(self.master, self.dockManager)
self.displayDock.dock_right()
self.dockWindows.append(self.displayDock)
self.displayDock.bind("<<WordWrapChanged>>", lambda *args:
self.editor.text.config(wrap=self.displayDock.word_wrap))
self.displayDock.bind("<<BlockCursorChanged>>", lambda *args:
self.editor.text.config(
blockcursor=self.displayDock.block_cursor))
self.displayDock.bind("<<LineSpacingChanged>>", lambda *args:
self.editor.text.config(
spacing3=self.displayDock.line_spacing))
def cd_hit_est(id2seq,
identity=0.9,
global_align=False,
band_width=20,
memory=800,
cpu=0,
word_length=10,
cluster_mode=0,
alignment_mode=1,
clean=True,
verbose=False):
"""
id2seq -- {id1:seq1, ...}
identity -- sequence identity threshold.
this is the default cd-hit's "global sequence identity" calculated as:
number of identical amino acids or bases in alignment
divided by the full length of the shorter sequence
global_align -- use global sequence identity
band_width -- band_width of alignment
memory -- memory limit (in MB) for the program, 0 for unlimited
cpu -- number of threads, with 0, all CPUs will be used
word_length -- word_length, default 10, see user's guide for choosing it
cluster_mode -- 1 or 0.
by cd-hit's default algorithm, a sequence is clustered to the first
cluster that meet the threshold (fast cluster). If set to 1, the program
will cluster it into the most similar cluster that meet the threshold
(accurate but slow mode)
alignment_mode -- 1 or 0, default 1, by default do both +/+ & +/- alignments
if set to 0, only +/+ strand alignment
clean -- Delete all tmp files
verbose -- Print command
Remove duplicated sequence from sequence
Return:
{id1:seq1,...}
Require: cd-hit-est
"""
import General, Colors
import shutil, tempfile
exe = General.require_exec("cd-hit-est", exception=True)
ROOT = tempfile.mkdtemp(prefix="cd_hit_est_")
#ROOT = "/tmp/predict_structure_%s/" % (randID, )
#os.mkdir(ROOT)
fa_file = os.path.join(ROOT, "input.fa")
output_file = os.path.join(ROOT, "output.fa")
General.write_fasta(id2seq, fa_file)
CMD = f"{exe} -i {fa_file} -o {output_file} -c {identity} -b {band_width} -M {memory} -T {cpu} -n {word_length} -g {cluster_mode} -r {alignment_mode} "
if global_align:
CMD += " -G "
if verbose:
print(Colors.f(CMD, fc='yellow'))
CMD += ' > /dev/null'
os.system(CMD)
cleaned_fasta = General.load_fasta(output_file)
if clean:
shutil.rmtree(ROOT)
return cleaned_fasta
def printNormalUsage(self):
print Colors.change_color(NormalUsage, 'OKGREEN')
def __init__(self, world, creature):
Overlay.__init__(self, world)
self.creature = creature
self.cursorPosX = 0
self.cursorPosY = 0
self.attackAttribute = Colors.getPairNumber('WHITE', 'RED') | curses.A_BOLD
def _processNeuron(self, file, neuron, options = {}):
"""
Part of the graphviz visualisation routines
Adds a single neuron and its connections into the graph
@type file: filehandle
@param file: handle of the graph file
@type neuron: neuron
@param neuron: the neuron
@type options: set
@param options: Set of options for visualisation
Further documentation: L{visualize}
"""
if (neuron != 0):
mass = normalize(neuron.getMass())
if (mass < 0):
mass_p = round(100+(mass*100))
else:
mass_p = round(100-(mass*100))
if 'useColor' in options:
color = int(neuron.getName().split('.')[1])
file.write('\t%s [shape="box" color="grey%i" penwidth="3" style="filled" fillcolor="%s"]\n' % (neuron.getName(),mass_p,Colors.getColor(color)))
else:
file.write('\t%s [shape="box" color="grey%i" penwidth="3"]\n' % (neuron.getName(),mass_p))
for x in range (0, neuron.getLinkCount()):
weight = normalize(neuron.getWeight(x))
if (weight < 0):
weight_p = round(100+(weight*100))
else:
weight_p = round(100-(weight*100))
file.write("\t%s -> %s " % (neuron.getName(),neuron.getLink(x)))
file.write(' [')
if 'showLabel' in options:
file.write('label="%.2f" ' % (weight))
if 'showHead' not in options:
file.write('arrowhead="none" ')
file.write('color="grey%i"] /* weight: %.2f */' % (weight_p,weight))
file.write('\n')
file.write('\n')