def record_temperatures(self):
p = Progress(self.num_tiles, 'Getting hot...')
iter_elevationfile = iter(self.parse(self.elevationfile))
iter_waterfile = iter(self.parse(self.waterfile, give_coords=False))
for tile in range(self.num_tiles):
p.update()
ele_char, coord = next(iter_elevationfile)
wat_char = next(iter_waterfile)
if coord[0] == 0 and self.temperaturefile.written == True:
self.temperaturefile._write('\n')
else:
pass
temp_lat = self.get_temperature_LATITUDE(coord[1])
temp_ele = self.get_temperature_ELEVATION(int(ele_char))
temp_wat = self.get_temperature_WATER(wat_char, coord[1])
total = temp_lat+temp_ele+temp_wat+random.randint(0, 2)/10.0
if total > 9:
total = 9
elif total < 0:
total = 0
else:
total = int(round(total))
self.temperaturefile._write(str(total))
p.close()
def load_seeds(self):
p = Progress(self.num_tiles, 'Loading seeds...')
for char, coord in self.parse(self.seedfile):
p.update()
if char == '1':
self.seeds.add(coord)
else:
continue
p.close()
def record_seeds(self):
p = Progress(self.map_size[1], 'Getting seeds...')
for y in range(self.map_size[1]):
p.update()
self.seedfile.skipline_if_written()
for x in range(self.map_size[0]):
test = (x, y)
if test in self.seeds:
self.seedfile._write('1')
else:
self.seedfile._write(' ')
p.close()
def draw_tiles(self):
p = Progress(self.map_size[1], 'Drawing tiles...')
y = -1
for line in self.tilefile._parse():
p.update()
y += 1
x = -1
for char in line.strip():
x += 1
tile = self.tm.tile_map[char]
position = (x*self.tile_length, y*self.tile_length)
CanvasTile(self, tile, position)
p.close()
raw_input()
def record_watercount(self):
p = Progress(self.num_tiles, 'Getting H2O...')
for char, coord in self.parse(self.elevationfile):
p.update()
if coord[0] == 0 and self.waterfile.written == True:
self.waterfile._write('\n')
else:
pass
elevation = int(char)
if elevation <= self.sealevel:
watercount = self.water_symbol
else:
watercount = self.get_watercount(coord)
self.waterfile._write(str(watercount))
p.close()
def record_tiles(self):
p = Progress(self.num_tiles, 'Building tiles...')
iter_elevationfile = iter(self.parse(self.elevationfile))
iter_temperaturefile = iter(self.parse(self.temperaturefile, give_coords=False))
for tile in range(self.num_tiles):
p.update()
ele_char, coord = next(iter_elevationfile)
temp_char = next(iter_temperaturefile)
corrected_temp = float(temp_char)/9*self.tRange+self.coldest
tile_symbol = self.tm.choose_tile(int(ele_char), corrected_temp)
if coord[0] == 0 and self.tilefile.written == True:
self.tilefile._write('\n')
else:
pass
if tile_symbol == None:
raise Exception(str(ele_char)+'\t'+str(corrected_temp))
else:
self.tilefile._write(str(tile_symbol))
p.close()
def __init__(self, app):
QDialog.__init__(self)
self.setupUi(self)
self.app = app
# init attributes
self.buttonBox.button(QDialogButtonBox.Ok).setEnabled(False)
self.filename = "/home/vagrant/Bureau/fork/qgisws/banskel/bano-75.csv"
self.browseButton.clicked.connect(self.__browse)
self.buttonBox.button(QDialogButtonBox.Ok).clicked.connect(self.__ok)
self.buttonBox.button(QDialogButtonBox.Cancel).clicked.connect(app.quit)
self.projector = Projector()
self.progress = Progress()
return os.system(cmd)
parser = argparse.ArgumentParser()
parser.add_argument('--out', type=str, required=True, nargs='+')
parser.add_argument('--chr', type=int, required=True)
parser.add_argument('--start', type=int, required=True)
parser.add_argument('--end', type=int, required=True)
parser.add_argument('--min-q', type=int, default=20)
parser.add_argument('--bam-list', type=str, required=True, nargs='+')
parser.add_argument('--projname', type=str, required=True)
if __name__ == '__main__':
args = parser.parse_args
n = len(args.bam_list)
pbar = Progress(n)
for i, bam, out in enumerate(zip(args.bam_list, args.out)):
if i % 20 == 0 or i == n:
pbar.update_progress(i)
# create tiny little bam
cmd = SUBSET_BAM.format(BAM=bam,
PROJ=args.projname,
CHR=args.chr,
START=args.start,
END=args.end,
OUT=out
)
if print_call(cmd):
print 'Error reading %s' % bam
continue
def cleanup_elevations(self):
total_entries = self.raw_elevationfile.get_total_entries()
p = Progress(total_entries, 'Getting high...')
dummymap = File('dummy')
if dummymap.written == True:
dummymap._delete()
elevationMEMORY = {}
memCOUNT = 0
for strcoord, floatelevation in self.raw_elevationfile.parse():
p.update()
coord = self.str2coord(strcoord)
#
elevation = int(round(float(floatelevation), 0))
if elevation > 9:
elevation = 9
elif elevation < 0:
elevation = 0
else:
pass
elevationMEMORY[coord] = elevation
memCOUNT += 1
if memCOUNT > self.memLIMIT or p.progress == total_entries:
if self.elevationfile.written == False:
for y in range(self.map_size[1]):
self.elevationfile.skipline_if_written()
for x in range(self.map_size[0]):
try:
elevation = elevationMEMORY[(x, y)]
except KeyError:
elevation = 0
self.elevationfile._write(str(elevation))
else:
y = -1
for line in self.elevationfile._parse():
dummymap.skipline_if_written()
y += 1
x = -1
for char in line:
x += 1
if char != '0':
dummymap._write(char)
else:
try:
elevation = elevationMEMORY[(x, y)]
except KeyError:
elevation = 0
dummymap._write(str(elevation))
self.elevationfile._delete()
dummymap._rename(self.elevationfile.filename)
self.elevationfile = dummymap
dummymap = File('dummy')
elevationMEMORY = {}
memCOUNT = 0
else:
continue
p.close()
def record_rawelevations(self):
if self.seeds == set():
self.load_seeds()
else:
pass
total_count = len(self.seeds)-1
p = Progress(total_count, 'Growing seeds...')
dummyfile = FaFile('dummy.fa')
if dummyfile.written == True:
dummyfile._delete()
elevation_MEMORY = {}
memCOUNT = 0
# ex. {coord:elevation}
for seed in self.seeds:
p.update()
for coord, rel_coord in self.get_tiles_within_radius(self.mountain_check_radius, seed):
randfactor = random.randint(0, 2)/10.0
dh = 5.0/(abs(rel_coord[0])+abs(rel_coord[1])+1)**(1.0/self.mountain_fatness)+randfactor
try:
elevation_MEMORY[coord] += dh
except KeyError:
elevation_MEMORY[coord] = dh
memCOUNT += 1
if memCOUNT > self.memLIMIT or p.progress == total_count:
if self.raw_elevationfile.written == False:
for key, value in self.coord2str(elevation_MEMORY):
self.raw_elevationfile.entry(key, str(value))
elevation_MEMORY = {}
memCOUNT = 0
else:
str_eleMEMORY = self.construct_str_eleMEMORY(elevation_MEMORY)
for key, value in self.raw_elevationfile.parse():
try:
str_eleMEMORY[key] += float(value)
except KeyError:
dummyfile.entry(key, str(value))
self.raw_elevationfile._delete()
dummyfile._rename(self.raw_elevationfile.filename)
self.raw_elevationfile = dummyfile
dummyfile = FaFile('dummy.fa')
for key, value in str_eleMEMORY.items():
self.raw_elevationfile.entry(key, str(value))
elevation_MEMORY = {}
memCOUNT = 0
else:
continue
p.close()
class Browser(QDialog, Ui_BrowseDialog):
# -------------------------------------------------------------------------
# public methods
# -------------------------------------------------------------------------
# -------------------------------------------------------------------------
def __init__(self, app):
QDialog.__init__(self)
self.setupUi(self)
self.app = app
# init attributes
self.buttonBox.button(QDialogButtonBox.Ok).setEnabled(False)
self.filename = "/home/vagrant/Bureau/fork/qgisws/banskel/bano-75.csv"
self.browseButton.clicked.connect(self.__browse)
self.buttonBox.button(QDialogButtonBox.Ok).clicked.connect(self.__ok)
self.buttonBox.button(QDialogButtonBox.Cancel).clicked.connect(app.quit)
self.projector = Projector()
self.progress = Progress()
# -------------------------------------------------------------------------
@property
def filename(self):
return self.__filename
# -------------------------------------------------------------------------
@filename.setter
def filename(self, filename):
if os.path.isfile(filename):
self.__filename = filename
self.urlEdit.setText(self.__filename)
self.buttonBox.button(QDialogButtonBox.Ok).setEnabled(True)
else:
self.buttonBox.button(QDialogButtonBox.Ok).setEnabled(False)
msg = QMessageBox()
msg.setText("Fichier introuvable")
# -------------------------------------------------------------------------
# private methods
# -------------------------------------------------------------------------
# -------------------------------------------------------------------------
def __in_progress(self):
self.progress.progressBar.setValue(self.progress.progressBar.value()+1)
# -------------------------------------------------------------------------
def __compute_done(self):
self.progress.close()
# -------------------------------------------------------------------------
def __ok(self):
self.projector.filename = self.__filename
self.projector.progressSignal.connect(self.__in_progress)
self.projector.finishSignal.connect(self.__compute_done)
self.projector.start()
self.progress.progressBar.setRange(0,count_lines(self.__filename))
self.progress.progressBar.setValue(0)
self.progress.show()
# -------------------------------------------------------------------------
def __browse(self):
self.filename = QFileDialog.getOpenFileName(self,"Sélectionner le fichier")
