def on_init(self):
pygame.init()
pygame.display.set_mode((SCREEN_WIDTH, SCREEN_HEIGHT),
pygame.DOUBLEBUF)
pygame.display.set_caption('Mandala Magic')
self.window = Window(pygame.display.get_surface(), pygame.time.Clock())
self._running = True
class Driver:
def __init__(self):
self._running = True
self.window = None
self.on_init()
def on_init(self):
pygame.init()
pygame.display.set_mode((SCREEN_WIDTH, SCREEN_HEIGHT),
pygame.DOUBLEBUF)
pygame.display.set_caption('Mandala Magic')
self.window = Window(pygame.display.get_surface(), pygame.time.Clock())
self._running = True
def on_event(self, event):
if event.type == pygame.QUIT:
self._running = False
def on_loop(self):
pass
def on_render(self):
self.window.draw()
def on_cleanup(self):
pygame.quit()
def on_execute(self):
while self._running:
for event in pygame.event.get():
self.on_event(event)
self.on_loop()
self.on_render()
self.on_cleanup()
class Driver:
def __init__(self, screen, clock):
self.window = Window(screen, clock)
self.stream = Stream
def run(self):
pa = PyAudio()
self.stream = pa.open(format=paFloat32,
channels=CHANNELS,
rate=SAMPLE_RATE,
output=False,
input=True,
stream_callback=self.callback,
input_device_index=INPUT_DEVICE_INDEX,
frames_per_buffer=CHUNK)
self.stream.start_stream()
pyquit = False
while self.stream.is_active() and not pyquit:
for event in pygame.event.get():
if event.type == pygame.QUIT:
pyquit = True
sleep(0.76) # 24 fps
self.stream.stop_stream()
self.stream.close()
pa.terminate()
pygame.quit()
def callback(self, in_data, frame_count, time_info, flag):
"""
:param in_data: audio data from input source
:param frame_count: 1024
:param time_info: {'input_buffer_adc_time': ..., 'current_time': ..., 'output_buffer_dac_time': ...}
:param flag: 0 or 1
"""
y = np.fromstring(in_data, dtype=np.float32)
with np.errstate(all='ignore'):
spectrum = np.nan_to_num(np.log(y))
self.window.draw(spectrum)
return in_data, paContinue
def main():
args = parse_args()
config = SafeConfigParser()
config.read([args.tracks_file, args.config_file])
if config.has_option("MAIN", "ASSEMBLY"):
assembly = config.get("MAIN", "ASSEMBLY")
gdb = genome.db.GenomeDB(assembly=assembly)
else:
gdb = genome.db.GenomeDB()
sys.stderr.write("using assembly %s\n" % gdb.assembly)
r = robjects.r
chrom_dict = gdb.get_chromosome_dict()
if config.getboolean("MAIN", "DRAW_GENES"):
tr_dict, gene_dict = get_genes(config, chrom_dict)
else:
tr_dict = {}
gene_dict = {}
regions = get_regions(config, gene_dict, chrom_dict)
track_types = get_track_types()
output_prefix = config.get("MAIN", "OUTPUT_PREFIX")
output_dir = config.get("MAIN", "OUTPUT_DIR")
single_file = config.getboolean("MAIN", "SINGLE_FILE")
width = config.getfloat("MAIN", "WINDOW_WIDTH")
output_format = config.get("MAIN", "OUTPUT_FORMAT").lower()
if output_dir:
if not output_dir.endswith("/"):
output_dir = output_dir + "/"
output_prefix = "%s%s" % (output_dir, output_prefix)
if single_file:
# get output file parameters
height = config.getfloat("MAIN", "WINDOW_HEIGHT")
if height < 5.0:
# make minimum height 5
height = 5.0
if output_format == "pdf":
filename = "%s.pdf" % output_prefix
grdevices.pdf(file=filename, width=width, height=height)
elif output_format == "png":
filename = "%s.png" % output_prefix
grdevices.png(file=filename, width=width, height=height)
else:
raise ValueError("unknown output format %s" % output_format)
sys.stderr.write("writing output to single file '%s'\n" % filename)
plot_num = 0
for i in range(len(regions)):
region = regions[i]
plot_num += 1
sys.stderr.write("DRAWING REGION %d (%s)\n" % (plot_num, str(region)))
# create window for this region
draw_grid = config.getboolean("MAIN", "DRAW_GRID")
if config.has_option("MAIN", "DRAW_MIDLINE"):
draw_midline = config.getboolean("MAIN", "DRAW_MIDLINE")
else:
draw_midline = False
# draw some vertical lines on this plot?
if config.has_option("MAIN", "DRAW_VERTLINES"):
vert_lines = [
float(x)
for x in config.get("MAIN", "DRAW_VERTLINES").split(",")
]
vert_lines_col = ["black"] * len(vert_lines)
else:
vert_lines = []
vert_lines_col = []
# region attributes can also be used to specify locations of
# vertical lines
if config.has_option("MAIN", "VERTLINES_ATTRIBUTES"):
attr_names = config.get("MAIN", "VERTLINES_ATTRIBUTES").split(",")
sys.stderr.write("drawing vertical lines corresponding to "
"region attrs %s\n" % ",".join(attr_names))
for a in attr_names:
if hasattr(region, a):
pos = int(getattr(region, a))
vert_lines.append(pos)
else:
sys.stderr.write("region is missing attribute %s\n" % a)
# colors can be specified for these lines
if config.has_option("MAIN", "VERTLINES_COLORS"):
cols = config.get("MAIN", "VERTLINES_COLORS").split(",")
vert_lines_col.extend(cols)
if len(vert_lines_col) < len(vert_lines):
# set extra lines to color black
diff = len(vert_lines) - len(vert_lines_col)
vert_lines_col.extend(["black"] * diff)
# sys.stderr.write("vert_lines: %s\n" % repr(vert_lines))
# sys.stderr.write("vert_lines_col: %s\n" % repr(vert_lines_col))
margin = config.getfloat("MAIN", "WINDOW_MARGIN")
cex = config.getfloat("MAIN", "CEX")
window = Window(region,
draw_grid=draw_grid,
draw_midline=draw_midline,
vert_lines=vert_lines,
vert_lines_col=vert_lines_col,
margin=margin,
cex=cex)
# add gene tracks to window
for genes_type in gene_dict.keys():
sys.stderr.write(" adding genes track %s\n" % genes_type)
options = dict(config.items(genes_type))
track_class = track_types[options['type']]
genes_track = track_class(tr_dict[genes_type], region, options)
window.add_track(genes_track)
# add other tracks to window
track_names = config.get("MAIN", "TRACKS").split(",")
for track_name in track_names:
if track_name.strip() == "":
continue
sys.stderr.write(" adding track %s\n" % track_name)
section_name = "TRACK_" + track_name
if not config.has_section(section_name):
sys.stderr.write("WARNING: no config section '%s' for "
"track '%s'\n" % (section_name, track_name))
continue
options = dict(config.items(section_name))
# add genome db to the options, so that it can
# be optionally used by tracks
options['gdb'] = gdb
if 'type' not in options:
sys.stderr.write("WARNING: track %s does not define "
"TYPE in configuration file\n" % track_name)
continue
track_type = options['type']
if track_type not in track_types:
sys.stderr.write(
"WARNING: don't how to create "
"track %s with type %s.\n"
" Known types are %s\n" %
(track_name, track_type, ", ".join(track_types.keys())))
continue
try:
track_class = track_types[track_type]
track = track_class(region, options)
window.add_track(track)
except TypeError as err:
sys.stderr.write(("-" * 60) + "\n")
sys.stderr.write("WARNING: could not init track %s of "
"type %s:\n%s\n" %
(track_name, track_type, str(err)))
traceback.print_exc()
sys.stderr.write(("-" * 60) + "\n")
except ValueError as err:
sys.stderr.write(("-" * 60) + "\n")
sys.stderr.write("WARNING: could not open track %s of "
"type %s:\n%s\n" %
(track_name, options['type'], str(err)))
traceback.print_exc()
sys.stderr.write(("-" * 60) + "\n")
if single_file:
# each region is a separate page of a single PDF
window.draw(r)
else:
# make a separate PDF for each region
# get output file parameters
height = config.getfloat("MAIN", "WINDOW_HEIGHT")
if height <= 0.0:
height = window.get_height() * 0.5
if height < 5.0:
# make minimum height 5 inches
height = 5.0
if output_format == "pdf":
filename = "%s%d.pdf" % (output_prefix, plot_num)
grdevices.pdf(file=filename, width=width, height=height)
# turn off clipping
r.par(xpd=True)
elif output_format == "png":
filename = "%s%d.png" % (output_prefix, plot_num)
grdevices.png(file=filename, width=width, height=height)
else:
raise ValueError("unknown output format %s" % output_format)
# render window
window.draw(r)
grdevices.dev_off()
if single_file:
grdevices.dev_off()
def main():
if len(sys.argv) != 2:
sys.stderr.write("usage: %s <config_file>\n" % sys.argv[0])
exit(2)
config = SafeConfigParser()
config.read(['conf/tracks.conf', sys.argv[1]])
if config.has_option("MAIN", "ASSEMBLY"):
assembly = config.get("MAIN", "ASSEMBLY")
gdb = genome.db.GenomeDB(assembly=assembly)
else:
gdb = genome.db.GenomeDB()
sys.stderr.write("using assembly %s\n" % gdb.assembly)
r = robjects.r
chrom_dict = gdb.get_chromosome_dict()
if config.getboolean("MAIN", "DRAW_GENES"):
tr_dict, gene_dict = get_genes(config, chrom_dict)
else:
tr_dict = {}
gene_dict = {}
regions = get_regions(config, gene_dict, chrom_dict)
track_types = get_track_types()
output_prefix = config.get("MAIN", "OUTPUT_PREFIX")
output_dir = config.get("MAIN", "OUTPUT_DIR")
single_file = config.getboolean("MAIN", "SINGLE_FILE")
width = config.getfloat("MAIN", "WINDOW_WIDTH")
output_format = config.get("MAIN", "OUTPUT_FORMAT").lower()
if output_dir:
if not output_dir.endswith("/"):
output_dir = output_dir + "/"
output_prefix = "%s%s" % (output_dir, output_prefix)
if single_file:
# get output file parameters
height = config.getfloat("MAIN", "WINDOW_HEIGHT")
if height < 5.0:
# make minimum height 5
height = 5.0
if output_format == "pdf":
filename = "%s.pdf" % output_prefix
grdevices.pdf(file=filename, width=width, height=height)
elif output_format == "png":
filename = "%s.png" % output_prefix
grdevices.png(file=filename, width=width, height=height)
else:
raise ValueError("unknown output format %s" % output_format)
sys.stderr.write("writing output to single file '%s'\n" % filename)
plot_num = 0
for i in range(len(regions)):
region = regions[i]
plot_num += 1
sys.stderr.write("DRAWING REGION %d (%s)\n" %
(plot_num, str(region)))
# create window for this region
draw_grid = config.getboolean("MAIN", "DRAW_GRID")
if config.has_option("MAIN", "DRAW_MIDLINE"):
draw_midline = config.getboolean("MAIN", "DRAW_MIDLINE")
else:
draw_midline = False
# draw some vertical lines on this plot?
if config.has_option("MAIN", "DRAW_VERTLINES"):
vert_lines = [float(x) for x in config.get("MAIN","DRAW_VERTLINES").split(",")]
else:
vert_lines = []
margin = config.getfloat("MAIN", "WINDOW_MARGIN")
cex = config.getfloat("MAIN", "CEX")
window = Window(region, draw_grid=draw_grid,
draw_midline=draw_midline,
vert_lines=vert_lines,
margin=margin, cex=cex)
# add gene tracks to window
for genes_type in gene_dict.keys():
sys.stderr.write(" adding genes track %s\n" % genes_type)
options = dict(config.items(genes_type))
track_class = track_types[options['type']]
genes_track = track_class(tr_dict[genes_type], region, options)
window.add_track(genes_track)
# add other tracks to window
track_names = config.get("MAIN", "TRACKS").split(",")
for track_name in track_names:
if track_name.strip() == "":
continue
sys.stderr.write(" adding track %s\n" % track_name)
section_name = "TRACK_" + track_name
if not config.has_section(section_name):
sys.stderr.write("WARNING: no config section '%s' for "
"track '%s'\n" % (section_name, track_name))
continue
options = dict(config.items(section_name))
# add genome db to the options, so that it can
# be optionally used by tracks
options['gdb'] = gdb
if 'type' not in options:
sys.stderr.write("WARNING: track %s does not define "
"TYPE in configuration file\n" % track_name)
continue
track_type = options['type']
if track_type not in track_types:
sys.stderr.write("WARNING: don't how to create "
"track %s with type %s.\n"
" Known types are %s\n"
% (track_name, track_type,
", ".join(track_types.keys())))
continue
try:
track_class = track_types[track_type]
track = track_class(region, options)
window.add_track(track)
except TypeError as err:
sys.stderr.write("WARNING: could not init track %s of "
"type %s:\n%s\n" %
(track_name, track_type, str(err)))
except ValueError as err:
sys.stderr.write("WARNING: could not open track %s of "
"type %s:\n%s\n" %
(track_name, options['type'], str(err)))
if single_file:
# each region is a separate page of a single PDF
window.draw(r)
else:
# make a separate PDF for each region
# get output file parameters
height = config.getfloat("MAIN", "WINDOW_HEIGHT")
if height <= 0.0:
height = window.get_height() * 0.5
if height < 5.0:
# make minimum height 5 inches
height = 5.0
if output_format == "pdf":
filename = "%s%d.pdf" % (output_prefix, plot_num)
grdevices.pdf(file=filename, width=width, height=height)
elif output_format == "png":
filename = "%s%d.png" % (output_prefix, plot_num)
grdevices.png(file=filename, width=width, height=height)
else:
raise ValueError("unknown output format %s" % output_format)
# render window
window.draw(r)
grdevices.dev_off()
if single_file:
grdevices.dev_off()
def __init__(self, screen, clock):
self.window = Window(screen, clock)
self.stream = Stream
def main():
args = parse_args()
config = ConfigParser()
config.read([args.tracks_file, args.config_file])
r = robjects.r
chrom_dict = genome.chrom.parse_chromosomes_dict(config.get("MAIN",
"CHROM_INFO"))
gene_types = []
if config.getboolean("MAIN", "DRAW_GENES"):
genes_str = config.get("MAIN", "GENES")
gene_types = genes_str.split(",")
gene_dict = get_genes(config, chrom_dict)
else:
gene_dict = {}
regions = region.get_regions(config, gene_dict, chrom_dict)
track_types = get_track_types()
output_prefix = config.get("MAIN", "OUTPUT_PREFIX")
output_dir = config.get("MAIN", "OUTPUT_DIR")
single_file = config.getboolean("MAIN", "SINGLE_FILE")
width = config.getfloat("MAIN", "WINDOW_WIDTH")
output_format = config.get("MAIN", "OUTPUT_FORMAT").lower()
if output_dir:
if not output_dir.endswith("/"):
output_dir = output_dir + "/"
output_prefix = "%s%s" % (output_dir, output_prefix)
if single_file:
# get output file parameters
height = config.getfloat("MAIN", "WINDOW_HEIGHT")
if height < 5.0:
# make minimum height 5
height = 5.0
if output_format == "pdf":
filename = "%s.pdf" % output_prefix
grdevices.pdf(file=filename, width=width, height=height)
elif output_format == "png":
filename = "%s.png" % output_prefix
grdevices.png(file=filename, width=width, height=height)
else:
raise ValueError("unknown output format %s" % output_format)
sys.stderr.write("writing output to single file '%s'\n" % filename)
plot_num = 0
for i in range(len(regions)):
reg = regions[i]
plot_num += 1
sys.stderr.write("DRAWING REGION %d (%s)\n" %
(plot_num, str(reg)))
# create window for this region
draw_grid = config.getboolean("MAIN", "DRAW_GRID")
if config.has_option("MAIN", "DRAW_MIDLINE"):
draw_midline = config.getboolean("MAIN", "DRAW_MIDLINE")
else:
draw_midline = False
# draw some vertical lines on this plot?
if config.has_option("MAIN", "DRAW_VERTLINES"):
vert_lines = [float(x) for x in config.get("MAIN","DRAW_VERTLINES").split(",")]
vert_lines_col = ["black"] * len(vert_lines)
else:
vert_lines = []
vert_lines_col = []
# region attributes can also be used to specify locations of
# vertical lines
if config.has_option("MAIN", "VERTLINES_ATTRIBUTES"):
attr_names = config.get("MAIN", "VERTLINES_ATTRIBUTES").split(",")
sys.stderr.write("drawing vertical lines corresponding to "
"region attrs %s\n" %",".join(attr_names))
for a in attr_names:
if hasattr(reg, a):
pos = int(getattr(reg, a))
vert_lines.append(pos)
else:
sys.stderr.write("region is missing attribute %s\n" % a)
# colors can be specified for these lines
if config.has_option("MAIN", "VERTLINES_COLORS"):
cols = config.get("MAIN", "VERTLINES_COLORS").split(",")
vert_lines_col.extend(cols)
if len(vert_lines_col) < len(vert_lines):
# set extra lines to color black
diff = len(vert_lines) - len(vert_lines_col)
vert_lines_col.extend(["black"] * diff)
# sys.stderr.write("vert_lines: %s\n" % repr(vert_lines))
# sys.stderr.write("vert_lines_col: %s\n" % repr(vert_lines_col))
margin = config.getfloat("MAIN", "WINDOW_MARGIN")
cex = config.getfloat("MAIN", "CEX")
window = Window(reg, draw_grid=draw_grid,
draw_midline=draw_midline,
vert_lines=vert_lines,
vert_lines_col=vert_lines_col,
margin=margin, cex=cex)
# add gene tracks to window
for genes_type in gene_types:
gene_label = "GENE_" + genes_type
sys.stderr.write(" adding genes track %s\n" % gene_label)
options = dict(config.items(gene_label))
track_class = track_types[options['type']]
genes_track = track_class(gene_dict[gene_label], reg, options)
window.add_track(genes_track)
# add other tracks to window
track_names = config.get("MAIN", "TRACKS").split(",")
for track_name in track_names:
if track_name.strip() == "":
continue
sys.stderr.write(" adding track %s\n" % track_name)
section_name = "TRACK_" + track_name
if not config.has_section(section_name):
sys.stderr.write("WARNING: no config section '%s' for "
"track '%s'\n" % (section_name, track_name))
continue
options = dict(config.items(section_name))
if 'type' not in options:
sys.stderr.write("WARNING: track %s does not define "
"TYPE in configuration file\n" % track_name)
continue
track_type = options['type']
if track_type not in track_types:
sys.stderr.write("WARNING: don't how to create "
"track %s with type %s.\n"
" Known types are %s\n"
% (track_name, track_type,
", ".join(list(track_types.keys()))))
continue
try:
track_class = track_types[track_type]
track = track_class(reg, options)
window.add_track(track)
except TypeError as err:
sys.stderr.write(("-" * 60) + "\n")
sys.stderr.write("WARNING: could not init track %s of "
"type %s:\n%s\n" %
(track_name, track_type, str(err)))
traceback.print_exc()
sys.stderr.write(("-" * 60) + "\n")
except ValueError as err:
sys.stderr.write(("-" * 60) + "\n")
sys.stderr.write("WARNING: could not open track %s of "
"type %s:\n%s\n" %
(track_name, options['type'], str(err)))
traceback.print_exc()
sys.stderr.write(("-" * 60) + "\n")
if single_file:
# each region is a separate page of a single PDF
window.draw(r)
else:
# make a separate PDF for each region
# get output file parameters
height = config.getfloat("MAIN", "WINDOW_HEIGHT")
if height <= 0.0:
height = window.get_height() * 0.5
if height < 5.0:
# make minimum height 5 inches
height = 5.0
if output_format == "pdf":
filename = "%s%d.pdf" % (output_prefix, plot_num)
grdevices.pdf(file=filename, width=width, height=height)
# turn off clipping
r.par(xpd=True)
elif output_format == "png":
filename = "%s%d.png" % (output_prefix, plot_num)
grdevices.png(file=filename, width=width, height=height)
else:
raise ValueError("unknown output format %s" % output_format)
# render window
window.draw(r)
grdevices.dev_off()
if single_file:
grdevices.dev_off()
output_filename = "%s.%s" % (tr_name, output_format)
width = 8
height = 5
sys.stderr.write("drawing transcript (filename=%s)\n" % output_filename)
grdevices.pdf(file=output_filename, width=width, height=height)
region = tr
options = {
'color': "#08306B",
'utr_color': '#DEEBF7',
'border': 'false',
'height': 0.1
}
window = Window(region, draw_grid=False)
tr_track = TranscriptTrack(tr, region, options)
window.add_track(tr_track)
window.draw(r)
# top = 0
# bottom = -1
# tr_track.set_position(tr.start, tr.end, top, bottom)
# tr_track.draw_track(r)
grdevices.dev_off()
output_filename = "%s.%s" % (tr_name, output_format)
width=8
height=5
sys.stderr.write("drawing transcript (filename=%s)\n" % output_filename)
grdevices.pdf(file=output_filename, width=width, height=height)
region = tr
options = {'color' : "#08306B",
'utr_color' : '#DEEBF7',
'border' : 'false',
'height' : 1}
window = Window(region, draw_grid=False)
tr_track = TranscriptTrack(tr, region, options)
window.add_track(tr_track)
window.draw(r)
# top = 0
# bottom = -1
# tr_track.set_position(tr.start, tr.end, top, bottom)
# tr_track.draw_track(r)
grdevices.dev_off()