def _build_logoformat(logodata, opts):
""" Extract and process relevant option values and return a
LogoFormat object."""
args = {}
direct_from_opts = [
# Logo Data Options.
"alphabet",
"unit_name",
"first_index",
"logo_start",
"logo_end",
# Logo Format Options.
"stack_width",
"stacks_per_line",
"logo_title",
"logo_label",
"show_xaxis",
"xaxis_label",
"annotate",
"rotate_numbers",
"number_interval",
"yaxis_scale",
"show_yaxis",
"yaxis_label",
"show_ends",
"fineprint",
"yaxis_tic_interval",
"show_errorbars",
"reverse_stacks",
# Color Options.
"color_scheme",
"default_color",
# Font Format Options.
"fontsize",
"title_fontsize",
"small_fontsize",
"number_fontsize",
"text_font",
"logo_font",
"title_font",
# Advanced Format Options.
"stack_aspect_ratio",
"show_boxes",
"resolution",
"scale_width",
"debug",
"errorbar_fraction",
"errorbar_width_fraction",
"errorbar_gray",
]
for k in direct_from_opts:
args[k] = opts.__dict__[k]
# logo_size = copy.copy(opts.__dict__['logo_size'])
# size_from_opts = ["stack_width", "stack_height"]
# for k in size_from_opts :
# length = getattr(opts, k)
# if length :
# setattr( logo_size, k, length )
# args["size"] = logo_size
if opts.colors:
color_scheme = ColorScheme()
for color, symbols, desc in opts.colors:
try:
# c = Color.from_string(color)
color_scheme.rules.append(SymbolColor(symbols, color, desc))
except ValueError:
raise ValueError(
"error: option --color: invalid value: '%s'" % color)
args["color_scheme"] = color_scheme
if opts.annotate:
args["annotate"] = opts.annotate.split(',')
logooptions = LogoOptions()
for a, v in iteritems(args):
setattr(logooptions, a, v)
theformat = LogoFormat(logodata, logooptions)
return theformat
def _build_logoformat(logodata, opts):
""" Extract and process relevant option values and return a
LogoFormat object."""
args = {}
direct_from_opts = [
# Logo Data Options.
"alphabet",
"unit_name",
"first_index",
"logo_start",
"logo_end",
# Logo Format Options.
"stack_width",
"stacks_per_line",
"logo_title",
"logo_label",
"show_xaxis",
"xaxis_label",
"annotate",
"rotate_numbers",
"number_interval",
"yaxis_scale",
"show_yaxis",
"yaxis_label",
"show_ends",
"fineprint",
"yaxis_tic_interval",
"show_errorbars",
"reverse_stacks",
# Color Options.
"color_scheme",
"default_color",
# Font Format Options.
"fontsize",
"title_fontsize",
"small_fontsize",
"number_fontsize",
"text_font",
"logo_font",
"title_font",
# Advanced Format Options.
"stack_aspect_ratio",
"show_boxes",
"resolution",
"scale_width",
"debug",
"errorbar_fraction",
"errorbar_width_fraction",
"errorbar_gray",
]
for k in direct_from_opts:
args[k] = opts.__dict__[k]
# logo_size = copy.copy(opts.__dict__['logo_size'])
# size_from_opts = ["stack_width", "stack_height"]
# for k in size_from_opts :
# length = getattr(opts, k)
# if length :
# setattr( logo_size, k, length )
# args["size"] = logo_size
if opts.colors:
color_scheme = ColorScheme()
for color, symbols, desc in opts.colors:
try:
# c = Color.from_string(color)
color_scheme.rules.append(SymbolColor(symbols, color, desc))
except ValueError:
raise ValueError(
"error: option --color: invalid value: '%s'" % color)
args["color_scheme"] = color_scheme
if opts.annotate:
args["annotate"] = opts.annotate.split(',')
logooptions = LogoOptions()
for a, v in iteritems(args):
setattr(logooptions, a, v)
theformat = LogoFormat(logodata, logooptions)
return theformat
def _build_logoformat( logodata, opts) :
""" Extract and process relevant option values and return a
LogoFormat object."""
args = {}
direct_from_opts = [
"stacks_per_line",
"logo_title",
"yaxis_label",
"show_xaxis",
"show_yaxis",
"xaxis_label",
"show_ends",
"fineprint",
"show_errorbars",
"show_boxes",
"yaxis_tic_interval",
"resolution",
"alphabet",
"debug",
"show_ends",
"default_color",
#"show_color_key",
"color_scheme",
"unit_name",
"logo_label",
"yaxis_scale",
"first_index",
"logo_start",
"logo_end",
"scale_width",
"annotate",
"stack_width",
"stack_aspect_ratio",
"reverse_stacks"
]
for k in direct_from_opts:
args[k] = opts.__dict__[k]
# logo_size = copy.copy(opts.__dict__['logo_size'])
# size_from_opts = ["stack_width", "stack_height"]
# for k in size_from_opts :
# length = getattr(opts, k)
# if length : setattr( logo_size, k, length )
# args["size"] = logo_size
if opts.colors:
color_scheme = ColorScheme()
for color, symbols, desc in opts.colors:
try :
#c = Color.from_string(color)
color_scheme.groups.append( ColorGroup(symbols, color, desc) )
except ValueError :
raise ValueError(
"error: option --color: invalid value: '%s'" % color )
##HY April 17
#color_scheme.groups.append(ColorGroup('.', 'white', '')) # removed symbols
#color_scheme.groups.append(ColorGroup('-', 'grey', '')) # grey gaps
args["color_scheme"] = color_scheme
if opts.annotate:
args["annotate"] = opts.annotate.split(',')
#HY 2015 FEB
if opts.color_group_file:
color_scheme = ColorScheme()
color_specified = {} # key: seq position + base, value: color number. eg. { '5A':'1', '6C':'1', '10G':'2'}
ccode=-1; # to make ccode start 0
for line in opts.color_group_file :
if line.isspace() : continue
l = line.lstrip().rstrip()
if l[-1] ==':' :
try :
ccode += 1
color_scheme.groups.append(ColorGroup(str(ccode), l[:-1], ''))
except ValueError :
raise ValueError(
"error: option custom color group: invalid value: '%s'" % l[:-1] )
else :
ptn = re.compile('\d+\s+[ACDEFGHIKLMNOPQRSTUVWYBJZX\*\-\#\.]+', re.IGNORECASE)
if (not ptn.match(l)): continue
s=l.split()
for x in s[1]:
color_specified[s[0]+x]=str(ccode)
#HY 25, Feb
color_scheme.groups.append(ColorGroup('.', 'white', '')) # removed symbols
color_scheme.groups.append(ColorGroup('-', 'grey', '')) # grey gaps
args["color_scheme"] = color_scheme
args["color_specified"] = color_specified
#HY 2015 FEB end
logooptions = LogoOptions()
for a, v in iteritems(args):
setattr(logooptions, a, v)
theformat = LogoFormat(logodata, logooptions )
return theformat