def _build_option_parser():
defaults = LogoOptions()
parser = DeOptionParser(
usage="%prog [options] < sequence_data.fa > sequence_logo.eps",
description=description,
version=release_description,
add_verbose_options=False)
io_grp = OptionGroup(
parser,
"Input/Output Options",
)
data_grp = OptionGroup(
parser,
"Logo Data Options",
)
trans_grp = OptionGroup(parser, "Transformations",
"Optional transformations of the sequence data.")
format_grp = OptionGroup(
parser, "Logo Format Options",
"These options control the format and display of the logo.")
color_grp = OptionGroup(
parser, "Color Options",
"Colors can be specified using CSS2 syntax. e.g. 'red', '#FF0000', etc."
)
advanced_grp = OptionGroup(
parser, "Advanced Format Options",
"These options provide fine control over the display of the logo. ")
server_grp = OptionGroup(parser, "WebLogo Server",
"Run a standalone webserver on a local port.")
parser.add_option_group(io_grp)
parser.add_option_group(data_grp)
parser.add_option_group(trans_grp)
parser.add_option_group(format_grp)
parser.add_option_group(color_grp)
parser.add_option_group(advanced_grp)
parser.add_option_group(server_grp)
# ========================== IO OPTIONS ==========================
io_grp.add_option("-f",
"--fin",
dest="fin",
action="store",
type="file_in",
default=None,
help="Sequence input file (default: stdin)",
metavar="FILENAME")
# Add position weight matrix formats to input parsers by hand
fin_choices = dict(seq_io.format_names())
fin_choices['transfac'] = 'transfac'
io_grp.add_option(
"-D",
"--datatype",
dest="input_parser",
action="store",
type="dict",
default=seq_io,
choices=fin_choices, # seq_io.format_names(),
help=
"Type of multiple sequence alignment or position weight matrix file: (%s, transfac)"
% ', '.join([f.names[0] for f in seq_io.formats]),
metavar="FORMAT")
io_grp.add_option("-o",
"--fout",
dest="fout",
type="file_out",
default=sys.stdout,
help="Output file (default: stdout)",
metavar="FILENAME")
io_grp.add_option(
"-F",
"--format",
dest="formatter",
action="store",
type="dict",
choices=formatters,
metavar="FORMAT",
help=
"Format of output: eps (default), png, png_print, pdf, jpeg, svg, logodata",
default=default_formatter)
# ========================== Data OPTIONS ==========================
data_grp.add_option(
"-A",
"--sequence-type",
dest="alphabet",
action="store",
type="dict",
choices=std_alphabets,
help="The type of sequence data: 'protein', 'rna' or 'dna'.",
metavar="TYPE")
data_grp.add_option(
"-a",
"--alphabet",
dest="alphabet",
action="store",
help="The set of symbols to count, e.g. 'AGTC'. "
"All characters not in the alphabet are ignored. "
"If neither the alphabet nor sequence-type are specified then weblogo will examine the input data and make an educated guess. "
"See also --sequence-type, --ignore-lower-case")
data_grp.add_option(
"-U",
"--units",
dest="unit_name",
action="store",
choices=std_units.keys(),
type="choice",
default=defaults.unit_name,
help=
"A unit of entropy ('bits' (default), 'nats', 'digits'), or a unit of free energy ('kT', 'kJ/mol', 'kcal/mol'), or 'probability' for probabilities",
metavar="NUMBER")
data_grp.add_option(
"",
"--composition",
dest="composition",
action="store",
type="string",
default="auto",
help=
"The expected composition of the sequences: 'auto' (default), 'equiprobable', 'none' (do not perform any compositional adjustment), a CG percentage, a species name (e.g. 'E. coli', 'H. sapiens'), or an explicit distribution (e.g. \"{'A':10, 'C':40, 'G':40, 'T':10}\"). The automatic option uses a typical distribution for proteins and equiprobable distribution for everything else. ",
metavar="COMP.")
data_grp.add_option(
"",
"--weight",
dest="weight",
action="store",
type="float",
default=None,
help="The weight of prior data. Default depends on alphabet length",
metavar="NUMBER")
data_grp.add_option(
"-i",
"--first-index",
dest="first_index",
action="store",
type="int",
default=1,
help="Index of first position in sequence data (default: 1)",
metavar="INDEX")
data_grp.add_option("-l",
"--lower",
dest="logo_start",
action="store",
type="int",
help="Lower bound of sequence to display",
metavar="INDEX")
data_grp.add_option("-u",
"--upper",
dest="logo_end",
action="store",
type="int",
help="Upper bound of sequence to display",
metavar="INDEX")
# ========================== Transformation OPTIONS ==========================
# FIXME Add test?
trans_grp.add_option(
"",
"--ignore-lower-case",
dest="ignore_lower_case",
action="store_true",
default=False,
help=
"Disregard lower case letters and only count upper case letters in sequences."
)
trans_grp.add_option(
"",
"--reverse",
dest="reverse",
action="store_true",
default=False,
help="reverse sequences",
)
trans_grp.add_option(
"",
"--complement",
dest="complement",
action="store_true",
default=False,
help="complement DNA sequences",
)
# ========================== FORMAT OPTIONS ==========================
format_grp.add_option(
"-s",
"--size",
dest="stack_width",
action="store",
type="dict",
choices=std_sizes,
metavar="LOGOSIZE",
default=defaults.stack_width,
help="Specify a standard logo size (small, medium (default), large)")
format_grp.add_option(
"-n",
"--stacks-per-line",
dest="stacks_per_line",
action="store",
type="int",
help="Maximum number of logo stacks per logo line. (default: %default)",
default=defaults.stacks_per_line,
metavar="COUNT")
format_grp.add_option("-t",
"--title",
dest="logo_title",
action="store",
type="string",
help="Logo title text.",
default=defaults.logo_title,
metavar="TEXT")
format_grp.add_option("",
"--label",
dest="logo_label",
action="store",
type="string",
help="A figure label, e.g. '2a'",
default=defaults.logo_label,
metavar="TEXT")
format_grp.add_option(
"-X",
"--show-xaxis",
action="store",
type="boolean",
default=defaults.show_xaxis,
metavar="YES/NO",
help="Display sequence numbers along x-axis? (default: %default)")
format_grp.add_option("-x",
"--xlabel",
dest="xaxis_label",
action="store",
type="string",
default=defaults.xaxis_label,
help="X-axis label",
metavar="TEXT")
format_grp.add_option(
"",
"--annotate",
dest="annotate",
action="store",
type="string",
default=None,
help=
"A comma separated list of custom stack annotations, e.g. '1,3,4,5,6,7'. Annotation list must be same length as sequences.",
metavar="TEXT")
format_grp.add_option(
"-S",
"--yaxis",
dest="yaxis_scale",
action="store",
type="float",
help=
"Height of yaxis in units. (Default: Maximum value with uninformative prior.)",
metavar="UNIT")
format_grp.add_option(
"-Y",
"--show-yaxis",
action="store",
type="boolean",
dest="show_yaxis",
default=defaults.show_yaxis,
metavar="YES/NO",
help="Display entropy scale along y-axis? (default: %default)")
format_grp.add_option(
"-y",
"--ylabel",
dest="yaxis_label",
action="store",
type="string",
help="Y-axis label (default depends on plot type and units)",
metavar="TEXT")
format_grp.add_option(
"-E",
"--show-ends",
action="store",
type="boolean",
default=defaults.show_ends,
metavar="YES/NO",
help="Label the ends of the sequence? (default: %default)")
format_grp.add_option("-P",
"--fineprint",
dest="fineprint",
action="store",
type="string",
default=defaults.fineprint,
help="The fine print (default: weblogo version)",
metavar="TEXT")
format_grp.add_option("",
"--ticmarks",
dest="yaxis_tic_interval",
action="store",
type="float",
default=defaults.yaxis_tic_interval,
help="Distance between ticmarks (default: %default)",
metavar="NUMBER")
format_grp.add_option("",
"--errorbars",
dest="show_errorbars",
action="store",
type="boolean",
default=defaults.show_errorbars,
metavar="YES/NO",
help="Display error bars? (default: %default)")
format_grp.add_option(
"",
"--reverse-stacks",
dest="reverse_stacks",
action="store",
type="boolean",
default=defaults.show_errorbars,
metavar="YES/NO",
help="Draw stacks with largest letters on top? (default: %default)")
# ========================== Color OPTIONS ==========================
# TODO: Future Feature
# color_grp.add_option( "-K", "--color-key",
# dest= "show_color_key",
# action="store",
# type = "boolean",
# default= defaults.show_color_key,
# metavar = "YES/NO",
# help="Display a color key (default: %default)")
color_scheme_choices = std_color_schemes.keys()
color_scheme_choices.sort()
color_grp.add_option( "-c", "--color-scheme",
dest="color_scheme",
action="store",
type ="dict",
choices = std_color_schemes,
metavar = "SCHEME",
default = None, # Auto
help="Specify a standard color scheme (%s)" % \
", ".join(color_scheme_choices) )
color_grp.add_option(
"-C",
"--color",
dest="colors",
action="append",
metavar="COLOR SYMBOLS DESCRIPTION ",
nargs=3,
default=[],
help=
"Specify symbol colors, e.g. --color black AG 'Purine' --color red TC 'Pyrimidine' "
)
color_grp.add_option("",
"--default-color",
dest="default_color",
action="store",
metavar="COLOR",
default=defaults.default_color,
help="Symbol color if not otherwise specified.")
# ========================== Advanced options =========================
advanced_grp.add_option("-W",
"--stack-width",
dest="stack_width",
action="store",
type="float",
default=defaults.stack_width,
help="Width of a logo stack (default: %s)" %
defaults.stack_width,
metavar="POINTS")
advanced_grp.add_option(
"",
"--aspect-ratio",
dest="stack_aspect_ratio",
action="store",
type="float",
default=defaults.stack_aspect_ratio,
help="Ratio of stack height to width (default: %s)" %
defaults.stack_aspect_ratio,
metavar="POINTS")
advanced_grp.add_option("",
"--box",
dest="show_boxes",
action="store",
type="boolean",
default=False,
metavar="YES/NO",
help="Draw boxes around symbols? (default: no)")
advanced_grp.add_option(
"",
"--resolution",
dest="resolution",
action="store",
type="float",
default=96,
help=
"Bitmap resolution in dots per inch (DPI). (Default: 96 DPI, except png_print, 600 DPI) Low resolution bitmaps (DPI<300) are antialiased.",
metavar="DPI")
advanced_grp.add_option(
"",
"--scale-width",
dest="scale_width",
action="store",
type="boolean",
default=True,
metavar="YES/NO",
help=
"Scale the visible stack width by the fraction of symbols in the column? (I.e. columns with many gaps of unknowns are narrow.) (Default: yes)"
)
advanced_grp.add_option(
"",
"--debug",
action="store",
type="boolean",
default=defaults.debug,
metavar="YES/NO",
help="Output additional diagnostic information. (Default: %default)")
# ========================== Server options =========================
server_grp.add_option(
"",
"--serve",
dest="serve",
action="store_true",
default=False,
help="Start a standalone WebLogo server for creating sequence logos.")
server_grp.add_option(
"",
"--port",
dest="port",
action="store",
type="int",
default=8080,
help="Listen to this local port. (Default: %default)",
metavar="PORT")
return parser
def _build_option_parser() :
defaults = LogoOptions()
parser = DeOptionParser(usage="%prog [options] < sequence_data.fa > sequence_logo.eps",
description = description,
version = release_description,
add_verbose_options = False
)
io_grp = OptionGroup(parser, "Input/Output Options",)
data_grp = OptionGroup(parser, "Logo Data Options",)
trans_grp = OptionGroup(parser, "Transformations", "Optional transformations of the sequence data.")
format_grp = OptionGroup(parser, "Logo Format Options",
"These options control the format and display of the logo.")
color_grp = OptionGroup(parser, "Color Options",
"Colors can be specified using CSS2 syntax. e.g. 'red', '#FF0000', etc.")
advanced_grp = OptionGroup(parser, "Advanced Format Options",
"These options provide fine control over the display of the logo. ")
server_grp = OptionGroup(parser, "WebLogo Server",
"Run a standalone webserver on a local port.")
parser.add_option_group(io_grp)
parser.add_option_group(data_grp)
parser.add_option_group(trans_grp)
parser.add_option_group(format_grp)
parser.add_option_group(color_grp)
parser.add_option_group(advanced_grp)
parser.add_option_group(server_grp)
# ========================== IO OPTIONS ==========================
io_grp.add_option( "-f", "--fin",
dest="fin",
action="store",
type="file_in",
default=None,
help="Sequence input file (default: stdin)",
metavar="FILENAME")
# Add position weight matrix formats to input parsers by hand
fin_choices = dict(seq_io.format_names())
fin_choices['transfac'] = 'transfac'
io_grp.add_option("-D", "--datatype",
dest="input_parser",
action="store", type ="dict",
default = seq_io,
choices = fin_choices, # seq_io.format_names(),
help="Type of multiple sequence alignment or position weight matrix file: (%s, transfac)" %
', '.join([ f.names[0] for f in seq_io.formats]),
metavar="FORMAT")
io_grp.add_option("-o", "--fout", dest="fout",
type="file_out",
default=sys.stdout,
help="Output file (default: stdout)",
metavar="FILENAME")
io_grp.add_option( "-F", "--format",
dest="formatter",
action="store",
type="dict",
choices = formatters,
metavar= "FORMAT",
help="Format of output: eps (default), png, png_print, pdf, jpeg, svg, logodata",
default = default_formatter)
# ========================== Data OPTIONS ==========================
data_grp.add_option( "-A", "--sequence-type",
dest="alphabet",
action="store",
type="dict",
choices = std_alphabets,
help="The type of sequence data: 'protein', 'rna' or 'dna'.",
metavar="TYPE")
data_grp.add_option( "-a", "--alphabet",
dest="alphabet",
action="store",
help="The set of symbols to count, e.g. 'AGTC'. "
"All characters not in the alphabet are ignored. "
"If neither the alphabet nor sequence-type are specified then weblogo will examine the input data and make an educated guess. "
"See also --sequence-type, --ignore-lower-case" )
data_grp.add_option( "-U", "--units",
dest="unit_name",
action="store",
choices = std_units.keys(),
type="choice",
default = defaults.unit_name,
help="A unit of entropy ('bits' (default), 'nats', 'digits'), or a unit of free energy ('kT', 'kJ/mol', 'kcal/mol'), or 'probability' for probabilities",
metavar = "NUMBER")
data_grp.add_option( "", "--composition",
dest="composition",
action="store",
type="string",
default = "auto",
help="The expected composition of the sequences: 'auto' (default), 'equiprobable', 'none' (do not perform any compositional adjustment), a CG percentage, a species name (e.g. 'E. coli', 'H. sapiens'), or an explicit distribution (e.g. \"{'A':10, 'C':40, 'G':40, 'T':10}\"). The automatic option uses a typical distribution for proteins and equiprobable distribution for everything else. ",
metavar="COMP.")
data_grp.add_option( "", "--weight",
dest="weight",
action="store",
type="float",
default = None,
help="The weight of prior data. Default depends on alphabet length",
metavar="NUMBER")
data_grp.add_option( "-i", "--first-index",
dest="first_index",
action="store",
type="int",
default = 1,
help="Index of first position in sequence data (default: 1)",
metavar="INDEX")
data_grp.add_option( "-l", "--lower",
dest="logo_start",
action="store",
type="int",
help="Lower bound of sequence to display",
metavar="INDEX")
data_grp.add_option( "-u", "--upper",
dest="logo_end",
action="store",
type="int",
help="Upper bound of sequence to display",
metavar="INDEX")
# ========================== Transformation OPTIONS ==========================
# FIXME Add test?
trans_grp.add_option( "", "--ignore-lower-case",
dest="ignore_lower_case",
action="store_true",
default=False,
help="Disregard lower case letters and only count upper case letters in sequences."
)
trans_grp.add_option( "", "--reverse",
dest="reverse",
action="store_true",
default=False,
help="reverse sequences",
)
trans_grp.add_option( "", "--complement",
dest="complement",
action="store_true",
default=False,
help="complement DNA sequences",
)
# ========================== FORMAT OPTIONS ==========================
format_grp.add_option( "-s", "--size",
dest="stack_width",
action="store",
type ="dict",
choices = std_sizes,
metavar = "LOGOSIZE",
default = defaults.stack_width,
help="Specify a standard logo size (small, medium (default), large)" )
format_grp.add_option( "-n", "--stacks-per-line",
dest="stacks_per_line",
action="store",
type="int",
help="Maximum number of logo stacks per logo line. (default: %default)",
default = defaults.stacks_per_line,
metavar="COUNT")
format_grp.add_option( "-t", "--title",
dest="logo_title",
action="store",
type="string",
help="Logo title text.",
default = defaults.logo_title,
metavar="TEXT")
format_grp.add_option( "", "--label",
dest="logo_label",
action="store",
type="string",
help="A figure label, e.g. '2a'",
default = defaults.logo_label,
metavar="TEXT")
format_grp.add_option( "-X", "--show-xaxis",
action="store",
type = "boolean",
default= defaults.show_xaxis,
metavar = "YES/NO",
help="Display sequence numbers along x-axis? (default: %default)")
format_grp.add_option( "-x", "--xlabel",
dest="xaxis_label",
action="store",
type="string",
default = defaults.xaxis_label,
help="X-axis label",
metavar="TEXT")
format_grp.add_option( "", "--annotate",
dest="annotate",
action="store",
type="string",
default = None,
help="A comma separated list of custom stack annotations, e.g. '1,3,4,5,6,7'. Annotation list must be same length as sequences.",
metavar="TEXT")
format_grp.add_option( "-S", "--yaxis",
dest="yaxis_scale",
action="store",
type="float",
help="Height of yaxis in units. (Default: Maximum value with uninformative prior.)",
metavar = "UNIT")
format_grp.add_option( "-Y", "--show-yaxis",
action="store",
type = "boolean",
dest = "show_yaxis",
default= defaults.show_yaxis,
metavar = "YES/NO",
help="Display entropy scale along y-axis? (default: %default)")
format_grp.add_option( "-y", "--ylabel",
dest="yaxis_label",
action="store",
type="string",
help="Y-axis label (default depends on plot type and units)",
metavar="TEXT")
format_grp.add_option( "-E", "--show-ends",
action="store",
type = "boolean",
default= defaults.show_ends,
metavar = "YES/NO",
help="Label the ends of the sequence? (default: %default)")
format_grp.add_option( "-P", "--fineprint",
dest="fineprint",
action="store",
type="string",
default= defaults.fineprint,
help="The fine print (default: weblogo version)",
metavar="TEXT")
format_grp.add_option( "", "--ticmarks",
dest="yaxis_tic_interval",
action="store",
type="float",
default= defaults.yaxis_tic_interval,
help="Distance between ticmarks (default: %default)",
metavar = "NUMBER")
format_grp.add_option( "", "--errorbars",
dest = "show_errorbars",
action="store",
type = "boolean",
default= defaults.show_errorbars,
metavar = "YES/NO",
help="Display error bars? (default: %default)")
format_grp.add_option( "", "--reverse-stacks",
dest = "reverse_stacks",
action="store",
type = "boolean",
default= defaults.show_errorbars,
metavar = "YES/NO",
help="Draw stacks with largest letters on top? (default: %default)")
# ========================== Color OPTIONS ==========================
# TODO: Future Feature
# color_grp.add_option( "-K", "--color-key",
# dest= "show_color_key",
# action="store",
# type = "boolean",
# default= defaults.show_color_key,
# metavar = "YES/NO",
# help="Display a color key (default: %default)")
color_scheme_choices = std_color_schemes.keys()
color_scheme_choices.sort()
color_grp.add_option( "-c", "--color-scheme",
dest="color_scheme",
action="store",
type ="dict",
choices = std_color_schemes,
metavar = "SCHEME",
default = None, # Auto
help="Specify a standard color scheme (%s)" % \
", ".join(color_scheme_choices) )
color_grp.add_option( "-C", "--color",
dest="colors",
action="append",
metavar="COLOR SYMBOLS DESCRIPTION ",
nargs = 3,
default=[],
help="Specify symbol colors, e.g. --color black AG 'Purine' --color red TC 'Pyrimidine' ")
color_grp.add_option( "", "--default-color",
dest="default_color",
action="store",
metavar="COLOR",
default= defaults.default_color,
help="Symbol color if not otherwise specified.")
# ========================== Advanced options =========================
advanced_grp.add_option( "-W", "--stack-width",
dest="stack_width",
action="store",
type="float",
default= defaults.stack_width,
help="Width of a logo stack (default: %s)"% defaults.stack_width,
metavar="POINTS" )
advanced_grp.add_option( "", "--aspect-ratio",
dest="stack_aspect_ratio",
action="store",
type="float",
default= defaults.stack_aspect_ratio ,
help="Ratio of stack height to width (default: %s)"%defaults.stack_aspect_ratio,
metavar="POINTS" )
advanced_grp.add_option( "", "--box",
dest="show_boxes",
action="store",
type = "boolean",
default=False,
metavar = "YES/NO",
help="Draw boxes around symbols? (default: no)")
advanced_grp.add_option( "", "--resolution",
dest="resolution",
action="store",
type="float",
default=96,
help="Bitmap resolution in dots per inch (DPI). (Default: 96 DPI, except png_print, 600 DPI) Low resolution bitmaps (DPI<300) are antialiased.",
metavar="DPI")
advanced_grp.add_option( "", "--scale-width",
dest="scale_width",
action="store",
type = "boolean",
default= True,
metavar = "YES/NO",
help="Scale the visible stack width by the fraction of symbols in the column? (I.e. columns with many gaps of unknowns are narrow.) (Default: yes)")
advanced_grp.add_option( "", "--debug",
action="store",
type = "boolean",
default= defaults.debug,
metavar = "YES/NO",
help="Output additional diagnostic information. (Default: %default)")
# Additional options by Omar Wagih
advanced_grp.add_option( "", "--rotate-numbers",
dest="rotate_numbers",
action="store",
type = "boolean",
default= False,
metavar = "YES/NO",
help="Rotate numbers on xaxis? (default: no)")
advanced_grp.add_option( "", "--tic-length",
dest="tic_length",
action="store",
type="float",
default= 5,
help="Length of tics (default: 5)",
metavar = "NUMBER")
# ========================== Server options =========================
server_grp.add_option( "", "--serve",
dest="serve",
action="store_true",
default= False,
help="Start a standalone WebLogo server for creating sequence logos.")
server_grp.add_option( "", "--port",
dest="port",
action="store",
type="int",
default= 8080,
help="Listen to this local port. (Default: %default)",
metavar="PORT")
return parser
def _build_option_parser():
defaults = LogoOptions()
parser = DeOptionParser(
usage="%prog [options] < sequence_data.fa > sequence_logo.eps",
description=description,
version=release_description,
add_verbose_options=False,
)
io_grp = OptionGroup(parser, "Input/Output Options")
data_grp = OptionGroup(parser, "Logo Data Options")
heat_grp = OptionGroup(
parser,
"Heat Map Options",
"These options affect the format of the sequence logo in the heat map mode (See also Color Options).",
)
color_grp = OptionGroup(
parser,
"Color Options",
"Colors can be specified using CSS2 syntax. e.g. 'red', '#FF0000', etc (See also Heat Map Options).",
)
trans_grp = OptionGroup(parser, "Transformations", "Optional transformations of the sequence data.")
format_grp = OptionGroup(
parser, "Logo Format Options", "These options control the format and display of the sequence logo."
)
advanced_grp = OptionGroup(
parser, "Advanced Format Options", "These options provide fine control over the display of the sequence logo."
)
server_grp = OptionGroup(parser, "HeatLogo Server", "Run a standalone webserver on a local port.")
parser.add_option_group(io_grp)
parser.add_option_group(data_grp)
parser.add_option_group(heat_grp)
parser.add_option_group(color_grp)
parser.add_option_group(trans_grp)
parser.add_option_group(format_grp)
parser.add_option_group(advanced_grp)
parser.add_option_group(server_grp)
# ========================== IO OPTIONS ==========================
io_grp.add_option(
"-i",
"--input",
dest="fin",
action="store",
type="file_in",
default=None,
help="Sequence input file (default: stdin)",
metavar="FILENAME",
)
# Add position weight matrix formats to input parsers by hand
fin_choices = dict(seq_io.format_names())
fin_choices["transfac"] = "transfac"
formatters_string = formatters.keys()
io_grp.add_option(
"-f",
"--input-format",
dest="input_parser",
action="store",
type="dict",
default=seq_io,
choices=fin_choices, # seq_io.format_names(),
help="Type of multiple sequence alignment or position weight matrix file: (%s, transfac)"
% ", ".join([f.names[0] for f in seq_io.formats]),
metavar="FORMAT",
)
io_grp.add_option(
"-o",
"--output",
dest="fout",
type="file_out",
default=sys.stdout,
help="Output file (default: stdout)",
metavar="FILENAME",
)
io_grp.add_option(
"-F",
"--output-format",
dest="formatter",
action="store",
type="dict",
metavar="FORMAT",
choices=formatters,
help="Format of output: eps (default), png, png_print, pdf, jpeg, svg, logodata",
default=default_formatter,
)
io_grp.add_option(
"",
"--pwm-prob",
dest="pwm_prob",
action="store",
type="string",
metavar="FILENAME",
default=None,
help="Output position weight matrix composed of logarithmic probabilities",
)
io_grp.add_option(
"",
"--pwm-pval",
dest="pwm_pval",
action="store",
type="string",
metavar="FILENAME",
default=None,
help="Output position weight matrix of P-values",
)
# ========================== Data OPTIONS ==========================
data_grp.add_option(
"-A",
"--sequence-type",
dest="alphabet",
action="store",
type="dict",
choices=std_alphabets,
help="The type of sequence data: 'protein', 'rna', 'dna', or 'codon' (See also: --codon-frame).",
metavar="TYPE",
)
data_grp.add_option(
"-a",
"--alphabet",
dest="alphabet",
action="store",
help="The set of symbols to count, e.g. 'AGTC'. All characters not in the alphabet are ignored. If neither the alphabet nor sequence-type are specified then heatlogo will examine the input data and make an educated guess. (See also: --sequence-type, --ignore-lower-case)",
)
data_grp.add_option(
"-R",
"--codon-frame",
dest="codon_frame",
action="store",
type="int",
default=defaults.codon_frame,
help="Codon reading frame (default: +1): [+1, +2, +3] indicate the forward strand frame, and [-1, -2, -3] indicate the reverse strand frame",
metavar="NUMBER",
)
data_grp.add_option(
"-b",
"--composition",
dest="composition",
action="store",
type="string",
default="auto",
help="The expected composition of the sequences. HeatLogo accepts four types of formats: (1) String: 'auto' (default), 'equiprobable', or 'none' (do not perform any compositional adjustment, Heatmap: off). The automatic option uses a typical distribution for proteins and equiprobable distribution for everything else. (2) CG percentage. (3) Explicit distribution of bases, amino acids, or codons (format: \"{'A':10, 'C':40, 'G':40, 'T':10}\"). (4) Tab-delimited file containing each symbol and its expected composition in each line.",
metavar="COMP.",
)
data_grp.add_option(
"-w",
"--weight",
dest="weight",
action="store",
type="float",
default=None,
help="The weight of prior data. Default depends on alphabet length",
metavar="NUMBER",
)
data_grp.add_option(
"-N",
"--second-data",
dest="second_data",
action="store",
type="file_in",
default=None,
help="Second dataset file to compare with the input. HeatLogo measures statistical significance at each column by comparing the number of symbols appered in input and second datasets. Accepted formats: %s."
% ", ".join([f.names[0] for f in seq_io.formats]),
metavar="FILENAME",
)
data_grp.add_option(
"-B",
"--second-composition",
dest="second_composition",
action="store",
type="string",
default="auto",
help="The expected composition of the second sample sequences. The supported formats are the same as those of '--composition'.",
metavar="2nd-COMP.",
)
data_grp.add_option(
"-W",
"--second-weight",
dest="second_weight",
action="store",
type="float",
default=None,
help="The prior weight for the second dataset. Default depends on alphabet length",
metavar="NUMBER",
)
data_grp.add_option(
"-U",
"--units",
dest="unit_name",
action="store",
choices=std_units.keys(),
type="choice",
default=defaults.unit_name,
help="A unit of entropy ('bits' (default), 'nats', 'digits'), or a unit of free energy ('kT', 'kJ/mol', 'kcal/mol'), or 'probability' for probabilities",
metavar="NUMBER",
)
# ======================== Heat Map OPTIONS =========================
stats_choices = stats_tests.keys()
stats_choices.sort()
heat_grp.add_option(
"-S",
"--stats-test",
dest="stats_func",
action="store",
type="dict",
choices=stats_tests,
metavar="TEST",
default=defaults.stats_func,
help="Specify a statistical test to calculate p-values: %s (default: t-test)" % ", ".join(stats_choices),
)
heat_color_choices = heat_color_schemes.keys()
heat_color_choices.sort()
heat_grp.add_option(
"-H",
"--heat-scheme",
dest="heat_scheme",
action="store",
type="dict",
choices=heat_color_schemes,
metavar="SCHEME",
default=defaults.heat_scheme,
help="Specify a heatmap color scheme (%s) (See also: '--p-color')" % ", ".join(heat_color_choices),
)
heat_grp.add_option(
"",
"--p-color",
dest="p_colors",
action="append",
metavar="COLOR PVALUE",
nargs=2,
default=[],
help="Specify a color for a p-value (p-value range: -1 < p < 1), e.g. --p-color blue 0.5 --p-color red 0.25",
)
heat_grp.add_option(
"",
"--hide-colorkey",
dest="show_colorkey",
action="store_false",
default=True,
help="Toggle switch to hide a heatmap color key on the right side of a sequence logo (default: off)",
)
# ========================== Color OPTIONS ==========================
color_scheme_choices = std_color_schemes.keys()
color_scheme_choices.sort()
color_grp.add_option(
"-C",
"--color-scheme",
dest="color_scheme",
action="store",
type="dict",
choices=std_color_schemes,
metavar="SCHEME",
default=None, # Auto
help="Specify a standard color scheme (%s) (Heatmap: off)" % ", ".join(color_scheme_choices),
)
color_grp.add_option(
"",
"--c-color",
dest="colors",
action="append",
metavar="COLOR SYMBOLS DESCRIPTION ",
nargs=3,
default=[],
help="Specify symbol colors, e.g. --c-color black AG 'Purine' --c-color red TC 'Pyrimidine', (Heatmap: off)",
)
color_grp.add_option(
"",
"--default-color",
dest="default_color",
action="store",
metavar="COLOR",
default=defaults.default_color,
help="Symbol color if not otherwise specified.",
)
# ========================== Transformation OPTIONS ==========================
# FIXME Add test?
trans_grp.add_option(
"",
"--ignore-lower-case",
dest="ignore_lower_case",
action="store_true",
default=False,
help="Disregard lower case letters and only count upper case letters in sequences.",
)
trans_grp.add_option("", "--reverse", dest="reverse", action="store_true", default=False, help="reverse sequences")
trans_grp.add_option(
"", "--complement", dest="complement", action="store_true", default=False, help="complement DNA sequences"
)
# ========================== FORMAT OPTIONS ==========================
format_grp.add_option(
"-I",
"--first-index",
dest="first_index",
action="store",
type="int",
default=1,
help="Index of first position in sequence data (default: 1)",
metavar="INDEX",
)
format_grp.add_option(
"-s",
"--start",
dest="logo_start",
action="store",
type="int",
help="Lower bound (i.e. start position) of sequence to display",
metavar="INDEX",
)
format_grp.add_option(
"-e",
"--end",
dest="logo_end",
action="store",
type="int",
help="Upper bound (i.e. end position) of sequence to display",
metavar="INDEX",
)
format_grp.add_option(
"-L",
"--size",
dest="stack_width",
action="store",
type="dict",
choices=std_sizes,
metavar="LOGOSIZE",
default=defaults.stack_width,
help="Specify a standard logo size (small, medium (default), large)",
)
format_grp.add_option(
"-n",
"--stacks-per-line",
dest="stacks_per_line",
action="store",
type="int",
help="Maximum number of logo stacks per logo line. (default: %default)",
default=defaults.stacks_per_line,
metavar="COUNT",
)
format_grp.add_option(
"-t",
"--title",
dest="logo_title",
action="store",
type="string",
help="Logo title text.",
default=defaults.logo_title,
metavar="TEXT",
)
format_grp.add_option(
"-l",
"--label",
dest="logo_label",
action="store",
type="string",
help="A figure label, e.g. '2a'",
default=defaults.logo_label,
metavar="TEXT",
)
format_grp.add_option(
"-X",
"--show-xaxis",
action="store",
type="boolean",
default=defaults.show_xaxis,
metavar="YES/NO",
help="Display sequence numbers along x-axis? (default: %default)",
)
format_grp.add_option(
"-x",
"--xlabel",
dest="xaxis_label",
action="store",
type="string",
default=defaults.xaxis_label,
help="X-axis label",
metavar="TEXT",
)
format_grp.add_option(
"",
"--annotate",
dest="annotate",
action="store",
type="string",
default=None,
help="A comma separated list of custom stack annotations, e.g. '1,3,4,5,6,7'. Annotation list must be same length as sequences.",
metavar="TEXT",
)
format_grp.add_option(
"-M",
"--yaxis",
dest="yaxis_scale",
action="store",
type="float",
help="Height of yaxis in units. (Default: Maximum value with uninformative prior.)",
metavar="UNIT",
)
format_grp.add_option(
"-Y",
"--show-yaxis",
action="store",
type="boolean",
dest="show_yaxis",
default=defaults.show_yaxis,
metavar="YES/NO",
help="Display entropy scale along y-axis? (default: %default)",
)
format_grp.add_option(
"-y",
"--ylabel",
dest="yaxis_label",
action="store",
type="string",
help="Y-axis label (default depends on plot type and units)",
metavar="TEXT",
)
format_grp.add_option(
"-E",
"--show-ends",
action="store",
type="boolean",
default=defaults.show_ends,
metavar="YES/NO",
help="Label the ends of the sequence? (default: %default)",
)
format_grp.add_option(
"-P",
"--fineprint",
dest="fineprint",
action="store",
type="string",
default=defaults.fineprint,
help="The fine print (default: heatlogo version)",
metavar="TEXT",
)
format_grp.add_option(
"",
"--ticmarks",
dest="yaxis_tic_interval",
action="store",
type="float",
default=defaults.yaxis_tic_interval,
help="Distance between ticmarks (default: %default)",
metavar="NUMBER",
)
format_grp.add_option(
"",
"--errorbars",
dest="show_errorbars",
action="store",
type="boolean",
default=defaults.show_errorbars,
metavar="YES/NO",
help="Display error bars? (default: %default)",
)
format_grp.add_option(
"",
"--reverse-stacks",
dest="reverse_stacks",
action="store",
type="boolean",
default=defaults.show_errorbars,
metavar="YES/NO",
help="Draw stacks with largest letters on top? (default: %default)",
)
# ========================== Advanced options =========================
advanced_grp.add_option(
"-k",
"--stack-width",
dest="stack_width",
action="store",
type="float",
default=defaults.stack_width,
help="Width of a logo stack (default: %s)" % defaults.stack_width,
metavar="POINTS",
)
advanced_grp.add_option(
"",
"--aspect-ratio",
dest="stack_aspect_ratio",
action="store",
type="float",
default=defaults.stack_aspect_ratio,
help="Ratio of stack height to width (default: %s)" % defaults.stack_aspect_ratio,
metavar="POINTS",
)
advanced_grp.add_option(
"",
"--box",
dest="show_boxes",
action="store",
type="boolean",
default=False,
metavar="YES/NO",
help="Draw boxes around symbols? (default: no)",
)
advanced_grp.add_option(
"",
"--resolution",
dest="resolution",
action="store",
type="float",
default=96,
help="Bitmap resolution in dots per inch (DPI). (Default: 96 DPI, except png_print, 600 DPI) Low resolution bitmaps (DPI<300) are antialiased.",
metavar="DPI",
)
advanced_grp.add_option(
"",
"--scale-width",
dest="scale_width",
action="store",
type="boolean",
default=True,
metavar="YES/NO",
help="Scale the visible stack width by the fraction of symbols in the column? (i.e. columns with many gaps of unknowns are narrow.) (Default: yes)",
)
# ========================== Server options =========================
server_grp.add_option(
"",
"--serve",
dest="serve",
action="store_true",
default=False,
help="Start a standalone HeatLogo server for creating sequence logos.",
)
server_grp.add_option(
"",
"--port",
dest="port",
action="store",
type="int",
default=8080,
help="Listen to this local port. (Default: %default)",
metavar="PORT",
)
return parser
