def weblogoPOIM(logofile, poim, max_len):
"""instead of plotting the POIM heatmap, create a weblogo from the 1st-degree poim"""
warnings.filterwarnings('ignore', ' This call to matplotlib.use()*')
from corebio.data import rna_letters, dna_letters, amino_acid_letters
from weblogolib import LogoData, LogoOptions, LogoFormat, classic, png_print_formatter
#print "WEBLOGO!"
#print "Writing ", logofile
#print poim[0]
positive_logo = []
negative_logo = []
for i in xrange(len(poim[0])):
positive_logo.append([])
negative_logo.append([])
for j in xrange(len(poim[0][i])):
if poim[0][i][j] < 0:
positive_logo[i].append(0)
negative_logo[i].append(poim[0][i][j] * -10000)
else:
negative_logo[i].append(0)
positive_logo[i].append(poim[0][i][j] * 1000)
#print "Positive logo: ", positive_logo
#print "Negative logo: ", negative_logo
pos_data = LogoData.from_counts('ACGT', numpy.array(positive_logo).T, None)
neg_data = LogoData.from_counts("ACGT", numpy.array(negative_logo).T, None)
neg_opt = LogoOptions()
neg_opt.fineprint += " from KIRMES POIM data"
#logoopt.number_interval = 5
neg_opt.small_fontsize = 4
neg_opt.title_fontsize = 8
neg_opt.scale_width = False
title = os.path.split(logofile)[1]
title = title[:title.rfind(".")]
if "_" in title:
title = title[title.rfind("_") + 1:]
neg_opt.logo_title = title + " Negative Logo"
neg_format = LogoFormat(neg_data, neg_opt)
pos_opt = LogoOptions()
#pos_opt.show_ends = True
pos_opt.scale_width = False
pos_opt.logo_title = title + " Positive Sequence Logo"
pos_opt.show_fineprint = False
pos_opt.color_scheme = classic
pos_format = LogoFormat(pos_data, pos_opt)
neg_logo = open(logofile + "n.png", 'w')
png_print_formatter(neg_data, neg_format, neg_logo)
neg_logo.close()
pos_logo = open(logofile + "p.png", 'w')
png_print_formatter(pos_data, pos_format, pos_logo)
pos_logo.close()
concatPNG(logofile, (logofile + "p.png", logofile + "n.png"))
os.remove(logofile + "n.png")
os.remove(logofile + "p.png")
def write_weblogo(self, filepath):
matrix_tuple = []
for distribution in self.values:
matrix_tuple.append(tuple(distribution))
dataArray = np.array(tuple(matrix_tuple))
alph = Alphabet(''.join(self.alphabet))
weblogoData = LogoData.from_counts(alph, dataArray)
weblogoOptions = LogoOptions(color_scheme=classic)
weblogoOptions.title = "PWM"
weblogoFormat = LogoFormat(weblogoData, weblogoOptions)
weblogo_file = open(filepath, 'w')
weblogo_file.write(png_print_formatter(weblogoData, weblogoFormat))
weblogo_file.close()
def outputMotif(theta_motif, theta_background_matrix, lambda_motif, logev, k, outstr):
from weblogolib import LogoData, LogoOptions, LogoFormat, png_formatter, eps_formatter, unambiguous_dna_alphabet
_pv_format = "%3.1fe%+04.0f"
f_string = sprint_logx(log(lambda_motif), 1, _pv_format)
g_string = sprint_logx(logev, 1, _pv_format)
print(("Motif {0:s} had a fraction of {1:s}").format(str(k), f_string))
print(("Motif {0:s} had an E-value of {1:s}").format(str(k), g_string))
print 'Saving motif as a png...'
data = LogoData.from_counts(counts=theta_motif,alphabet=unambiguous_dna_alphabet)#,prior=theta_background_matrix[0])#Does prior mess things up?
options = LogoOptions()
options.title = 'Motif'
forma = LogoFormat(data, options)
fout = open(outstr + "Motif_" + str(k) + '.png', 'w')
png_formatter(data, forma, fout)
fout.close()
print 'Saving motif as an eps...'
fout = open(outstr + "Motif_" + str(k) + '.eps', 'w')
eps_formatter(data, forma, fout)
fout.close()
def outputMotif(theta_motif, theta_background_matrix, lambda_motif, logev, k, outstr):
from weblogolib import LogoData, LogoOptions, LogoFormat, png_formatter, eps_formatter, unambiguous_dna_alphabet
_pv_format = "%3.1fe%+04.0f"
f_string = sprint_logx(log(lambda_motif), 1, _pv_format)
g_string = sprint_logx(logev, 1, _pv_format)
print(("Motif {0:s} had a fraction of {1:s}").format(str(k), f_string))
print(("Motif {0:s} had an E-value of {1:s}").format(str(k), g_string))
print 'Saving motif as a png...'
data = LogoData.from_counts(counts=theta_motif,alphabet=unambiguous_dna_alphabet)#,prior=theta_background_matrix[0])#Does prior mess things up?
options = LogoOptions()
options.title = 'Motif'
forma = LogoFormat(data, options)
fout = open(outstr + "Motif_" + str(k) + '.png', 'w')
png_formatter(data, forma, fout)
fout.close()
print 'Saving motif as an eps...'
fout = open(outstr + "Motif_" + str(k) + '.eps', 'w')
eps_formatter(data, forma, fout)
fout.close()
def createSeqLogo(pfm, filename, fformat='eps'):
"""Create sequence logo for an individual cRBM motif.
Parameters
-----------
pfm : numpy-array
2D numpy array representing a PFM. See :meth:`CRBM.getPFMs`
path : str
Output folder.
fformat : str
File format for storing the sequence logos. Default: 'eps'.
"""
alph = Alphabet('ACGT')
weblogoData = LogoData.from_counts(
alph, pfm.T) #, c)#, learner.c.get_value().reshape(-1))
weblogoOptions = LogoOptions(color_scheme=classic)
weblogoFormat = LogoFormat(weblogoData, weblogoOptions)
content = formatters[fformat](weblogoData, weblogoFormat)
f = open(filename, "wb")
f.write(content)
f.close()
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_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)
args["color_scheme"] = color_scheme
if opts.annotate:
args["annotate"] = opts.annotate.split(',')
logooptions = LogoOptions()
for a, v in args.iteritems():
setattr(logooptions, a, v)
theformat = LogoFormat(logodata, logooptions)
return theformat
