def weblogo_from_dist(dist, filename='logo.eps'):
"""Generate a weblogo from a pssm distribution"""
import weblogolib
data = weblogo_data_from_dist(dist)
options = weblogolib.LogoOptions()
options.size = weblogolib.LogoSize(stack_width=5.4 * 12,
stack_height=5.4 * 12 * 5)
options.color_scheme = weblogolib.std_color_schemes["classic"]
format = weblogolib.LogoFormat(data, options)
weblogolib.eps_formatter(data, format, open(filename, 'w'))
def create_logo(self, seqs=[]):
"""Create sequence logo for input sequences."""
# seperate headers
headers, instances = [list(x)
for x in zip(*seqs)]
if self.options.sequence_type is 'rna':
alphabet = Alphabet('ACGU')
elif self.options.sequence_type is 'protein':
alphabet = Alphabet('ACDEFGHIKLMNPQRSTVWY')
else:
alphabet = Alphabet('AGCT')
motif_corebio = SeqList(alist=instances, alphabet=alphabet)
data = wbl.LogoData().from_seqs(motif_corebio)
format = wbl.LogoFormat(data, self.options)
if self.output_format == 'png':
return wbl.png_formatter(data, format)
elif self.output_format == 'png_print':
return wbl.png_print_formatter(data, format)
elif self.output_format == 'jpeg':
return wbl.jpeg_formatter(data, format)
else:
return wbl.eps_formatter(data, format)
def generate_logo(seqfile, title):
'''
Generate the sequence logo from the specified sequences.
Args:
seqfile (str): The path to a sequence file.
'''
with open(seqfile, 'r') as fh:
seqlen = len(fh.readline().rstrip('\n'))
fh.seek(0)
seqs = wl.read_seq_data(fh)
data = wl.LogoData.from_seqs(seqs)
options = wl.LogoOptions()
options.title = title
options.fineprint = ''
#options.stack_width = 16
options.first_index = -1 * int(seqlen / 2)
form = wl.LogoFormat(data, options)
eps = wl.eps_formatter(data, form)
eps_file = seqfile[:-4] + '.eps'
with open(eps_file, 'wb') as fh:
fh.write(eps)
def create_logo(self, seqs=[]):
"""Create sequence logo for input sequences."""
# seperate headers
headers, instances = [list(x)
for x in zip(*seqs)]
if self.options.sequence_type is 'rna':
alphabet = Alphabet('ACGU')
elif self.options.sequence_type is 'protein':
alphabet = Alphabet('ACDEFGHIKLMNPQRSTVWY')
else:
alphabet = Alphabet('AGCT')
motif_corebio = SeqList(alist=instances, alphabet=alphabet)
data = wbl.LogoData().from_seqs(motif_corebio)
format = wbl.LogoFormat(data, self.options)
if self.output_format == 'png':
return wbl.png_formatter(data, format)
elif self.output_format == 'png_print':
return wbl.png_print_formatter(data, format)
elif self.output_format == 'jpeg':
return wbl.jpeg_formatter(data, format)
else:
return wbl.eps_formatter(data, format)
def weblogo_from_dist( dist, filename = 'logo.eps' ):
"""Generate a weblogo from a pssm distribution"""
import weblogolib
data = weblogo_data_from_dist( dist )
options = weblogolib.LogoOptions()
options.size = weblogolib.LogoSize(
stack_width = 5.4*12,
stack_height = 5.4*12*5
)
options.color_scheme = weblogolib.std_color_schemes[ "classic" ]
#format = weblogolib.LogoFormat( data, options )
weblogolib.eps_formatter(
data,
#format,
open( filename, 'w' )
)
def make_pdf_weblogo(
self,
pdf_path,
prior=None
): # prior could also be = weblogolib.parse_prior('equiprobable', corebio.seq.unambiguous_protein_alphabet) )
assert (pdf_path.endswith('.pdf'))
assert (self.design_positions != None)
assert (self.starting_seq != None)
pdf_basedir = os.path.dirname(pdf_path)
if not os.path.isdir(pdf_basedir):
os.makedirs(pdf_basedir)
eps_logo_filename = pdf_path[:-4] + '.eps'
data = weblogolib.LogoData.from_seqs(self.raw_seqs, prior=prior)
options = weblogolib.LogoOptions()
options.show_fineprint = False
options.xaxis_tic_interval = 1
options.number_interval = 1
options.number_fontsize = 3
options.stacks_per_line = 40
options.show_errorbars = False
logo_format = weblogolib.LogoFormat(data, options)
eps_binary = weblogolib.eps_formatter(data, logo_format)
eps_str = eps_binary.decode()
eps_str = replace_logo_numbers(eps_str, self.design_positions,
self.starting_seq)
with open(eps_logo_filename, 'w') as f:
f.write(eps_str)
eps_to_pdf(eps_logo_filename)
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 generate_weblogo(seq_id, seq_strs):
seqs = weblogolib.read_seq_data(io.StringIO('\n'.join(seq_strs)),
input_parser=array_io.read)
data = weblogolib.LogoData.from_seqs(seqs)
options = weblogolib.LogoOptions()
options.title = seq_id
options.unit_name = "probability"
format = weblogolib.LogoFormat(data, options)
eps = weblogolib.eps_formatter(data, format)
with open(os.path.join(WEBLOGO_PATH, seq_id + '.eps'), 'wb') as f:
f.write(eps)
def logo(dist, tag, make_png=False, make_eps=True, write_title=True):
"Generate a logo with the given tag in the given directory."
import weblogolib as W
import corebio.seq
data = W.LogoData.from_counts(corebio.seq.unambiguous_dna_alphabet, dist)
scale = 5.4 * 4
options = W.LogoOptions(
logo_title=write_title and tag or None,
stack_width=scale,
stack_aspect_ratio=5,
color_scheme=W.colorscheme.nucleotide,
show_xaxis=False,
show_yaxis=False,
show_fineprint=False,
)
format_ = W.LogoFormat(data, options)
filename = 'logo-%s' % tag
if make_eps:
W.eps_formatter(data, format_, open('%s.eps' % filename, 'w'))
if make_png:
W.png_formatter(data, format_, open('%s.png' % filename, 'w'))
def generate_weblogo(file_path, seq_strs, unit_name=None):
seqs = weblogolib.read_seq_data(
io.StringIO('\n'.join(seq_strs)),
input_parser=array_io.read,
alphabet=corebio_seq.reduced_protein_alphabet)
data = weblogolib.LogoData.from_seqs(seqs)
options = weblogolib.LogoOptions(color_scheme=get_color_scheme())
if unit_name is not None:
options.unit_name = unit_name
format = weblogolib.LogoFormat(data, options)
eps = weblogolib.eps_formatter(data, format)
with open(file_path, 'wb') as f:
f.write(eps)
def logo(dist, tag, make_png=True, make_eps=False, write_title=True):
"Generate a logo named with the given tag."
import corebio.seq
import weblogolib as W
if tuple(map(int, W.__version__.split('.'))) < (3, 4):
raise ValueError('weblogolib version 3.4 or higher required')
data = W.LogoData.from_counts(corebio.seq.unambiguous_dna_alphabet, dist)
scale = 5.4 * 4
options = W.LogoOptions(
logo_title=write_title and tag or None,
stack_width=scale,
stack_aspect_ratio=5,
color_scheme=W.colorscheme.nucleotide,
show_xaxis=False,
show_yaxis=False,
show_fineprint=False,
)
format_ = W.LogoFormat(data, options)
filename = 'logo-%s' % tag
if make_eps:
open('%s.eps' % filename, 'w').write(W.eps_formatter(data, format_))
if make_png:
open('%s.png' % filename, 'w').write(W.png_formatter(data, format_))