def _build_logodata(options):
motif_flag = False
fin = options.fin
if options.upload is None:
if fin is None:
fin = StringIO(sys.stdin.read())
else:
if fin is None:
from . import _from_URL_fileopen
fin = _from_URL_fileopen(options.upload)
else:
raise ValueError(
"error: options --fin and --upload are incompatible")
try:
# Try reading data in transfac format first.
from corebio.matrix import Motif
motif = Motif.read_transfac(fin, alphabet=options.alphabet)
motif_flag = True
except ValueError as motif_err:
# Failed reading Motif, try reading as multiple sequence data.
if options.input_parser == "transfac":
raise motif_err # Adding transfac as str insted of parser is a bit of a ugly kludge
seqs = read_seq_data(fin,
options.input_parser.read,
alphabet=options.alphabet,
ignore_lower_case=options.ignore_lower_case)
if motif_flag:
if options.ignore_lower_case:
raise ValueError(
"error: option --ignore-lower-case incompatible with matrix input"
)
if options.reverse or options.revcomp:
motif.reverse()
if options.complement or options.revcomp:
motif.complement()
prior = parse_prior(options.composition, motif.alphabet,
options.weight)
data = LogoData.from_counts(motif.alphabet, motif, prior)
else:
if options.reverse or options.revcomp:
seqs = SeqList([s.reverse() for s in seqs], seqs.alphabet)
if options.complement or options.revcomp:
if not nucleic_alphabet.alphabetic(seqs.alphabet):
raise ValueError('non-nucleic sequence cannot be complemented')
aaa = seqs.alphabet
seqs.alphabet = nucleic_alphabet
seqs = SeqList([Seq(s, seqs.alphabet).complement() for s in seqs],
seqs.alphabet)
seqs.alphabet = aaa
prior = parse_prior(options.composition, seqs.alphabet, options.weight)
data = LogoData.from_seqs(seqs, prior)
return data
def profile(self, alphabet=None):
"""Counts the occurrences of characters in each column.
Returns: Motif(counts, alphabet)
"""
if not alphabet: alphabet = self.alphabet
if not alphabet: raise ValueError("No alphabet")
N = len(alphabet)
ords = self.ords(alphabet)
L = len(ords[0])
counts = [[
0,
] * N for l in range(0, L)]
for o in ords:
if len(o) != L:
raise ValueError(
"Sequences are of incommensurate lengths. Cannot tally.")
for j, n in enumerate(o):
if n < N: counts[j][n] += 1
from corebio.matrix import Motif
return Motif(alphabet, counts)
def _build_logodata(options):
motif_flag = False
fin = options.fin
if options.upload is None:
if fin is None:
fin = StringIO(sys.stdin.read())
else:
if fin is None:
from . import _from_URL_fileopen
fin = _from_URL_fileopen(options.upload)
else:
raise ValueError("error: options --fin and --upload are incompatible")
try:
# Try reading data in transfac format first.
from corebio.matrix import Motif
motif = Motif.read_transfac(fin, alphabet=options.alphabet)
motif_flag = True
except ValueError as motif_err:
# Failed reading Motif, try reading as multiple sequence data.
if options.input_parser == "transfac":
raise motif_err # Adding transfac as str insted of parser is a bit of a ugly kludge
seqs = read_seq_data(fin,
options.input_parser.read,
alphabet=options.alphabet,
ignore_lower_case=options.ignore_lower_case)
if motif_flag:
if options.ignore_lower_case:
raise ValueError("error: option --ignore-lower-case incompatible with matrix input")
if options.reverse or options.revcomp:
motif.reverse()
if options.complement or options.revcomp:
motif.complement()
prior = parse_prior(options.composition, motif.alphabet, options.weight)
data = LogoData.from_counts(motif.alphabet, motif, prior)
else:
if options.reverse or options.revcomp:
seqs = SeqList([s.reverse() for s in seqs], seqs.alphabet)
if options.complement or options.revcomp:
if not nucleic_alphabet.alphabetic(seqs.alphabet):
raise ValueError('non-nucleic sequence cannot be complemented')
aaa = seqs.alphabet
seqs.alphabet = nucleic_alphabet
seqs = SeqList([Seq(s, seqs.alphabet).complement() for s in seqs], seqs.alphabet)
seqs.alphabet = aaa
prior = parse_prior(options.composition, seqs.alphabet, options.weight)
data = LogoData.from_seqs(seqs, prior)
return data
def _build_logodata_core(fin, fin_compos, fin_weight, options, second_data=None):
motif_flag = False
isCodon = False
try:
# Try reading data in transfac format first.
from corebio.matrix import Motif
motif = Motif.read_transfac(fin, alphabet=options.alphabet)
motif_flag = True
except ValueError, motif_err:
# Failed reading Motif, try reading as multiple sequence data.
if options.alphabet is True:
isCodon = True
options.alphabet = None
seqs = read_seq_data(
fin, options.input_parser.read, alphabet=options.alphabet, ignore_lower_case=options.ignore_lower_case
)
def _build_logodata(options):
motif_flag = False
fin = options.fin
if fin is None:
from StringIO import StringIO
fin = StringIO(sys.stdin.read())
try:
# Try reading data in transfac format first.
from corebio.matrix import Motif
motif = Motif.read_transfac(fin, alphabet=options.alphabet)
motif_flag = True
except ValueError, motif_err:
# Failed reading Motif, try reading as multiple sequence data.
seqs = read_seq_data(fin,
options.input_parser.read,
alphabet=options.alphabet,
ignore_lower_case=options.ignore_lower_case)
def _build_logodata(options):
if options.input_parser != "transfac":
seqs = read_seq_data(options.fin,
options.input_parser.read,
alphabet=options.alphabet,
ignore_lower_case=options.ignore_lower_case)
if options.reverse:
seqs = SeqList([s.reverse() for s in seqs], seqs.alphabet)
if options.complement:
seqs = SeqList([Seq(s, seqs.alphabet).complement() for s in seqs],
seqs.alphabet)
prior = parse_prior(options.composition, seqs.alphabet, options.weight)
data = LogoData.from_seqs(seqs, prior)
else:
from corebio.matrix import Motif
if options.ignore_lower_case:
raise ValueError(
"error: option --ignore-lower-case incompatible with matrix input"
)
#FIXME : implement
if options.reverse:
raise ValueError(
"error: option --reverse incompatible with matrix input")
#FIXME : implement
if options.complement:
raise ValueError(
"error: option --complement incompatible with matrix input")
motif = Motif.read_transfac(options.fin, alphabet=options.alphabet)
prior = parse_prior(options.composition, motif.alphabet,
options.weight)
data = LogoData.from_counts(motif.alphabet, motif, prior)
return data
def _build_logodata(options) :
motif_flag=False
fin = options.fin;
if fin is None :
from StringIO import StringIO
fin = StringIO(sys.stdin.read())
try:
# Try reading data in transfac format first.
from corebio.matrix import Motif
motif = Motif.read_transfac(fin, alphabet=options.alphabet)
motif_flag = True
except ValueError, motif_err :
# Failed reading Motif, try reading as multiple sequence data.
seqs = read_seq_data(fin,
options.input_parser.read,
alphabet=options.alphabet,
ignore_lower_case = options.ignore_lower_case)
def main(htdocs_directory=None):
logooptions = weblogolib.LogoOptions()
# A list of form fields.
# The default for checkbox values must be False (irrespective of
# the default in logooptions) since a checked checkbox returns 'true'
# but an unchecked checkbox returns nothing.
controls = [
Field('sequences', ''),
Field(
'format',
'png',
weblogolib.formatters.get,
options=[
'png_print', 'png', 'jpeg', 'eps', 'pdf', 'svg', 'logodata'
], #TODO: Should copy list from __init__.formatters
errmsg="Unknown format option."),
Field('stacks_per_line',
logooptions.stacks_per_line,
int,
errmsg='Invalid number of stacks per line.'),
Field('stack_width',
'medium',
weblogolib.std_sizes.get,
options=['small', 'medium', 'large'],
errmsg='Invalid logo size.'),
Field('alphabet',
'alphabet_auto',
alphabets.get,
options=[
'alphabet_auto', 'alphabet_protein', 'alphabet_dna',
'alphabet_rna'
],
errmsg="Unknown sequence type."),
Field('unit_name',
'bits',
options=[
'probability', 'bits', 'nats', 'kT', 'kJ/mol', 'kcal/mol'
]),
Field('first_index', 1, int_or_none),
Field('logo_start', '', int_or_none),
Field('logo_end', '', int_or_none),
Field('composition',
'comp_auto',
composition.get,
options=[
'comp_none', 'comp_auto', 'comp_equiprobable', 'comp_CG',
'comp_Celegans', 'comp_Dmelanogaster', 'comp_Ecoli',
'comp_Hsapiens', 'comp_Mmusculus', 'comp_Scerevisiae'
],
errmsg="Illegal sequence composition."),
Field('percentCG', '', float_or_none, errmsg="Invalid CG percentage."),
Field('show_errorbars', False, truth),
Field('logo_title', logooptions.logo_title),
Field('logo_label', logooptions.logo_label),
Field('show_xaxis', False, truth),
Field('xaxis_label', logooptions.xaxis_label),
Field('show_yaxis', False, truth),
Field('yaxis_label', logooptions.yaxis_label, string_or_none),
Field('yaxis_scale',
logooptions.yaxis_scale,
float_or_none,
errmsg="The yaxis scale must be a positive number."),
Field('yaxis_tic_interval', logooptions.yaxis_tic_interval,
float_or_none),
Field('show_ends', False, truth),
Field('show_fineprint', False, truth),
Field('color_scheme',
'color_auto',
color_schemes.get,
options=color_schemes.keys(),
errmsg='Unknown color scheme'),
Field('color0', ''),
Field('symbols0', ''),
Field('desc0', ''),
Field('color1', ''),
Field('symbols1', ''),
Field('desc1', ''),
Field('color2', ''),
Field('symbols2', ''),
Field('desc2', ''),
Field('color3', ''),
Field('symbols3', ''),
Field('desc3', ''),
Field('color4', ''),
Field('symbols4', ''),
Field('desc4', ''),
Field('ignore_lower_case', False, truth),
Field('scale_width', False, truth),
]
form = {}
for c in controls:
form[c.name] = c
form_values = cgilib.FieldStorage()
# Send default form?
if len(form_values) == 0 or "cmd_reset" in form_values:
# Load default truth values now.
form['show_errorbars'].value = logooptions.show_errorbars
form['show_xaxis'].value = logooptions.show_xaxis
form['show_yaxis'].value = logooptions.show_yaxis
form['show_ends'].value = logooptions.show_ends
form['show_fineprint'].value = logooptions.show_fineprint
form['scale_width'].value = logooptions.scale_width
send_form(controls, htdocs_directory=htdocs_directory)
return
# Get form content
for c in controls:
c.value = form_values.getfirst(c.name, c.default)
options_from_form = [
'format', 'stacks_per_line', 'stack_width', 'alphabet', 'unit_name',
'first_index', 'logo_start', 'logo_end', 'composition',
'show_errorbars', 'logo_title', 'logo_label', 'show_xaxis',
'xaxis_label', 'show_yaxis', 'yaxis_label', 'yaxis_scale',
'yaxis_tic_interval', 'show_ends', 'show_fineprint', 'scale_width'
]
errors = []
for optname in options_from_form:
try:
value = form[optname].get_value()
if value != None: setattr(logooptions, optname, value)
except ValueError as err:
errors.append(err.args)
# Construct custom color scheme
custom = ColorScheme()
for i in range(0, 5):
color = form["color%d" % i].get_value()
symbols = form["symbols%d" % i].get_value()
desc = form["desc%d" % i].get_value()
if color:
try:
custom.groups.append(
weblogolib.ColorGroup(symbols, color, desc))
except ValueError as e:
errors.append(('color%d' % i, "Invalid color: %s" % color))
if form["color_scheme"].value == 'color_custom':
logooptions.color_scheme = custom
else:
try:
logooptions.color_scheme = form["color_scheme"].get_value()
except ValueError as err:
errors.append(err.args)
sequences = None
# FIXME: Ugly fix: Must check that sequence_file key exists
# FIXME: Sending malformed or missing form keys should not cause a crash
# sequences_file = form["sequences_file"]
if "sequences_file" in form_values:
sequences = form_values.getvalue("sequences_file")
#assert type(sequences) == str
if not sequences or len(sequences) == 0:
sequences = form["sequences"].get_value()
if not sequences or len(sequences) == 0:
errors.append((
"sequences",
"Please enter a multiple-sequence alignment in the box above, or select a file to upload."
))
# If we have uncovered errors or we want the chance to edit the logo
# ("cmd_edit" command from examples page) then we return the form now.
# We do not proceed to the time consuming logo creation step unless
# required by a 'create' or 'validate' command, and no errors have been
# found yet.
if errors or "cmd_edit" in form_values:
send_form(controls, errors, htdocs_directory)
return
try:
comp = form["composition"].get_value()
percentCG = form["percentCG"].get_value()
ignore_lower_case = ("ignore_lower_case" in form_values)
if comp == 'percentCG':
comp = str(percentCG / 100)
from corebio.matrix import Motif
try:
# Try reading data in transfac format first.
# TODO Refactor this code
motif = Motif.read_transfac(StringIO(sequences),
alphabet=logooptions.alphabet)
prior = weblogolib.parse_prior(comp, motif.alphabet)
data = weblogolib.LogoData.from_counts(motif.alphabet, motif,
prior)
except ValueError as motif_err:
seqs = weblogolib.read_seq_data(
StringIO(sequences),
alphabet=logooptions.alphabet,
ignore_lower_case=ignore_lower_case)
prior = weblogolib.parse_prior(comp, seqs.alphabet)
data = weblogolib.LogoData.from_seqs(seqs, prior)
logoformat = weblogolib.LogoFormat(data, logooptions)
format = form["format"].value
logo = weblogolib.formatters[format](data, logoformat)
except ValueError as err:
errors.append(err.args)
except IOError as err:
errors.append(err.args)
except RuntimeError as err:
errors.append(err.args)
if errors or "cmd_validate" in form_values:
send_form(controls, errors, htdocs_directory)
return
#
# RETURN LOGO OVER HTTP
#
print("Content-Type:", mime_type[format])
# Content-Disposition: inline Open logo in browser window
# Content-Disposition: attachment Download logo
if "download" in form_values:
print('Content-Disposition: attachment; ' \
'filename="logo.%s"' % extension[format])
else:
print('Content-Disposition: inline; ' \
'filename="logo.%s"' % extension[format])
# Separate header from data
print()
# Finally, and at last, send the logo.
if sys.version_info[0] >= 3:
sys.stdout.buffer.write(logo)
else:
sys.stdout.write(logo)
# We write the logo into a local buffer so that we can catch and
# handle any errors. Once the "Content-Type:" header has been sent
# we can't send any useful feedback
logo = StringIO()
try:
comp = form["composition"].get_value()
percentCG = form["percentCG"].get_value()
ignore_lower_case = form_values.has_key("ignore_lower_case")
if comp == 'percentCG': comp = str(percentCG / 100)
from corebio.matrix import Motif
try:
# Try reading data in transfac format first.
# TODO Refactor this code
motif = Motif.read_transfac(StringIO(sequences),
alphabet=logooptions.alphabet)
prior = weblogolib.parse_prior(comp, motif.alphabet)
data = weblogolib.LogoData.from_counts(motif.alphabet, motif,
prior)
except ValueError, motif_err:
seqs = weblogolib.read_seq_data(
StringIO(sequences),
alphabet=logooptions.alphabet,
ignore_lower_case=ignore_lower_case)
prior = weblogolib.parse_prior(comp, seqs.alphabet)
data = weblogolib.LogoData.from_seqs(seqs, prior)
logoformat = weblogolib.LogoFormat(data, logooptions)
format = form["format"].value
weblogolib.formatters[format](data, logoformat, logo)
except ValueError, err:
def main(htdocs_directory=None):
logooptions = weblogolib.LogoOptions()
# A list of form fields.
# The default for checkbox values must be False (irrespective of
# the default in logooptions) since a checked checkbox returns 'true'
# but an unchecked checkbox returns nothing.
controls = [
Field("sequences", ""),
Field(
"format",
"png",
weblogolib.formatters.get,
options=[
"png_print",
"png",
"jpeg",
"eps",
"pdf",
"svg",
"logodata",
], # TODO: Should copy list from __init__.formatters
errmsg="Unknown format option.",
),
Field("stacks_per_line", logooptions.stacks_per_line, int, errmsg="Invalid number of stacks per line."),
Field(
"stack_width",
"medium",
weblogolib.std_sizes.get,
options=["small", "medium", "large"],
errmsg="Invalid logo size.",
),
Field(
"alphabet",
"alphabet_auto",
alphabets.get,
options=["alphabet_auto", "alphabet_protein", "alphabet_dna", "alphabet_rna"],
errmsg="Unknown sequence type.",
),
Field("unit_name", "bits", options=["probability", "bits", "nats", "kT", "kJ/mol", "kcal/mol"]),
Field("first_index", 1, int_or_none),
Field("logo_start", "", int_or_none),
Field("logo_end", "", int_or_none),
Field(
"composition",
"comp_auto",
composition.get,
options=[
"comp_none",
"comp_auto",
"comp_equiprobable",
"comp_CG",
"comp_Celegans",
"comp_Dmelanogaster",
"comp_Ecoli",
"comp_Hsapiens",
"comp_Mmusculus",
"comp_Scerevisiae",
],
errmsg="Illegal sequence composition.",
),
Field("percentCG", "", float_or_none, errmsg="Invalid CG percentage."),
Field("show_errorbars", False, truth),
Field("logo_title", logooptions.logo_title),
Field("logo_label", logooptions.logo_label),
Field("show_xaxis", False, truth),
Field("xaxis_label", logooptions.xaxis_label),
Field("show_yaxis", False, truth),
Field("yaxis_label", logooptions.yaxis_label, string_or_none),
Field(
"yaxis_scale", logooptions.yaxis_scale, float_or_none, errmsg="The yaxis scale must be a positive number."
),
Field("yaxis_tic_interval", logooptions.yaxis_tic_interval, float_or_none),
Field("show_ends", False, truth),
Field("show_fineprint", False, truth),
Field(
"color_scheme", "color_auto", color_schemes.get, options=color_schemes.keys(), errmsg="Unknown color scheme"
),
Field("color0", ""),
Field("symbols0", ""),
Field("desc0", ""),
Field("color1", ""),
Field("symbols1", ""),
Field("desc1", ""),
Field("color2", ""),
Field("symbols2", ""),
Field("desc2", ""),
Field("color3", ""),
Field("symbols3", ""),
Field("desc3", ""),
Field("color4", ""),
Field("symbols4", ""),
Field("desc4", ""),
Field("ignore_lower_case", False, truth),
Field("scale_width", False, truth),
]
form = {}
for c in controls:
form[c.name] = c
form_values = cgilib.FieldStorage()
# Send default form?
if len(form_values) == 0 or "cmd_reset" in form_values:
# Load default truth values now.
form["show_errorbars"].value = logooptions.show_errorbars
form["show_xaxis"].value = logooptions.show_xaxis
form["show_yaxis"].value = logooptions.show_yaxis
form["show_ends"].value = logooptions.show_ends
form["show_fineprint"].value = logooptions.show_fineprint
form["scale_width"].value = logooptions.scale_width
send_form(controls, htdocs_directory=htdocs_directory)
return
# Get form content
for c in controls:
c.value = form_values.getfirst(c.name, c.default)
options_from_form = [
"format",
"stacks_per_line",
"stack_width",
"alphabet",
"unit_name",
"first_index",
"logo_start",
"logo_end",
"composition",
"show_errorbars",
"logo_title",
"logo_label",
"show_xaxis",
"xaxis_label",
"show_yaxis",
"yaxis_label",
"yaxis_scale",
"yaxis_tic_interval",
"show_ends",
"show_fineprint",
"scale_width",
]
errors = []
for optname in options_from_form:
try:
value = form[optname].get_value()
if value != None:
setattr(logooptions, optname, value)
except ValueError as err:
errors.append(err.args)
# Construct custom color scheme
custom = ColorScheme()
for i in range(0, 5):
color = form["color%d" % i].get_value()
symbols = form["symbols%d" % i].get_value()
desc = form["desc%d" % i].get_value()
if color:
try:
custom.groups.append(weblogolib.ColorGroup(symbols, color, desc))
except ValueError as e:
errors.append(("color%d" % i, "Invalid color: %s" % color))
if form["color_scheme"].value == "color_custom":
logooptions.color_scheme = custom
else:
try:
logooptions.color_scheme = form["color_scheme"].get_value()
except ValueError as err:
errors.append(err.args)
sequences = None
# FIXME: Ugly fix: Must check that sequence_file key exists
# FIXME: Sending malformed or missing form keys should not cause a crash
# sequences_file = form["sequences_file"]
if "sequences_file" in form_values:
sequences = form_values.getvalue("sequences_file")
# assert type(sequences) == str
if not sequences or len(sequences) == 0:
sequences = form["sequences"].get_value()
# If a user tries to paste a very large file into sequence textarea,
# then WebLogo runs very slow for no apparently good reason. (Might be client side bug?)
# So we limit the maximum sequence size.
# Form field also limits size, but not necessarly respected. Also can truncate data
# without warning, so we'll set textarea maximum to be larger than MAX_SEQUENCE_SIZE
SEQUENCES_MAXLENGTH = 100000
if len(sequences) > SEQUENCES_MAXLENGTH:
errors.append(("sequences", "Sequence data too large for text input. Use file upload instead."))
controls[0] = Field("sequences", "")
if not sequences or len(sequences) == 0:
errors.append(
("sequences", "Please enter a multiple-sequence alignment in the box above, or select a file to upload.")
)
# If we have uncovered errors or we want the chance to edit the logo
# ("cmd_edit" command from examples page) then we return the form now.
# We do not proceed to the time consuming logo creation step unless
# required by a 'create' or 'validate' command, and no errors have been
# found yet.
if errors or "cmd_edit" in form_values:
send_form(controls, errors, htdocs_directory)
return
try:
comp = form["composition"].get_value()
percentCG = form["percentCG"].get_value()
ignore_lower_case = "ignore_lower_case" in form_values
if comp == "percentCG":
comp = str(percentCG / 100)
from corebio.matrix import Motif
try:
# Try reading data in transfac format first.
# TODO Refactor this code
motif = Motif.read_transfac(StringIO(sequences), alphabet=logooptions.alphabet)
prior = weblogolib.parse_prior(comp, motif.alphabet)
data = weblogolib.LogoData.from_counts(motif.alphabet, motif, prior)
except ValueError as motif_err:
seqs = weblogolib.read_seq_data(
StringIO(sequences), alphabet=logooptions.alphabet, ignore_lower_case=ignore_lower_case
)
prior = weblogolib.parse_prior(comp, seqs.alphabet)
data = weblogolib.LogoData.from_seqs(seqs, prior)
logoformat = weblogolib.LogoFormat(data, logooptions)
format = form["format"].value
logo = weblogolib.formatters[format](data, logoformat)
except ValueError as err:
errors.append(err.args)
except IOError as err:
errors.append(err.args)
except RuntimeError as err:
errors.append(err.args)
if errors or "cmd_validate" in form_values:
send_form(controls, errors, htdocs_directory)
return
#
# RETURN LOGO OVER HTTP
#
print("Content-Type:", mime_type[format])
# Content-Disposition: inline Open logo in browser window
# Content-Disposition: attachment Download logo
if "download" in form_values:
print("Content-Disposition: attachment; " 'filename="logo.%s"' % extension[format])
else:
print("Content-Disposition: inline; " 'filename="logo.%s"' % extension[format])
# Separate header from data
print()
# Finally, and at last, send the logo.
if sys.version_info[0] >= 3:
sys.stdout.buffer.write(logo)
else:
sys.stdout.write(logo)
# We write the logo into a local buffer so that we can catch and
# handle any errors. Once the "Content-Type:" header has been sent
# we can't send any useful feedback
logo = StringIO()
try :
comp = form["composition"].get_value()
percentCG = form["percentCG"].get_value()
ignore_lower_case = form_values.has_key("ignore_lower_case")
if comp=='percentCG': comp = str(percentCG/100)
from corebio.matrix import Motif
try:
# Try reading data in transfac format first.
# TODO Refactor this code
motif = Motif.read_transfac(StringIO( sequences), alphabet=logooptions.alphabet)
prior = weblogolib.parse_prior( comp,motif.alphabet)
data = weblogolib.LogoData.from_counts(motif.alphabet, motif, prior)
except ValueError, motif_err :
seqs = weblogolib.read_seq_data(StringIO( sequences),
alphabet=logooptions.alphabet,
ignore_lower_case=ignore_lower_case
)
prior = weblogolib.parse_prior(comp, seqs.alphabet)
data = weblogolib.LogoData.from_seqs(seqs, prior)
logoformat = weblogolib.LogoFormat(data, logooptions)
format = form["format"].value
weblogolib.formatters[format](data, logoformat, logo)
except ValueError, err :
errors.append( err.args )
def main(htdocs_directory = None) :
logooptions = weblogolib.LogoOptions()
# A list of form fields.
# The default for checkbox values must be False (irrespective of
# the default in logooptions) since a checked checkbox returns 'true'
# but an unchecked checkbox returns nothing.
controls = [
Field( 'sequences', ''),
Field( 'format', 'png', weblogolib.formatters.get ,
options=['png_print', 'png', 'jpeg', 'eps', 'pdf', 'svg', 'logodata'] , #TODO: Should copy list from __init__.formatters
errmsg="Unknown format option."),
Field( 'stacks_per_line', logooptions.stacks_per_line , int,
errmsg='Invalid number of stacks per line.'),
Field( 'stack_width','medium', weblogolib.std_sizes.get,
options=['small', 'medium', 'large'], errmsg='Invalid logo size.'),
Field( 'alphabet','alphabet_auto', alphabets.get,
options=['alphabet_auto', 'alphabet_protein', 'alphabet_dna',
'alphabet_rna'],
errmsg="Unknown sequence type."),
Field( 'unit_name', 'bits',
options=[ 'probability', 'bits', 'nats', 'kT', 'kJ/mol',
'kcal/mol']),
Field( 'first_index', 1, int_or_none),
Field( 'logo_start', '', int_or_none),
Field( 'logo_end', '', int_or_none),
Field( 'composition', 'comp_auto', composition.get,
options=['comp_none','comp_auto','comp_equiprobable','comp_CG',
'comp_Celegans','comp_Dmelanogaster','comp_Ecoli',
'comp_Hsapiens','comp_Mmusculus','comp_Scerevisiae'],
errmsg= "Illegal sequence composition."),
Field( 'percentCG', '', float_or_none, errmsg="Invalid CG percentage."),
Field( 'show_errorbars', False , truth),
Field( 'logo_title', logooptions.logo_title ),
Field( 'logo_label', logooptions.logo_label ),
Field( 'show_xaxis', False, truth),
Field( 'xaxis_label', logooptions.xaxis_label ),
Field( 'show_yaxis', False, truth),
Field( 'yaxis_label', logooptions.yaxis_label, string_or_none ),
Field( 'yaxis_scale', logooptions.yaxis_scale , float_or_none,
errmsg="The yaxis scale must be a positive number." ),
Field( 'yaxis_tic_interval', logooptions.yaxis_tic_interval ,
float_or_none),
Field( 'show_ends', False, truth),
Field( 'show_fineprint', False , truth),
Field( 'color_scheme', 'color_auto', color_schemes.get,
options=color_schemes.keys() ,
errmsg = 'Unknown color scheme'),
Field( 'color0', ''),
Field( 'symbols0', ''),
Field( 'desc0', ''),
Field( 'color1', ''),
Field( 'symbols1', ''),
Field( 'desc1', ''),
Field( 'color2', ''),
Field( 'symbols2', ''),
Field( 'desc2', ''),
Field( 'color3', ''),
Field( 'symbols3', ''),
Field( 'desc3', ''),
Field( 'color4', ''),
Field( 'symbols4', ''),
Field( 'desc4', ''),
Field( 'ignore_lower_case', False, truth),
Field( 'scale_width', False, truth),
]
form = {}
for c in controls :
form[c.name] = c
form_values = cgilib.FieldStorage()
# Send default form?
if len(form_values) == 0 or "cmd_reset" in form_values:
# Load default truth values now.
form['show_errorbars'].value = logooptions.show_errorbars
form['show_xaxis'].value = logooptions.show_xaxis
form['show_yaxis'].value = logooptions.show_yaxis
form['show_ends'].value = logooptions.show_ends
form['show_fineprint'].value = logooptions.show_fineprint
form['scale_width'].value = logooptions.scale_width
send_form(controls, htdocs_directory = htdocs_directory)
return
# Get form content
for c in controls :
c.value = form_values.getfirst( c.name, c.default)
options_from_form = ['format', 'stacks_per_line', 'stack_width',
'alphabet', 'unit_name', 'first_index', 'logo_start','logo_end',
'composition',
'show_errorbars', 'logo_title', 'logo_label', 'show_xaxis',
'xaxis_label',
'show_yaxis', 'yaxis_label', 'yaxis_scale', 'yaxis_tic_interval',
'show_ends', 'show_fineprint', 'scale_width']
errors = []
for optname in options_from_form :
try :
value = form[optname].get_value()
if value!=None : setattr(logooptions, optname, value)
except ValueError as err :
errors.append(err.args)
# Construct custom color scheme
custom = ColorScheme()
for i in range(0,5) :
color = form["color%d"%i].get_value()
symbols = form["symbols%d"%i].get_value()
desc = form["desc%d"%i].get_value()
if color :
try :
custom.groups.append(weblogolib.ColorGroup(symbols, color, desc))
except ValueError as e:
errors.append( ('color%d'%i, "Invalid color: %s" % color) )
if form["color_scheme"].value == 'color_custom' :
logooptions.color_scheme = custom
else :
try :
logooptions.color_scheme = form["color_scheme"].get_value()
except ValueError as err:
errors.append(err.args)
sequences = None
# FIXME: Ugly fix: Must check that sequence_file key exists
# FIXME: Sending malformed or missing form keys should not cause a crash
# sequences_file = form["sequences_file"]
if "sequences_file" in form_values:
sequences = form_values.getvalue("sequences_file")
#assert type(sequences) == str
if not sequences or len(sequences) ==0:
sequences = form["sequences"].get_value()
if not sequences or len(sequences) ==0:
errors.append( ("sequences", "Please enter a multiple-sequence alignment in the box above, or select a file to upload."))
# If we have uncovered errors or we want the chance to edit the logo
# ("cmd_edit" command from examples page) then we return the form now.
# We do not proceed to the time consuming logo creation step unless
# required by a 'create' or 'validate' command, and no errors have been
# found yet.
if errors or "cmd_edit" in form_values:
send_form(controls, errors, htdocs_directory)
return
try :
comp = form["composition"].get_value()
percentCG = form["percentCG"].get_value()
ignore_lower_case = ("ignore_lower_case" in form_values)
if comp == 'percentCG':
comp = str(percentCG / 100)
from corebio.matrix import Motif
try:
# Try reading data in transfac format first.
# TODO Refactor this code
motif = Motif.read_transfac(StringIO( sequences), alphabet=logooptions.alphabet)
prior = weblogolib.parse_prior( comp,motif.alphabet)
data = weblogolib.LogoData.from_counts(motif.alphabet, motif, prior)
except ValueError as motif_err:
seqs = weblogolib.read_seq_data(StringIO( sequences),
alphabet=logooptions.alphabet,
ignore_lower_case=ignore_lower_case
)
prior = weblogolib.parse_prior(comp, seqs.alphabet)
data = weblogolib.LogoData.from_seqs(seqs, prior)
logoformat = weblogolib.LogoFormat(data, logooptions)
format = form["format"].value
logo = weblogolib.formatters[format](data, logoformat)
except ValueError as err:
errors.append(err.args)
except IOError as err:
errors.append(err.args)
except RuntimeError as err:
errors.append(err.args)
if errors or "cmd_validate" in form_values:
send_form(controls, errors, htdocs_directory)
return
#
# RETURN LOGO OVER HTTP
#
print("Content-Type:", mime_type[format])
# Content-Disposition: inline Open logo in browser window
# Content-Disposition: attachment Download logo
if "download" in form_values:
print('Content-Disposition: attachment; ' \
'filename="logo.%s"' % extension[format])
else:
print('Content-Disposition: inline; ' \
'filename="logo.%s"' % extension[format])
# Separate header from data
print()
# Finally, and at last, send the logo.
if sys.version_info[0] >= 3:
sys.stdout.buffer.write(logo)
else:
sys.stdout.write(logo)
send_form(controls, errors, htdocs_directory)
return
try:
comp = form["composition"].get_value()
percentCG = form["percentCG"].get_value()
ignore_lower_case = ("ignore_lower_case" in form_values)
if comp == 'percentCG':
comp = str(percentCG / 100)
from corebio.matrix import Motif
try:
# Try reading data in transfac format first.
# TODO Refactor this code
motif = Motif.read_transfac(seq_file,
alphabet=logooptions.alphabet)
prior = weblogolib.parse_prior(comp, motif.alphabet)
data = weblogolib.LogoData.from_counts(motif.alphabet, motif,
prior)
except ValueError as motif_err:
seqs = weblogolib.read_seq_data(
seq_file,
alphabet=logooptions.alphabet,
ignore_lower_case=ignore_lower_case)
prior = weblogolib.parse_prior(comp, seqs.alphabet)
data = weblogolib.LogoData.from_seqs(seqs, prior)
logoformat = weblogolib.LogoFormat(data, logooptions)
format = form["format"].value
logo = weblogolib.formatters[format](data, logoformat)
except ValueError as err:
