def weblogo(self, fname, format="PNG", **kwds):
"""
uses the Berkeley weblogo service to download and save a weblogo of itself
requires an internet connection.
The parameters from **kwds are passed directly to the weblogo server.
"""
from Bio._py3k import urlopen, urlencode, Request
al = self._to_fasta()
url = 'http://weblogo.berkeley.edu/logo.cgi'
values = {
'sequence': al,
'format': format,
'logowidth': '18',
'logoheight': '5',
'logounits': 'cm',
'kind': 'AUTO',
'firstnum': "1",
'command': 'Create Logo',
'smallsamplecorrection': "on",
'symbolsperline': 32,
'res': '96',
'res_units': 'ppi',
'antialias': 'on',
'title': '',
'barbits': '',
'xaxis': 'on',
'xaxis_label': '',
'yaxis': 'on',
'yaxis_label': '',
'showends': 'on',
'shrink': '0.5',
'fineprint': 'on',
'ticbits': '1',
'colorscheme': 'DEFAULT',
'color1': 'green',
'color2': 'blue',
'color3': 'red',
'color4': 'black',
'color5': 'purple',
'color6': 'orange',
'color1': 'black',
}
for k, v in kwds.items():
values[k] = str(v)
data = urlencode(values)
req = Request(url, data)
response = urlopen(req)
f = open(fname, "w")
im = response.read()
f.write(im)
f.close()
def _open(cgi, params={}, get=1):
"""_open(cgi, params={}, get=1) -> UndoHandle
Open a handle to SCOP. cgi is the URL for the cgi script to access.
params is a dictionary with the options to pass to it. get is a boolean
that describes whether a GET should be used. Does some
simple error checking, and will raise an IOError if it encounters one.
"""
from Bio._py3k import urlopen, urlencode
# Open a handle to SCOP.
options = urlencode(params)
if get: # do a GET
if options:
cgi += "?" + options
handle = urlopen(cgi)
else: # do a POST
handle = urlopen(cgi, data=options)
return handle
def _open(cgi, params={}, get=1):
"""_open(cgi, params={}, get=1) -> UndoHandle
Open a handle to SCOP. cgi is the URL for the cgi script to access.
params is a dictionary with the options to pass to it. get is a boolean
that describes whether a GET should be used. Does some
simple error checking, and will raise an IOError if it encounters one.
"""
from Bio._py3k import urlopen, urlencode
# Open a handle to SCOP.
options = urlencode(params)
if get: # do a GET
if options:
cgi += "?" + options
handle = urlopen(cgi)
else: # do a POST
handle = urlopen(cgi, data=options)
return handle
def weblogo(self,fname,format="PNG",**kwds):
"""
uses the Berkeley weblogo service to download and save a weblogo of itself
requires an internet connection.
The parameters from **kwds are passed directly to the weblogo server.
"""
from Bio._py3k import urlopen, urlencode, Request
al= self._to_fasta()
url = 'http://weblogo.berkeley.edu/logo.cgi'
values = {'sequence': al,
'format': format,
'logowidth': '18',
'logoheight': '5',
'logounits': 'cm',
'kind': 'AUTO',
'firstnum': "1",
'command': 'Create Logo',
'smallsamplecorrection': "on",
'symbolsperline': 32,
'res': '96',
'res_units': 'ppi',
'antialias': 'on',
'title': '',
'barbits': '',
'xaxis': 'on',
'xaxis_label': '',
'yaxis': 'on',
'yaxis_label': '',
'showends': 'on',
'shrink': '0.5',
'fineprint': 'on',
'ticbits': '1',
'colorscheme': 'DEFAULT',
'color1': 'green',
'color2': 'blue',
'color3': 'red',
'color4': 'black',
'color5': 'purple',
'color6': 'orange',
'color1': 'black',
}
for k, v in kwds.items():
values[k]=str(v)
data = urlencode(values)
req = Request(url, data)
response = urlopen(req)
f=open(fname,"w")
im=response.read()
f.write(im)
f.close()
def _open(cgi, params=None, get=1):
"""Open a handle to SCOP and return it (PRIVATE).
Open a handle to SCOP. cgi is the URL for the cgi script to access.
params is a dictionary with the options to pass to it. get is a boolean
that describes whether a GET should be used.
"""
from Bio._py3k import urlopen, urlencode
# Open a handle to SCOP.
if params is None:
params = {}
options = urlencode(params)
if get: # do a GET
if options:
cgi += "?" + options
handle = urlopen(cgi)
else: # do a POST
handle = urlopen(cgi, data=options)
return handle
def setUp(self):
# We are using the files of the Drosophila Gateway Vector Collection
# (<https://emb.carnegiescience.edu/drosophila-gateway-vector-collection>)
# as sample Gck files. We cannot redistribute those files along with
# Biopython, so we need to download them now for the tests to run.
if not os.path.exists("Gck/DGVC_GCK.zip"):
try:
requires_internet.check()
except MissingExternalDependencyError:
self.skipTest("Sample files missing and no Internet access")
return
try:
src = urlopen("https://emb.carnegiescience.edu/sites/default/files/DGVC_GCK.zip")
with open("Gck/DGVC_GCK.zip", "wb") as dst:
shutil.copyfileobj(src, dst)
src.close()
except HTTPError:
self.skipTest("Cannot download the sample files")
return
self.zipdata = ZipFile("Gck/DGVC_GCK.zip")
def weblogo(self, fname, format="PNG", version="2.8.2", **kwds):
"""Download and save a weblogo using the Berkeley weblogo service.
Requires an internet connection.
The parameters from ``**kwds`` are passed directly to the weblogo server.
Currently, this method uses WebLogo version 3.3.
These are the arguments and their default values passed to
WebLogo 3.3; see their website at http://weblogo.threeplusone.com
for more information::
'stack_width' : 'medium',
'stacks_per_line' : '40',
'alphabet' : 'alphabet_dna',
'ignore_lower_case' : True,
'unit_name' : "bits",
'first_index' : '1',
'logo_start' : '1',
'logo_end': str(self.length),
'composition' : "comp_auto",
'percentCG' : '',
'scale_width' : True,
'show_errorbars' : True,
'logo_title' : '',
'logo_label' : '',
'show_xaxis': True,
'xaxis_label': '',
'show_yaxis': True,
'yaxis_label': '',
'yaxis_scale': 'auto',
'yaxis_tic_interval' : '1.0',
'show_ends' : True,
'show_fineprint' : True,
'color_scheme': 'color_auto',
'symbols0': '',
'symbols1': '',
'symbols2': '',
'symbols3': '',
'symbols4': '',
'color0': '',
'color1': '',
'color2': '',
'color3': '',
'color4': '',
"""
from Bio._py3k import urlopen, urlencode, Request
from Bio import Alphabet
if isinstance(self.alphabet, Alphabet.ProteinAlphabet):
alpha = "alphabet_protein"
elif isinstance(self.alphabet, Alphabet.RNAAlphabet):
alpha = "alphabet_rna"
elif isinstance(self.alphabet, Alphabet.DNAAlphabet):
alpha = "alphabet_dna"
else:
alpha = "auto"
frequencies = self.format('transfac')
url = 'http://weblogo.threeplusone.com/create.cgi'
values = {
'sequences': frequencies,
'format': format.lower(),
'stack_width': 'medium',
'stacks_per_line': '40',
'alphabet': alpha,
'ignore_lower_case': True,
'unit_name': "bits",
'first_index': '1',
'logo_start': '1',
'logo_end': str(self.length),
'composition': "comp_auto",
'percentCG': '',
'scale_width': True,
'show_errorbars': True,
'logo_title': '',
'logo_label': '',
'show_xaxis': True,
'xaxis_label': '',
'show_yaxis': True,
'yaxis_label': '',
'yaxis_scale': 'auto',
'yaxis_tic_interval': '1.0',
'show_ends': True,
'show_fineprint': True,
'color_scheme': 'color_auto',
'symbols0': '',
'symbols1': '',
'symbols2': '',
'symbols3': '',
'symbols4': '',
'color0': '',
'color1': '',
'color2': '',
'color3': '',
'color4': '',
}
values.update(
dict((k, "" if v is False else str(v)) for k, v in kwds.items()))
data = urlencode(values).encode("utf-8")
req = Request(url, data)
response = urlopen(req)
with open(fname, "wb") as f:
im = response.read()
f.write(im)
def weblogo(self,fname,format="PNG",version="2.8.2", **kwds):
"""
uses the Berkeley weblogo service to download and save a weblogo of
itself
requires an internet connection.
The parameters from **kwds are passed directly to the weblogo server.
Currently, this method uses WebLogo version 3.3.
These are the arguments and their default values passed to
WebLogo 3.3; see their website at http://weblogo.threeplusone.com
for more information:
'stack_width' : 'medium',
'stack_per_line' : '40',
'alphabet' : 'alphabet_dna',
'ignore_lower_case' : True,
'unit_name' : "bits",
'first_index' : '1',
'logo_start' : '1',
'logo_end': str(self.length),
'composition' : "comp_auto",
'percentCG' : '',
'scale_width' : True,
'show_errorbars' : True,
'logo_title' : '',
'logo_label' : '',
'show_xaxis': True,
'xaxis_label': '',
'show_yaxis': True,
'yaxis_label': '',
'yaxis_scale': 'auto',
'yaxis_tic_interval' : '1.0',
'show_ends' : True,
'show_fineprint' : True,
'color_scheme': 'color_auto',
'symbols0': '',
'symbols1': '',
'symbols2': '',
'symbols3': '',
'symbols4': '',
'color0': '',
'color1': '',
'color2': '',
'color3': '',
'color4': '',
"""
from Bio._py3k import urlopen, urlencode, Request
frequencies = self.format('transfac')
url = 'http://weblogo.threeplusone.com/create.cgi'
values = {'sequences': frequencies,
'format': format.lower(),
'stack_width': 'medium',
'stack_per_line': '40',
'alphabet': 'alphabet_dna',
'ignore_lower_case': True,
'unit_name': "bits",
'first_index': '1',
'logo_start': '1',
'logo_end': str(self.length),
'composition': "comp_auto",
'percentCG': '',
'scale_width': True,
'show_errorbars': True,
'logo_title': '',
'logo_label': '',
'show_xaxis': True,
'xaxis_label': '',
'show_yaxis': True,
'yaxis_label': '',
'yaxis_scale': 'auto',
'yaxis_tic_interval': '1.0',
'show_ends': True,
'show_fineprint': True,
'color_scheme': 'color_auto',
'symbols0': '',
'symbols1': '',
'symbols2': '',
'symbols3': '',
'symbols4': '',
'color0': '',
'color1': '',
'color2': '',
'color3': '',
'color4': '',
}
for k, v in kwds.items():
if isinstance(values[k], bool):
if not v:
v = ""
values[k]=str(v)
data = urlencode(values)
req = Request(url, data)
response = urlopen(req)
with open(fname,"w") as f:
im = response.read()
f.write(im)
def weblogo(self, fname, format="PNG", version="2.8.2", **kwds):
"""Download and save a weblogo using the Berkeley weblogo service.
Requires an internet connection.
The parameters from ``**kwds`` are passed directly to the weblogo server.
Currently, this method uses WebLogo version 3.3.
These are the arguments and their default values passed to
WebLogo 3.3; see their website at http://weblogo.threeplusone.com
for more information::
'stack_width' : 'medium',
'stacks_per_line' : '40',
'alphabet' : 'alphabet_dna',
'ignore_lower_case' : True,
'unit_name' : "bits",
'first_index' : '1',
'logo_start' : '1',
'logo_end': str(self.length),
'composition' : "comp_auto",
'percentCG' : '',
'scale_width' : True,
'show_errorbars' : True,
'logo_title' : '',
'logo_label' : '',
'show_xaxis': True,
'xaxis_label': '',
'show_yaxis': True,
'yaxis_label': '',
'yaxis_scale': 'auto',
'yaxis_tic_interval' : '1.0',
'show_ends' : True,
'show_fineprint' : True,
'color_scheme': 'color_auto',
'symbols0': '',
'symbols1': '',
'symbols2': '',
'symbols3': '',
'symbols4': '',
'color0': '',
'color1': '',
'color2': '',
'color3': '',
'color4': '',
"""
from Bio._py3k import urlopen, urlencode, Request
if self.alphabet == "ACDEFGHIKLMNPQRSTVWY":
alpha = "alphabet_protein"
elif self.alphabet == "ACGU":
alpha = "alphabet_rna"
elif self.alphabet == "ACGT":
alpha = "alphabet_dna"
else:
alpha = "auto"
frequencies = self.format("transfac")
url = "http://weblogo.threeplusone.com/create.cgi"
values = {
"sequences": frequencies,
"format": format.lower(),
"stack_width": "medium",
"stacks_per_line": "40",
"alphabet": alpha,
"ignore_lower_case": True,
"unit_name": "bits",
"first_index": "1",
"logo_start": "1",
"logo_end": str(self.length),
"composition": "comp_auto",
"percentCG": "",
"scale_width": True,
"show_errorbars": True,
"logo_title": "",
"logo_label": "",
"show_xaxis": True,
"xaxis_label": "",
"show_yaxis": True,
"yaxis_label": "",
"yaxis_scale": "auto",
"yaxis_tic_interval": "1.0",
"show_ends": True,
"show_fineprint": True,
"color_scheme": "color_auto",
"symbols0": "",
"symbols1": "",
"symbols2": "",
"symbols3": "",
"symbols4": "",
"color0": "",
"color1": "",
"color2": "",
"color3": "",
"color4": "",
}
values.update(
{k: "" if v is False else str(v)
for k, v in kwds.items()})
data = urlencode(values).encode("utf-8")
req = Request(url, data)
response = urlopen(req)
with open(fname, "wb") as f:
im = response.read()
f.write(im)
import gzip
import inspect
import os
import warnings
from Bio._py3k import urlopen
url = "ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz"
# extract name of gzip file
gzname = os.path.basename(url)
# extract name of cif file (split by sep, remove last, rejoin)
cifname = os.extsep.join(gzname.split(os.extsep)[:-1])
url_handle = urlopen(url)
with open(gzname, 'wb') as gzh:
print("Downloading file... (approx. 29 MB)")
while True:
data = url_handle.read(1024)
if len(data) == 0:
break
gzh.write(data)
# size as of 13 April 2012
if os.path.getsize(gzname) < 29944258:
warnings.warn("ERROR: Downloaded file is too small", RuntimeWarning)
fh = gzip.open(gzname, 'rb')
def weblogo(self, fname, format="PNG", version="2.8.2", **kwds):
"""Download and save a weblogo using the Berkeley weblogo service.
Requires an internet connection.
The parameters from ``**kwds`` are passed directly to the weblogo server.
Currently, this method uses WebLogo version 3.3.
These are the arguments and their default values passed to
WebLogo 3.3; see their website at http://weblogo.threeplusone.com
for more information::
'stack_width' : 'medium',
'stacks_per_line' : '40',
'alphabet' : 'alphabet_dna',
'ignore_lower_case' : True,
'unit_name' : "bits",
'first_index' : '1',
'logo_start' : '1',
'logo_end': str(self.length),
'composition' : "comp_auto",
'percentCG' : '',
'scale_width' : True,
'show_errorbars' : True,
'logo_title' : '',
'logo_label' : '',
'show_xaxis': True,
'xaxis_label': '',
'show_yaxis': True,
'yaxis_label': '',
'yaxis_scale': 'auto',
'yaxis_tic_interval' : '1.0',
'show_ends' : True,
'show_fineprint' : True,
'color_scheme': 'color_auto',
'symbols0': '',
'symbols1': '',
'symbols2': '',
'symbols3': '',
'symbols4': '',
'color0': '',
'color1': '',
'color2': '',
'color3': '',
'color4': '',
"""
from Bio._py3k import urlopen, urlencode, Request
if self.alphabet == 'ACDEFGHIKLMNPQRSTVWY':
alpha = "alphabet_protein"
elif self.alphabet == 'ACGU':
alpha = "alphabet_rna"
elif self.alphabet == 'ACGT':
alpha = "alphabet_dna"
else:
alpha = "auto"
frequencies = self.format('transfac')
url = 'http://weblogo.threeplusone.com/create.cgi'
values = {'sequences': frequencies,
'format': format.lower(),
'stack_width': 'medium',
'stacks_per_line': '40',
'alphabet': alpha,
'ignore_lower_case': True,
'unit_name': "bits",
'first_index': '1',
'logo_start': '1',
'logo_end': str(self.length),
'composition': "comp_auto",
'percentCG': '',
'scale_width': True,
'show_errorbars': True,
'logo_title': '',
'logo_label': '',
'show_xaxis': True,
'xaxis_label': '',
'show_yaxis': True,
'yaxis_label': '',
'yaxis_scale': 'auto',
'yaxis_tic_interval': '1.0',
'show_ends': True,
'show_fineprint': True,
'color_scheme': 'color_auto',
'symbols0': '',
'symbols1': '',
'symbols2': '',
'symbols3': '',
'symbols4': '',
'color0': '',
'color1': '',
'color2': '',
'color3': '',
'color4': '',
}
values.update(
dict((k, "" if v is False else str(v)) for k, v in kwds.items()))
data = urlencode(values).encode("utf-8")
req = Request(url, data)
response = urlopen(req)
with open(fname, "wb") as f:
im = response.read()
f.write(im)
import inspect
import os
import warnings
from Bio._py3k import urlopen
__docformat__ = "restructuredtext en"
url = "ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz"
# extract name of gzip file
gzname = os.path.basename(url)
# extract name of cif file (split by sep, remove last, rejoin)
cifname = os.extsep.join(gzname.split(os.extsep)[:-1])
url_handle = urlopen(url)
with open(gzname, 'wb') as gzh:
print("Downloading file... (approx. 29 MB)")
while True:
data = url_handle.read(1024)
if len(data) == 0:
break
gzh.write(data)
# size as of 13 April 2012
if os.path.getsize(gzname) < 29944258:
warnings.warn("ERROR: Downloaded file is too small",
RuntimeWarning)
fh = gzip.open(gzname, 'rb')
def weblogo(self,fname,format="PNG",version="2.8.2", **kwds):
"""
uses the Berkeley weblogo service to download and save a weblogo of
itself
requires an internet connection.
The parameters from **kwds are passed directly to the weblogo server.
Currently, this method uses WebLogo version 3.3.
These are the arguments and their default values passed to
WebLogo 3.3; see their website at http://weblogo.threeplusone.com
for more information:
'stack_width' : 'medium',
'stack_per_line' : '40',
'alphabet' : 'alphabet_dna',
'ignore_lower_case' : True,
'unit_name' : "bits",
'first_index' : '1',
'logo_start' : '1',
'logo_end': str(self.length),
'composition' : "comp_auto",
'percentCG' : '',
'scale_width' : True,
'show_errorbars' : True,
'logo_title' : '',
'logo_label' : '',
'show_xaxis': True,
'xaxis_label': '',
'show_yaxis': True,
'yaxis_label': '',
'yaxis_scale': 'auto',
'yaxis_tic_interval' : '1.0',
'show_ends' : True,
'show_fineprint' : True,
'color_scheme': 'color_auto',
'symbols0': '',
'symbols1': '',
'symbols2': '',
'symbols3': '',
'symbols4': '',
'color0': '',
'color1': '',
'color2': '',
'color3': '',
'color4': '',
"""
from Bio._py3k import urlopen, urlencode, Request
frequencies = self.format('transfac')
url = 'http://weblogo.threeplusone.com/create.cgi'
values = {'sequences': frequencies,
'format': format.lower(),
'stack_width': 'medium',
'stack_per_line': '40',
'alphabet': 'alphabet_dna',
'ignore_lower_case': True,
'unit_name': "bits",
'first_index': '1',
'logo_start': '1',
'logo_end': str(self.length),
'composition': "comp_auto",
'percentCG': '',
'scale_width': True,
'show_errorbars': True,
'logo_title': '',
'logo_label': '',
'show_xaxis': True,
'xaxis_label': '',
'show_yaxis': True,
'yaxis_label': '',
'yaxis_scale': 'auto',
'yaxis_tic_interval': '1.0',
'show_ends': True,
'show_fineprint': True,
'color_scheme': 'color_auto',
'symbols0': '',
'symbols1': '',
'symbols2': '',
'symbols3': '',
'symbols4': '',
'color0': '',
'color1': '',
'color2': '',
'color3': '',
'color4': '',
}
for k, v in kwds.items():
if isinstance(values[k], bool):
if not v:
v = ""
values[k]=str(v)
data = urlencode(values)
req = Request(url, data)
response = urlopen(req)
f = open(fname,"w")
im = response.read()
f.write(im)
f.close()