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def __set_angular_version(self, startpoint):
"""Find and set the AngularJS version as class attribute
Args:
startpoint (:class:`nyawc.http.Request`): The startpoint request.
Returns:
str: True if found and set, False otherwise.
"""
if self.__args.angular_version:
self.__angular_version = self.__args.angular_version
colorlog.getLogger().info("Found AngularJS version " + self.__angular_version + " in the arguments.")
return True
colorlog.getLogger().info("Looking for AngularJS version using a headless browser.")
colorlog.getLogger().info("Waiting until DOM is completely loaded.")
self.__angular_version = BrowserHelper.javascript(
QueueItem(startpoint, Response(self.__args.domain)),
"return angular.version.full"
)
if self.__angular_version:
colorlog.getLogger().info("Found AngularJS version " + self.__angular_version + ".")
return True
colorlog.getLogger().error("Couldn't determine the AngularJS version (`angular.version.full` threw an exception).")
colorlog.getLogger().error("If you are certain this URL uses AngularJS, specify the version via the `--angular-version` argument.")
# #
# You should have received a copy of the GNU General Public License #
# along with this program (COPYING file). #
# If not, see . #
###########################################################################
"""PHYLOXML2NEXUS converter"""
import os
import colorlog
from Bio import SeqIO
from bioconvert import ConvBase
from bioconvert.core.decorators import requires
_log = colorlog.getLogger(__name__)
__all__ = ['PHYLOXML2NEXUS']
class PHYLOXML2NEXUS(ConvBase):
"""
Converts a tree file from :term:`PHYLOXML` format to :term:`NEXUS` format. ::
"""
_default_method = 'gotree'
def __init__(self, infile, outfile=None, alphabet=None, *args, **kwargs):
""".. rubric:: constructor
:param str infile: input :term:`PHYLOXML` file.
# #
# You should have received a copy of the GNU General Public License #
# along with this program (COPYING file). #
# If not, see . #
###########################################################################
"""Convert :term:`XLS` format to :term:`CSV` format"""
import csv
import colorlog
from bioconvert.core.base import ConvArg
from bioconvert.core.decorators import requires, requires_nothing
from bioconvert import ConvBase
logger = colorlog.getLogger(__name__)
class ODS2CSV(ConvBase):
"""Convert :term:`XLS` file into :term:`CSV` file
Method based on pyexcel [PYEXCEL].
"""
_default_method = "pyexcel"
DEFAULT_OUT_SEP = ','
DEFAULT_LINE_TERMINATOR = '\n'
def __init__(self, infile, outfile):
""".. rubric:: constructor
:param str infile:
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with this program (COPYING file). #
# If not, see . #
###########################################################################
"""Convert :term:`SAM` file to :term:`BAM` file"""
from bioconvert import ConvBase
from bioconvert.core.decorators import requires
import colorlog
logger = colorlog.getLogger(__name__)
__all__ = ["SAM2BAM"]
class SAM2BAM(ConvBase):
"""Convert :term:`SAM` file to :term:`BAM` file"""
_threading = True
def __init__(self, infile, outfile, *args, **kargs):
""".. rubric:: constructor
:param str infile:
:param str outfile:
"""
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with this program (COPYING file). #
# If not, see . #
###########################################################################
"""Convert :term:`BPLINK` to :term:`PLINK`"""
import colorlog
from bioconvert import ConvBase
from bioconvert.core.decorators import requires
from bioconvert.core.utils import generate_outfile_name
_log = colorlog.getLogger(__name__)
class BPLINK2PLINK(ConvBase):
"""Converts a genotype dataset bed+bim+fam in :term:`BPLINK` format to
ped+map :term:`PLINK` format.
Conversion is based on plink [PLINK]_ executable.
.. warning:: **plink** takes several inputs and outputs and does not need
extensions. What is required is a prefix. Bioconvert usage is therefore::
bioconvert bplink2plink plink_toy
Since there is no extension, you must be explicit by providing the
conversion name (bplink2plink). This command will search for 3 input
files plink_toy.bed, plink_toy.bim and plink_toy.fam. It will then
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with this program (COPYING file). #
# If not, see . #
###########################################################################
"""Convert :term:`CLUSTAL` to :term:`PHYLIP` format"""
import colorlog
from Bio import SeqIO
from bioconvert import ConvBase
from bioconvert.core.decorators import requires
from bioconvert.core.decorators import compressor
_log = colorlog.getLogger(__name__)
__all__ = ["CLUSTAL2PHYLIP"]
class CLUSTAL2PHYLIP(ConvBase):
"""
Converts a sequence alignment from :term:`CLUSTAL` format to :term:`PHYLIP` format.
Methods available are based on squizz [SQUIZZ]_ or biopython [BIOPYTHON]_, and
goalign [GOALIGN]_.
"""
_default_method = 'biopython'
def __init__(self, infile, outfile=None, alphabet=None, *args, **kwargs):
""".. rubric:: constructor
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with this program (COPYING file). #
# If not, see . #
###########################################################################
"""Convert :term:`BPLINK` to :term:`VCF`"""
import colorlog
import os
from bioconvert import ConvBase
from bioconvert.core.decorators import requires
from bioconvert.core.utils import generate_outfile_name
_log = colorlog.getLogger(__name__)
class BPLINK2VCF(ConvBase):
"""Converts a genotype dataset bed+bim+fam in :term:`BPLINK` format to
vcf :term:`VCF` format
Conversion is based on plink [PLINK]_ executable.
.. warning:: **plink** takes several inputs and outputs and does not need
extensions. What is required is a prefix. Bioconvert usage is therefore::
bioconvert bplink2vcf plink_toy plink_toy.vcf
Since there is no extension, you must be explicit by providing the
conversion name (bplink2plink). This command will search for 3 input
files plink_toy.bed, plink_toy.bim and plink_toy.fam. It will then
filename_error = False
while os.path.isfile(filename) and not filename_error:
filename_changed = True
filename_append += 1
filename = filename_backup + "." + str(filename_append)
if filename_append == sys.maxsize:
filename_error = True
if filename_error:
colorlog.getLogger().error("The output log file already exists and therefore no logs will be written.")
return
if filename_changed:
colorlog.getLogger().warning("The output log filename was changed to `" + filename + "` since `" + filename_backup + "` already exists.")
FileLoggingHelper.__filename = filename
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with this program (COPYING file). #
# If not, see . #
###########################################################################
"""Converts :term:`NEWICK` file to :term:`PHYLOXML` file."""
import colorlog
from bioconvert import ConvBase
from bioconvert.core.decorators import requires
from bioconvert.core.decorators import compressor
_log = colorlog.getLogger(__name__)
__all__ = ['NEWICK2PHYLOXML']
class NEWICK2PHYLOXML(ConvBase):
"""
Converts a tree file from :term:`NEWICK` format to :term:`PHYLOXML` format.
Methods available are based on gotree [GOTREE]_.
"""
_default_method = 'gotree'
def __init__(self, infile, outfile=None, alphabet=None, *args, **kwargs):
""".. rubric:: constructor
def init_logger(self):
self._mylogger = colorlog.getLogger("sequanix")
"""self._fh = open(self._logger_output, "w")
self._handler = colorlog.StreamHandler(self._fh)