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tsnaomi/finnsyll | finnsyll/phonology.py | sonseq | def sonseq(word):
'''Return True if 'word' does not violate sonority sequencing.'''
parts = re.split(r'([ieaouäöy]+)', word, flags=re.I | re.U)
onset, coda = parts[0], parts[-1]
# simplex onset Finnish complex onset
if len(onset) <= 1 or onset.lower() in ONSETS:
# simplex coda ... | python | def sonseq(word):
'''Return True if 'word' does not violate sonority sequencing.'''
parts = re.split(r'([ieaouäöy]+)', word, flags=re.I | re.U)
onset, coda = parts[0], parts[-1]
# simplex onset Finnish complex onset
if len(onset) <= 1 or onset.lower() in ONSETS:
# simplex coda ... | [
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tsnaomi/finnsyll | finnsyll/phonology.py | harmonic | def harmonic(word):
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depths = (depth[x.lower()] for x in vowels)
return len(set(depths)) < 2 | python | def harmonic(word):
'''Return True if the word's vowels agree in frontness/backness.'''
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saltant-org/saltant-py | saltant/models/executable_task_type.py | ExecutableTaskType.put | def put(self):
"""Updates this task type on the saltant server.
Returns:
:class:`saltant.models.container_task_type.ExecutableTaskType`:
An executable task type model instance representing the task type
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"""
return self.manager.pu... | python | def put(self):
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Returns:
:class:`saltant.models.container_task_type.ExecutableTaskType`:
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required_arguments_default_values=None,
json_file_option=None,
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required_arguments_default_values=None,
json_file_option=None,
extra_data_to_post=None,
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OLC-Bioinformatics/sipprverse | sipprverse_reporter/reports.py | Reports.reporter | def reporter(self, analysistype='genesippr'):
"""
Creates a report of the genesippr results
:param analysistype: The variable to use when accessing attributes in the metadata object
"""
logging.info('Creating {} report'.format(analysistype))
# Create a dictionary to link ... | python | def reporter(self, analysistype='genesippr'):
"""
Creates a report of the genesippr results
:param analysistype: The variable to use when accessing attributes in the metadata object
"""
logging.info('Creating {} report'.format(analysistype))
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OLC-Bioinformatics/sipprverse | sipprverse_reporter/reports.py | Reports.genusspecific | def genusspecific(self, analysistype='genesippr'):
"""
Creates simplified genus-specific reports. Instead of the % ID and the fold coverage, a simple +/- scheme is
used for presence/absence
:param analysistype: The variable to use when accessing attributes in the metadata object
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Creates simplified genus-specific reports. Instead of the % ID and the fold coverage, a simple +/- scheme is
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:param analysistype: The variable to use when accessing attributes in the metadata object
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OLC-Bioinformatics/sipprverse | sipprverse_reporter/reports.py | Reports.gdcsreporter | def gdcsreporter(self, analysistype='GDCS'):
"""
Creates a report of the GDCS results
:param analysistype: The variable to use when accessing attributes in the metadata object
"""
logging.info('Creating {} report'.format(analysistype))
# Initialise list to store all the G... | python | def gdcsreporter(self, analysistype='GDCS'):
"""
Creates a report of the GDCS results
:param analysistype: The variable to use when accessing attributes in the metadata object
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logging.info('Creating {} report'.format(analysistype))
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OLC-Bioinformatics/sipprverse | sipprverse_reporter/reports.py | Reports.gdcs_fai | def gdcs_fai(sample, analysistype='GDCS'):
"""
GDCS analyses need to use the .fai file supplied in the targets folder rather than the one created following
reverse baiting
:param sample: sample object
:param analysistype: current analysis being performed
"""
try:
... | python | def gdcs_fai(sample, analysistype='GDCS'):
"""
GDCS analyses need to use the .fai file supplied in the targets folder rather than the one created following
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:param sample: sample object
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OLC-Bioinformatics/sipprverse | sipprverse_reporter/reports.py | Reports.sixteensreporter | def sixteensreporter(self, analysistype='sixteens_full'):
"""
Creates a report of the results
:param analysistype: The variable to use when accessing attributes in the metadata object
"""
# Create the path in which the reports are stored
make_path(self.reportpath)
... | python | def sixteensreporter(self, analysistype='sixteens_full'):
"""
Creates a report of the results
:param analysistype: The variable to use when accessing attributes in the metadata object
"""
# Create the path in which the reports are stored
make_path(self.reportpath)
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OLC-Bioinformatics/sipprverse | sipprverse_reporter/reports.py | Reports.confindr_reporter | def confindr_reporter(self, analysistype='confindr'):
"""
Creates a final report of all the ConFindr results
"""
# Initialise the data strings
data = 'Strain,Genus,NumContamSNVs,ContamStatus,PercentContam,PercentContamSTD\n'
with open(os.path.join(self.reportpath, analysi... | python | def confindr_reporter(self, analysistype='confindr'):
"""
Creates a final report of all the ConFindr results
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data = 'Strain,Genus,NumContamSNVs,ContamStatus,PercentContam,PercentContamSTD\n'
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OLC-Bioinformatics/sipprverse | sipprverse_reporter/reports.py | Reports.methodreporter | def methodreporter(self):
"""
Create final reports collating results from all the individual iterations through the method pipeline
"""
# Ensure that the analyses are set to complete
self.analysescomplete = True
# Reset the report path to original value
self.repor... | python | def methodreporter(self):
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Create final reports collating results from all the individual iterations through the method pipeline
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OLC-Bioinformatics/sipprverse | sipprverse_reporter/reports.py | ReportImage.main | def main(self):
"""
Run the methods required to create the genesippr report summary image
"""
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self.image_report,
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OLC-Bioinformatics/sipprverse | sipprverse_reporter/reports.py | ReportImage.data_sanitise | def data_sanitise(self, inputstring, header=None):
"""
Format the data to be consistent with heatmaps
:param inputstring: string containing data to be formatted
:param header: class of the data - certain categories have specific formatting requirements
:return: the formatted outp... | python | def data_sanitise(self, inputstring, header=None):
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OLC-Bioinformatics/sipprverse | sipprverse_reporter/reports.py | ReportImage.dataframe_setup | def dataframe_setup(self):
"""
Set-up a report to store the desired header: sanitized string combinations
"""
# Initialise a dictionary to store the sanitized headers and strings
genesippr_dict = dict()
# Try to open all the reports - use pandas to extract the results fro... | python | def dataframe_setup(self):
"""
Set-up a report to store the desired header: sanitized string combinations
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OLC-Bioinformatics/sipprverse | sipprverse_reporter/reports.py | ReportImage.figure_populate | def figure_populate(outputpath, csv, xlabels, ylabels, analysistype, description, fail=False):
"""
Create the report image from the summary report created in self.dataframesetup
:param outputpath: Path in which the outputs are to be created
:param csv: Name of the report file from which ... | python | def figure_populate(outputpath, csv, xlabels, ylabels, analysistype, description, fail=False):
"""
Create the report image from the summary report created in self.dataframesetup
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pyBookshelf/bookshelf | bookshelf/api_v2/os_helpers.py | add_usr_local_bin_to_path | def add_usr_local_bin_to_path(log=False):
""" adds /usr/local/bin to $PATH """
if log:
bookshelf2.logging_helpers.log_green('inserts /usr/local/bin into PATH')
with settings(hide('warnings', 'running', 'stdout', 'stderr'),
capture=True):
try:
sudo('echo "export... | python | def add_usr_local_bin_to_path(log=False):
""" adds /usr/local/bin to $PATH """
if log:
bookshelf2.logging_helpers.log_green('inserts /usr/local/bin into PATH')
with settings(hide('warnings', 'running', 'stdout', 'stderr'),
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pyBookshelf/bookshelf | bookshelf/api_v2/os_helpers.py | dir_attribs | def dir_attribs(location, mode=None, owner=None,
group=None, recursive=False, use_sudo=False):
""" cuisine dir_attribs doesn't do sudo, so we implement our own
Updates the mode/owner/group for the given remote directory."""
args = ''
if recursive:
args = args + ' -R '
if... | python | def dir_attribs(location, mode=None, owner=None,
group=None, recursive=False, use_sudo=False):
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pyBookshelf/bookshelf | bookshelf/api_v2/os_helpers.py | dir_ensure | def dir_ensure(location, recursive=False, mode=None,
owner=None, group=None, use_sudo=False):
""" cuisine dir_ensure doesn't do sudo, so we implement our own
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pyBookshelf/bookshelf | bookshelf/api_v2/os_helpers.py | dir_exists | def dir_exists(location, use_sudo=False):
"""Tells if there is a remote directory at the given location."""
with settings(hide('running', 'stdout', 'stderr'), warn_only=True):
if use_sudo:
# convert return code 0 to True
return not bool(sudo('test -d %s' % (location)).return_code... | python | def dir_exists(location, use_sudo=False):
"""Tells if there is a remote directory at the given location."""
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if use_sudo:
# convert return code 0 to True
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pyBookshelf/bookshelf | bookshelf/api_v2/os_helpers.py | disable_env_reset_on_sudo | def disable_env_reset_on_sudo(log=False):
""" updates /etc/sudoers so that users from %wheel keep their
environment when executing a sudo call
"""
if log:
bookshelf2.logging_helpers.log_green('disabling env reset on sudo')
file_append('/etc/sudoers',
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""" updates /etc/sudoers so that users from %wheel keep their
environment when executing a sudo call
"""
if log:
bookshelf2.logging_helpers.log_green('disabling env reset on sudo')
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pyBookshelf/bookshelf | bookshelf/api_v2/os_helpers.py | disable_requiretty_on_sudoers | def disable_requiretty_on_sudoers(log=False):
""" allow sudo calls through ssh without a tty """
if log:
bookshelf2.logging_helpers.log_green(
'disabling requiretty on sudo calls')
comment_line('/etc/sudoers',
'^Defaults.*requiretty', use_sudo=True)
return True | python | def disable_requiretty_on_sudoers(log=False):
""" allow sudo calls through ssh without a tty """
if log:
bookshelf2.logging_helpers.log_green(
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comment_line('/etc/sudoers',
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pyBookshelf/bookshelf | bookshelf/api_v2/os_helpers.py | file_attribs | def file_attribs(location,
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pyBookshelf/bookshelf | bookshelf/api_v2/os_helpers.py | os_release | def os_release():
""" returns /etc/os-release in a dictionary """
with settings(hide('warnings', 'running', 'stderr'),
warn_only=True, capture=True):
release = {}
data = run('cat /etc/os-release')
for line in data.split('\n'):
if not line:
c... | python | def os_release():
""" returns /etc/os-release in a dictionary """
with settings(hide('warnings', 'running', 'stderr'),
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pyBookshelf/bookshelf | bookshelf/api_v2/os_helpers.py | linux_distribution | def linux_distribution():
""" returns the linux distribution in lower case """
with settings(hide('warnings', 'running', 'stdout', 'stderr'),
warn_only=True, capture=True):
data = os_release()
return(data['ID']) | python | def linux_distribution():
""" returns the linux distribution in lower case """
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data = os_release()
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pyBookshelf/bookshelf | bookshelf/api_v2/os_helpers.py | lsb_release | def lsb_release():
""" returns /etc/lsb-release in a dictionary """
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_lsb_release = {}
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for line in data.split('\n'):
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""" returns /etc/lsb-release in a dictionary """
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pyBookshelf/bookshelf | bookshelf/api_v2/os_helpers.py | restart_service | def restart_service(service, log=False):
""" restarts a service """
with settings():
if log:
bookshelf2.logging_helpers.log_yellow(
'stoping service %s' % service)
sudo('service %s stop' % service)
if log:
bookshelf2.logging_helpers.log_yellow(
... | python | def restart_service(service, log=False):
""" restarts a service """
with settings():
if log:
bookshelf2.logging_helpers.log_yellow(
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sudo('service %s stop' % service)
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pyBookshelf/bookshelf | bookshelf/api_v2/os_helpers.py | systemd | def systemd(service, start=True, enabled=True, unmask=False, restart=False):
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""" manipulates systemd services """
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pyBookshelf/bookshelf | bookshelf/api_v2/os_helpers.py | install_os_updates | def install_os_updates(distribution, force=False):
""" installs OS updates """
if ('centos' in distribution or
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bookshelf2.logging_helpers.log_green('installing OS updates')
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""" installs OS updates """
if ('centos' in distribution or
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'redhat' in distribution):
bookshelf2.logging_helpers.log_green('installing OS updates')
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moralrecordings/mrcrowbar | mrcrowbar/statistics.py | Stats.ansi_format | def ansi_format( self, width=64, height=12 ):
"""Return a human readable ANSI-terminal printout of the stats.
width
Custom width for the graph (in characters).
height
Custom height for the graph (in characters).
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Custom height for the graph (in characters).
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saltant-org/saltant-py | saltant/models/task_whitelist.py | TaskWhitelist.put | def put(self):
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A task whitelist model instance representing the task
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"""
return self.manager.put(
... | python | def put(self):
"""Updates this task whitelist on the saltant server.
Returns:
:class:`saltant.models.task_whitelist.TaskWhitelist`:
A task whitelist model instance representing the task
whitelist just updated.
"""
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moralrecordings/mrcrowbar | mrcrowbar/utils.py | enable_logging | def enable_logging( level='WARNING' ):
"""Enable sending logs to stderr. Useful for shell sessions.
level
Logging threshold, as defined in the logging module of the Python
standard library. Defaults to 'WARNING'.
"""
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log = logging.getLogger( 'mrcrowbar' )
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moralrecordings/mrcrowbar | mrcrowbar/utils.py | basic_diff | def basic_diff( source1, source2, start=None, end=None ):
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moralrecordings/mrcrowbar | mrcrowbar/utils.py | hexdump_iter | def hexdump_iter( source, start=None, end=None, length=None, major_len=8, minor_len=4, colour=True, address_base=None ):
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moralrecordings/mrcrowbar | mrcrowbar/utils.py | hexdump_diff_iter | def hexdump_diff_iter( source1, source2, start=None, end=None, length=None, major_len=8, minor_len=4, colour=True, before=2, after=2, address_base=None ):
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moralrecordings/mrcrowbar | mrcrowbar/utils.py | hexdump_diff | def hexdump_diff( source1, source2, start=None, end=None, length=None, major_len=8, minor_len=4, colour=True, before=2, after=2, address_base=None ):
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moralrecordings/mrcrowbar | mrcrowbar/utils.py | BitReader.set_offset | def set_offset( self, offset ):
"""Set the current read offset (in bytes) for the instance."""
assert offset in range( len( self.buffer ) )
self.pos = offset
self._fill_buffer() | python | def set_offset( self, offset ):
"""Set the current read offset (in bytes) for the instance."""
assert offset in range( len( self.buffer ) )
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moralrecordings/mrcrowbar | mrcrowbar/utils.py | BitWriter.put_bits | def put_bits( self, value, count ):
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Integer containing bits to push, ordered from least-significant bit to
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count
Number of bits to push to the target.
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Number of bits to push to the target.
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Riffstation/Flask-Philo-SQLAlchemy | flask_philo_sqlalchemy/orm.py | BaseManager.get_for_update | def get_for_update(self, connection_name='DEFAULT', **kwargs):
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tsnaomi/finnsyll | finnsyll/prev/v07.py | syllabify | def syllabify(word, compound=None):
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compound = bool(re.search(r'(-| |=)', word))
syllabify = _syllabify_compound if compound else _syllabify
syll, rules = syllabify(word)
yield syll, rules
n = 7
if '... | python | def syllabify(word, compound=None):
'''Syllabify the given word, whether simplex or complex.'''
if compound is None:
compound = bool(re.search(r'(-| |=)', word))
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danishabdullah/algen | algen/compilers.py | ModelCompiler.convert_case | def convert_case(name):
"""Converts name from CamelCase to snake_case"""
s1 = re.sub('(.)([A-Z][a-z]+)', r'\1_\2', name)
return re.sub('([a-z0-9])([A-Z])', r'\1_\2', s1).lower() | python | def convert_case(name):
"""Converts name from CamelCase to snake_case"""
s1 = re.sub('(.)([A-Z][a-z]+)', r'\1_\2', name)
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danishabdullah/algen | algen/compilers.py | ModelCompiler.table_name | def table_name(self):
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danishabdullah/algen | algen/compilers.py | ModelCompiler.types | def types(self):
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res.append(ModelCompiler.get_column_type(tmp)) if tmp else False
res = list(set(res))
return res | python | def types(self):
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res = []
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danishabdullah/algen | algen/compilers.py | ModelCompiler.basic_types | def basic_types(self):
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"""Returns non-postgres types referenced in user supplied model """
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danishabdullah/algen | algen/compilers.py | ModelCompiler.primary_keys | def primary_keys(self):
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danishabdullah/algen | algen/compilers.py | ModelCompiler.compiled_named_imports | def compiled_named_imports(self):
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res = []
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module='sqlalchemy.dialects.postgresql',
... | python | def compiled_named_imports(self):
"""Returns compiled named imports required for the model"""
res = []
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... | [
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danishabdullah/algen | algen/compilers.py | ModelCompiler.compiled_orm_imports | def compiled_orm_imports(self):
"""Returns compiled named imports required for the model"""
module = 'sqlalchemy.orm'
labels = []
if self.relationship_definitions:
labels.append("relationship")
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"""Returns compiled named imports required for the model"""
module = 'sqlalchemy.orm'
labels = []
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labels.append("relationship")
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danishabdullah/algen | algen/compilers.py | ModelCompiler.compiled_columns | def compiled_columns(self):
"""Returns compiled column definitions"""
def get_column_args(column):
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if arg_name not in ('name', 'type'):
if arg_name in ('server_default', 'server_onupdate'):
... | python | def compiled_columns(self):
"""Returns compiled column definitions"""
def get_column_args(column):
tmp = []
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danishabdullah/algen | algen/compilers.py | ModelCompiler.compiled_foreign_keys | def compiled_foreign_keys(self):
"""Returns compiled foreign key definitions"""
def get_column_args(column):
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if arg_name not in ('name', 'type', 'reference'):
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"""Returns compiled foreign key definitions"""
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danishabdullah/algen | algen/compilers.py | ModelCompiler.compiled_relationships | def compiled_relationships(self):
"""Returns compiled relationship definitions"""
def get_column_args(column):
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danishabdullah/algen | algen/compilers.py | ModelCompiler.columns | def columns(self):
"""Return names of all the addressable columns (including foreign keys) referenced in user supplied model"""
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res.extend([col['name'] for col in self.foreign_key_definitions])
return res | python | def columns(self):
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OLC-Bioinformatics/sipprverse | sixteenS/sixteens_full.py | SixteenSBait.main | def main(self):
"""
Run the required methods in the appropriate order
"""
self.targets()
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self.reversebait(maskmiddle='t', k=19)
self.subsample_reads() | python | def main(self):
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Run the required methods in the appropriate order
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OLC-Bioinformatics/sipprverse | sixteenS/sixteens_full.py | SixteenS.subsample | def subsample(self):
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OLC-Bioinformatics/sipprverse | sixteenS/sixteens_full.py | SixteenS.fasta | def fasta(self):
"""
Convert the subsampled reads to FASTA format using reformat.sh
"""
logging.info('Converting FASTQ files to FASTA format')
# Create the threads for the analysis
for _ in range(self.cpus):
threads = Thread(target=self.fastathreads, args=())
... | python | def fasta(self):
"""
Convert the subsampled reads to FASTA format using reformat.sh
"""
logging.info('Converting FASTQ files to FASTA format')
# Create the threads for the analysis
for _ in range(self.cpus):
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OLC-Bioinformatics/sipprverse | sixteenS/sixteens_full.py | SixteenS.makeblastdb | def makeblastdb(self):
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OLC-Bioinformatics/sipprverse | sixteenS/sixteens_full.py | SixteenS.blast | def blast(self):
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Run BLAST analyses of the subsampled FASTQ reads against the NCBI 16S reference database
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Run BLAST analyses of the subsampled FASTQ reads against the NCBI 16S reference database
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OLC-Bioinformatics/sipprverse | sixteenS/sixteens_full.py | SixteenS.blastparse | def blastparse(self):
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OLC-Bioinformatics/sipprverse | sixteenS/sixteens_full.py | SixteenS.reporter | def reporter(self):
"""
Creates a report of the results
"""
# Create the path in which the reports are stored
make_path(self.reportpath)
logging.info('Creating {} report'.format(self.analysistype))
# Initialise the header and data strings
header = 'Strain,... | python | def reporter(self):
"""
Creates a report of the results
"""
# Create the path in which the reports are stored
make_path(self.reportpath)
logging.info('Creating {} report'.format(self.analysistype))
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QunarOPS/qg.core | qg/core/observer.py | Observable.add_listener | def add_listener(self, evt_name, fn):
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self._listeners.setdefault(evt_name, [])
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允许一个函数多次注册，多次注册意味着一次 :func:`fire_event` 多次调用。
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QunarOPS/qg.core | qg/core/observer.py | Observable.remove_listener | def remove_listener(self, evt_name, fn, remove_all=False):
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.. note::
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QunarOPS/qg.core | qg/core/observer.py | Observable.has_listener | def has_listener(self, evt_name, fn):
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:params evt_name: 事件名称
:params fn: 要注册的触发函数函数
"""
listeners = self.__get_listeners(evt_name)
return fn in listeners | python | def has_listener(self, evt_name, fn):
"""指定listener是否存在
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QunarOPS/qg.core | qg/core/observer.py | Observable.fire_event | def fire_event(self, evt_name, *args, **kwargs):
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:params args: 给事件接受者的参数
:params kwargs: 给事件接受者的参数
"""
listeners = self.__get_listeners(evt_name)
evt = self.generate_event(evt_name)
for listener in listeners:
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pyBookshelf/bookshelf | bookshelf/api_v2/ec2.py | create_server_ec2 | def create_server_ec2(connection,
region,
disk_name,
disk_size,
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instance_type,
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security_groups=None,
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pyBookshelf/bookshelf | bookshelf/api_v2/ec2.py | destroy_ebs_volume | def destroy_ebs_volume(connection, region, volume_id, log=False):
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log_yellow('destroying EBS volume ...')
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region=region)
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pyBookshelf/bookshelf | bookshelf/api_v2/ec2.py | down_ec2 | def down_ec2(connection, instance_id, region, log=False):
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pyBookshelf/bookshelf | bookshelf/api_v2/ec2.py | get_ec2_info | def get_ec2_info(connection,
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pyBookshelf/bookshelf | bookshelf/api_v2/ec2.py | up_ec2 | def up_ec2(connection,
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tsnaomi/finnsyll | finnsyll/prev/v03.py | apply_T4 | def apply_T4(word):
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[va.ka.ut.taa].'''
WORD = word.split('.')
for i, v in enumerate(WORD):
# i % 2 != 0 prevents this rule from applying to first, third, etc.
... | python | def apply_T4(word):
'''An agglutination diphthong that ends in /u, y/ usually contains a
syllable boundary when -C# or -CCV follow, e.g., [lau.ka.us],
[va.ka.ut.taa].'''
WORD = word.split('.')
for i, v in enumerate(WORD):
# i % 2 != 0 prevents this rule from applying to first, third, etc.
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OLC-Bioinformatics/sipprverse | cgecore/utility.py | seqs_from_file | def seqs_from_file(filename, exit_on_err=False, return_qual=False):
"""Extract sequences from a file
Name:
seqs_from_file
Author(s):
Martin C F Thomsen
Date:
18 Jul 2013
Description:
Iterator which extract sequence data from the input file
Args:
filename: string which... | python | def seqs_from_file(filename, exit_on_err=False, return_qual=False):
"""Extract sequences from a file
Name:
seqs_from_file
Author(s):
Martin C F Thomsen
Date:
18 Jul 2013
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Iterator which extract sequence data from the input file
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OLC-Bioinformatics/sipprverse | cgecore/utility.py | open_ | def open_(filename, mode=None, compresslevel=9):
"""Switch for both open() and gzip.open().
Determines if the file is normal or gzipped by looking at the file
extension.
The filename argument is required; mode defaults to 'rb' for gzip and 'r'
for normal and compresslevel defaults to 9 for gzip.
... | python | def open_(filename, mode=None, compresslevel=9):
"""Switch for both open() and gzip.open().
Determines if the file is normal or gzipped by looking at the file
extension.
The filename argument is required; mode defaults to 'rb' for gzip and 'r'
for normal and compresslevel defaults to 9 for gzip.
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>>> from contextlib import cl... | [
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OLC-Bioinformatics/sipprverse | cgecore/utility.py | load_json | def load_json(json_object):
''' Load json from file or file name '''
content = None
if isinstance(json_object, str) and os.path.exists(json_object):
with open_(json_object) as f:
try:
content = json.load(f)
except Exception as e:
debug.log("Warning: Content of '%... | python | def load_json(json_object):
''' Load json from file or file name '''
content = None
if isinstance(json_object, str) and os.path.exists(json_object):
with open_(json_object) as f:
try:
content = json.load(f)
except Exception as e:
debug.log("Warning: Content of '%... | [
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OLC-Bioinformatics/sipprverse | cgecore/utility.py | sort2groups | def sort2groups(array, gpat=['_R1','_R2']):
""" Sort an array of strings to groups by patterns """
groups = [REGroup(gp) for gp in gpat]
unmatched = []
for item in array:
matched = False
for m in groups:
if m.match(item):
matched = True
break
if not matched... | python | def sort2groups(array, gpat=['_R1','_R2']):
""" Sort an array of strings to groups by patterns """
groups = [REGroup(gp) for gp in gpat]
unmatched = []
for item in array:
matched = False
for m in groups:
if m.match(item):
matched = True
break
if not matched... | [
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OLC-Bioinformatics/sipprverse | cgecore/utility.py | sort_and_distribute | def sort_and_distribute(array, splits=2):
""" Sort an array of strings to groups by alphabetically continuous
distribution
"""
if not isinstance(array, (list,tuple)): raise TypeError("array must be a list")
if not isinstance(splits, int): raise TypeError("splits must be an integer")
remaining = so... | python | def sort_and_distribute(array, splits=2):
""" Sort an array of strings to groups by alphabetically continuous
distribution
"""
if not isinstance(array, (list,tuple)): raise TypeError("array must be a list")
if not isinstance(splits, int): raise TypeError("splits must be an integer")
remaining = so... | [
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OLC-Bioinformatics/sipprverse | cgecore/utility.py | mkpath | def mkpath(filepath, permissions=0o777):
""" This function executes a mkdir command for filepath and with permissions
(octal number with leading 0 or string only)
# eg. mkpath("path/to/file", "0o775")
"""
# Converting string of octal to integer, if string is given.
if isinstance(permissions, str):
... | python | def mkpath(filepath, permissions=0o777):
""" This function executes a mkdir command for filepath and with permissions
(octal number with leading 0 or string only)
# eg. mkpath("path/to/file", "0o775")
"""
# Converting string of octal to integer, if string is given.
if isinstance(permissions, str):
... | [
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