def _guess_scheduler(self):
from easydev import cmd_exists
if cmd_exists("sbatch") and cmd_exists("srun"):
return 'slurm'
else:
return 'local'
def guess_scheduler():
"""Guesses whether we are on a SLURM cluster or not.
If not, we assume a local run is expected.
"""
from easydev import cmd_exists
if cmd_exists("sbatch") and cmd_exists("srun"):
return 'slurm'
else:
return 'local'
def __init__(self, RExecutable='R', max_len=1000,
use_dict=None, host='localhost', user=None, ssh='ssh',
verbose=False, return_err=True):
"""
:param str RCMD: the name of the R executable
:param max_len: define the upper limitation for the length of command string. A
command string will be passed to R by a temporary file if it is longer
than this value.
:param host: The computer name (or IP) on which the R interpreter is
installed. The value "localhost" means that the R locates on the
the localhost computer. On POSIX systems (including Cygwin
environment on Windows), it is possible to use R on a remote
computer if the command "ssh" works. To do that, the user need set
this value, and perhaps the parameter "user".
:param user: The user name on the remote computer. This value need to be set
only if the user name is different on the remote computer. In
interactive environment, the password can be input by the user if
prompted. If running in a program, the user need to be able to
login without typing password! (i.e., you need to set your SSH keys)
:param ssh: The program to login to remote computer.
:param kargs: must be empty. Error raised otherwise
"""
from easydev import cmd_exists
if host == 'localhost' and cmd_exists(RExecutable) is False:
raise Exception('Could not find the R executable %s in your path' % RExecutable)
super(RSession, self).__init__(RCMD=RExecutable, max_len=max_len,
use_dict=use_dict, host=host, user=user, ssh=ssh, return_err=return_err,
dump_stdout=verbose)
def __init__(
self,
RExecutable="R",
max_len=1000,
use_dict=None,
host="localhost",
user=None,
ssh="ssh",
verbose=False,
return_err=True,
):
"""
:param str RCMD: the name of the R executable
:param max_len: define the upper limitation for the length of command string. A
command string will be passed to R by a temporary file if it is longer
than this value.
:param host: The computer name (or IP) on which the R interpreter is
installed. The value "localhost" means that the R locates on the
the localhost computer. On POSIX systems (including Cygwin
environment on Windows), it is possible to use R on a remote
computer if the command "ssh" works. To do that, the user need set
this value, and perhaps the parameter "user".
:param user: The user name on the remote computer. This value need to be set
only if the user name is different on the remote computer. In
interactive environment, the password can be input by the user if
prompted. If running in a program, the user need to be able to
login without typing password! (i.e., you need to set your SSH keys)
:param ssh: The program to login to remote computer.
:param kargs: must be empty. Error raised otherwise
"""
from easydev import cmd_exists
if host == "localhost" and cmd_exists(RExecutable) is False:
raise Exception(
"Could not find the R executable %s in your path" % RExecutable
)
super(RSession, self).__init__(
RCMD=RExecutable,
max_len=max_len,
use_dict=use_dict,
host=host,
user=user,
ssh=ssh,
return_err=return_err,
dump_stdout=verbose,
)
self.run("options(warn=-1)")
# the :class:`sequana.kraken.KrakenResults`. See following example.
##############################################
# Example
# --------
#
# In the following example, we use the results of a kraken analysis. The
# original toy data files contains 1500 reads mostly related to Measles virus
#
from sequana import KrakenResults, sequana_data
test_file = sequana_data("test_kraken.out", "testing")
k = KrakenResults(test_file)
df = k.plot(kind='pie')
print(df)
####################################################
# Note that only a subset of taxons are shown in the pie chart
# that is those that cover at least 1% of the total reads. Others
# are put together and labelled "others"
#
# A more interactive plot can be obtained using Krona if installed:
from sequana import KrakenResults, sequana_data
test_file = sequana_data("test_kraken.out", "testing")
import easydev
if easydev.cmd_exists("ktImportText"):
k = KrakenResults(test_file)
k.to_js(onweb=False) # The output filame is krona.html by default
#######################################################################
# An example is available in `Krona example <../_static/krona.html>`_