def sanity_check(self, skip_warnings=False):
A = lambda x, t: t(args.__dict__[x]
) if x in self.args.__dict__ else None
null = lambda x: x
# the directory files will be dumped into (can exist but must be empty)
if filesnpaths.is_file_exists(self.directory, dont_raise=True):
filesnpaths.is_output_dir_writable(self.directory)
if not filesnpaths.is_dir_empty(self.directory):
raise ModellerError(
"You cannot give MODELLER a non-empty directory to work in."
)
else:
filesnpaths.gen_output_directory(self.directory)
if not self.lazy_init:
self.executable = check_MODELLER(self.executable)
# does target_fasta_path point to a fasta file?
utils.filesnpaths.is_file_fasta_formatted(self.target_fasta_path)
# make sure target_fasta is valid
target_fasta = u.SequenceSource(self.target_fasta_path,
lazy_init=False)
if target_fasta.total_seq != 1:
raise ConfigError(
"MODELLER :: The input FASTA file must have exactly one sequence. "
"You provided one with {}.".format(target_fasta.total_seq))
try:
while next(target_fasta):
int(target_fasta.id)
except:
raise ConfigError(
"MODELLER :: The defline of this fasta file must be an integer"
)
target_fasta.close()
# parameter consistencies
if self.deviation < 0.5 or self.deviation > 20:
self.run.warning(
"You realize that deviation is given in angstroms, right? You chose {}"
.format(self.deviation))
if self.very_fast and self.num_models > 1:
self.num_models = 1
self.run.warning(
"Since you chose --very-fast, there will be little difference, if at all, between models. Anvi'o "
"authoritatively sets --num-models to 1 to save you time.")
def sanity_check(self):
A = lambda x, t: t(args.__dict__[x]) if x in self.args.__dict__ else None
null = lambda x: x
# the directory files will be dumped into (can exist but must be empty)
if filesnpaths.is_file_exists(self.directory, dont_raise=True):
filesnpaths.is_output_dir_writable(self.directory)
if not filesnpaths.is_dir_empty(self.directory):
raise ModellerError("You cannot give MODELLER a non-empty directory to work in.")
else:
filesnpaths.gen_output_directory(self.directory)
# All MODELLER scripts are housed in self.script_folder
self.scripts_folder = J(os.path.dirname(anvio.__file__), 'data/misc/MODELLER/scripts')
if utils.filesnpaths.is_dir_empty(self.scripts_folder):
raise ConfigError("Anvi'o houses all its MODELLER scripts in {}, but your directory \
contains no scripts. Why you do dat?")
# check that MODELLER exists
if self.args.__dict__['modeller_executable'] if 'modeller_executable' in self.args.__dict__ else None:
self.run.info_single("As per your request, anvi'o will use `%s` to run MODELLER." % self.executable, nl_before=1)
utils.is_program_exists(self.executable)
else:
try:
utils.is_program_exists(self.executable)
except ConfigError as e:
raise ConfigError("Anvi'o needs a MODELLER program to be installed on your system. You didn't specify one\
(which can be done with `--modeller-executable`), so anvi'o tried the most recent version\
it knows about: '%s'. If you are certain you have it on your system (for instance you can run it\
by typing '%s' in your terminal window), you may want to send a detailed bug report. If you\
don't have it on your system, check out these installation instructions on our website:\
http://merenlab.org/2016/06/18/installing-third-party-software/#modeller" % (self.executable, self.executable))
self.run.info_single("Anvi'o found the default executable for MODELLER, `%s`, and will\
use it." % self.executable, nl_before=1)
self.is_executable_a_MODELLER_program()
# does target_fasta_path point to a fasta file?
utils.filesnpaths.is_file_fasta_formatted(self.target_fasta_path)
# make sure target_fasta is valid
target_fasta = u.SequenceSource(self.target_fasta_path, lazy_init=False)
if target_fasta.total_seq != 1:
raise ConfigError("MODELLER::The input FASTA file must have exactly one sequence.\
You provided one with {}.".format(target_fasta.total_seq))
# (not sanity check but we get self.corresponding_gene_call since target_fasta is opened)
while next(target_fasta):
self.corresponding_gene_call = target_fasta.id
target_fasta.close()
# parameter consistencies
if self.deviation < 0.5 or self.deviation > 20:
self.run.warning("You realize that deviation is given in angstroms, right? You chose {}".format(self.deviation))
if self.very_fast and self.num_models > 1:
self.run.warning("Since you chose --very-fast, there will be little difference, if at all, between models. You \
can potentially save a lot of time by setting --num-models to 1.")
if self.percent_identical_cutoff <= 20:
self.run.warning("Two completely unrelated sequences of same length can expect to have around 10% proper \
percent identicalness... Having this parameter below 20% is probably a bad idea.")
def sanity_check(self):
A = lambda x, t: t(args.__dict__[x]) if x in self.args.__dict__ else None
null = lambda x: x
# the directory files will be dumped into (can exist but must be empty)
if filesnpaths.is_file_exists(self.directory, dont_raise=True):
filesnpaths.is_output_dir_writable(self.directory)
if not filesnpaths.is_dir_empty(self.directory):
raise ModellerError("You cannot give MODELLER a non-empty directory to work in.")
else:
filesnpaths.gen_output_directory(self.directory)
# All MODELLER scripts are housed in self.script_folder
self.scripts_folder = J(os.path.dirname(anvio.__file__), 'data/misc/MODELLER/scripts')
if utils.filesnpaths.is_dir_empty(self.scripts_folder):
raise ConfigError("Anvi'o houses all its MODELLER scripts in {}, but your directory \
contains no scripts. Why you do dat?")
# check that MODELLER exists
if self.args.__dict__['modeller_executable'] if 'modeller_executable' in self.args.__dict__ else None:
self.run.info_single("As per your request, anvi'o will use `%s` to run MODELLER." % self.executable, nl_before=1)
utils.is_program_exists(self.executable)
else:
try:
utils.is_program_exists(self.executable)
except ConfigError as e:
raise ConfigError("Anvi'o needs a MODELLER program to be installed on your system. You didn't specify one\
(which can be done with `--modeller-executable`), so anvi'o tried the most recent version\
it knows about: '%s'. If you are certain you have it on your system (for instance you can run it\
by typing '%s' in your terminal window), you may want to send a detailed bug report. If you\
don't have it on your system, check out these installation instructions on our website:\
http://merenlab.org/2016/06/18/installing-third-party-software/#modeller" % (self.executable, self.executable))
self.run.info_single("Anvi'o found the default executable for MODELLER, `%s`, and will\
use it." % self.executable, nl_before=1)
self.is_executable_a_MODELLER_program()
# does target_fasta_path point to a fasta file?
utils.filesnpaths.is_file_fasta_formatted(self.target_fasta_path)
# make sure target_fasta is valid
target_fasta = u.SequenceSource(self.target_fasta_path, lazy_init=False)
if target_fasta.total_seq != 1:
raise ConfigError("MODELLER::The input FASTA file must have exactly one sequence.\
You provided one with {}.".format(target_fasta.total_seq))
# (not sanity check but we get self.corresponding_gene_call since target_fasta is opened)
while next(target_fasta):
self.corresponding_gene_call = target_fasta.id
target_fasta.close()
# parameter consistencies
if self.deviation < 0.5 or self.deviation > 20:
self.run.warning("You realize that deviation is given in angstroms, right? You chose {}".format(self.deviation))
if self.very_fast and self.num_models > 1:
self.run.warning("Since you chose --very-fast, there will be little difference, if at all, between models. You \
can potentially save a lot of time by setting --num-models to 1.")
if self.percent_identical_cutoff <= 20:
self.run.warning("Two completely unrelated sequences of same length can expect to have around 10% proper \
percent identicalness... Having this parameter below 20% is probably a bad idea.")