def check_options(self, supply=[]):
if (options().reference_pkg is not None):
self.load_reference(os.path.join(options().reference.path, 'refpkg/%s.refpkg/' % options().reference_pkg))
if (options().taxonomy_file is None):
supply = supply + ["taxonomy file"]
if (options().taxonomy_name_mapping_file is None):
supply = supply + ["taxonomy name mapping file"]
ExhaustiveAlgorithm.check_options(self, supply)
def check_options(self):
options().info_file = "A_dummy_value"
if options().tree_file is None or options().alignment_file is None:
_LOG.error("Specify the backbone alignment and tree and query sequences")
exit(-1)
sequences = MutableAlignment()
sequences.read_file_object(open(self.options.alignment_file.name))
return ExhaustiveAlgorithm.check_options(self)
def check_options(self):
options().info_file = "A_dummy_value"
#Check to see if tree/alignment/fragment file provided, if not, generate it
#from sequence file
if not options().tree_file is None and not options().alignment_file is None and not options().sequence_file is None:
options().fragment_file = options().sequence_file
elif options().tree_file is None and options().alignment_file is None and not options().sequence_file is None:
self.generate_backbone()
else:
_LOG.error("Either specify the backbone alignment and tree and query sequences or only the query sequences. Any other combination is invalid")
exit(-1)
sequences = MutableAlignment()
sequences.read_file_object(open(self.options.alignment_file.name))
backbone_size = sequences.get_num_taxa()
if options().backbone_size is None:
options().backbone_size = backbone_size
assert options().backbone_size == backbone_size, ("Backbone parameter needs to match actual size of backbone; backbone parameter:%s backbone_size:%s"
%(options().backbone_size, backbone_size))
if options().placement_size is None:
options().placement_size = options().backbone_size
return ExhaustiveAlgorithm.check_options(self)
def check_options(self):
options().info_file = "A_dummy_value"
#Check to see if tree/alignment/fragment file provided, if not, generate it
#from sequence file
if not options().tree_file is None and not options().alignment_file is None and not options().sequence_file is None:
options().fragment_file = options().sequence_file
elif options().tree_file is None and options().alignment_file is None and not options().sequence_file is None:
self.generate_backbone()
else:
_LOG.error("Either specify the backbone alignment and tree and query sequences or only the query sequences. Any other combination is invalid")
exit(-1)
sequences = MutableAlignment()
sequences.read_file_object(open(self.options.alignment_file.name))
backbone_size = sequences.get_num_taxa()
if options().backbone_size is None:
options().backbone_size = backbone_size
assert options().backbone_size == backbone_size, ("Backbone parameter needs to match actual size of backbone; backbone parameter:%s backbone_size:%s"
%(options().backbone_size, backbone_size))
if options().placement_size is None:
options().placement_size = options().backbone_size
if options().alignment_size is None:
_LOG.info("Alignment subset size not given. Calculating subset size. ")
alignment = MutableAlignment()
alignment.read_file_object(open(self.options.alignment_file.name))
if (options().molecule == 'amino'):
_LOG.warning("Automated alignment subset selection not implemented for protein alignment. Setting to 10.")
options().alignment_size = 10
else:
(averagep,maxp) = alignment.get_p_distance()
align_size = 10
if (averagep > .60):
while (align_size*2 < alignment.get_num_taxa()):
align_size = align_size * 2
_LOG.info("Average p-distance of backbone is %f0.2. Alignment subset size set to %d. " % (averagep,align_size))
options().alignment_size = align_size
return ExhaustiveAlgorithm.check_options(self)
def check_options(self):
self.check_outputprefix()
options().info_file = "A_dummy_value"
# Check to see if tree/alignment/fragment file provided, if not,
# generate it from sequence file
if (
(not options().tree_file is None) and
(not options().alignment_file is None) and
(not options().sequence_file is None)
):
options().fragment_file = options().sequence_file
elif (
(options().tree_file is None) and
(options().alignment_file is None) and
(not options().sequence_file is None)
):
self.generate_backbone()
else:
_LOG.error(
("Either specify the backbone alignment and tree and query "
"sequences or only the query sequences. Any other "
"combination is invalid"))
exit(-1)
sequences = MutableAlignment()
sequences.read_file_object(open(self.options.alignment_file.name))
backbone_size = sequences.get_num_taxa()
if options().backbone_size is None:
options().backbone_size = backbone_size
assert options().backbone_size == backbone_size, (
("Backbone parameter needs to match actual size of backbone; "
"backbone parameter:%s backbone_size:%s")
% (options().backbone_size, backbone_size))
if options().placement_size is None:
options().placement_size = options().backbone_size
return ExhaustiveAlgorithm.check_options(self)
def check_options(self, supply=[]):
if (options().taxonomy_file is None):
supply = supply + ["taxonomy file"]
if (options().taxonomy_name_mapping_file is None):
supply = supply + ["taxonomy name mapping file"]
ExhaustiveAlgorithm.check_options(self, supply)
