def make_tree(self, user_path):
# Begin by making a filtered alignment, containing ONLY those columns
# that are defined in the subsets
subset_with_everything = subset.Subset(*list(self.cfg.partitions))
self.filtered_alignment = SubsetAlignment(self.alignment,
subset_with_everything)
self.filtered_alignment_path = os.path.join(self.cfg.start_tree_path,
'filtered_source.phy')
self.filtered_alignment.write(self.filtered_alignment_path)
# Now we've written this alignment, we need to lock everything in
# place, no more adding partitions, or changing them from now on.
self.cfg.partitions.check_against_alignment(self.alignment)
self.cfg.partitions.finalise()
# We start by copying the alignment
self.alignment_path = os.path.join(self.cfg.start_tree_path,
'source.phy')
# Now check for the tree
tree_path = self.cfg.processor.make_tree_path(
self.filtered_alignment_path)
if self.need_new_tree(tree_path) == True:
log.debug("Estimating new starting tree, no old tree found")
# If we have a user tree, then use that, otherwise, create a topology
util.clean_out_folder(self.cfg.start_tree_path,
keep=["filtered_source.phy", "source.phy"])
if user_path is not None and user_path != "":
# Copy it into the start tree folder
log.info("Using user supplied topology at %s", user_path)
topology_path = os.path.join(self.cfg.start_tree_path,
'user_topology.phy')
self.cfg.processor.dupfile(user_path, topology_path)
else:
log.debug("didn't find tree at %s, making a new one" %
tree_path)
topology_path = self.cfg.processor.make_topology(
self.filtered_alignment_path, self.cfg.datatype,
self.cfg.cmdline_extras)
# Now estimate branch lengths
tree_path = self.cfg.processor.make_branch_lengths(
self.filtered_alignment_path, topology_path, self.cfg.datatype,
self.cfg.cmdline_extras)
self.tree_path = tree_path
log.info("Starting tree with branch lengths is here: %s",
self.tree_path)
def make_tree(self, user_path):
# Begin by making a filtered alignment, containing ONLY those columns
# that are defined in the subsets
subset_with_everything = subset_ops.merge_subsets(self.cfg.user_subsets)
self.filtered_alignment = SubsetAlignment(
self.alignment, subset_with_everything)
self.filtered_alignment_path = os.path.join(
self.cfg.start_tree_path, 'filtered_source.phy')
self.filtered_alignment.write(self.filtered_alignment_path)
# Now we've written this alignment, we need to lock everything in
# place, no more adding partitions, or changing them from now on.
# TODO: This checking should still be done...
# self.cfg.partitions.check_against_alignment(self.alignment)
# self.cfg.partitions.finalise()
# We start by copying the alignment
self.alignment_path = os.path.join(
self.cfg.start_tree_path, 'source.phy')
# Now check for the tree
tree_path = self.cfg.processor.make_tree_path(
self.filtered_alignment_path)
if self.need_new_tree(tree_path):
log.debug("Estimating new starting tree, no old tree found")
# If we have a user tree, then use that, otherwise, create a topology
util.clean_out_folder(self.cfg.start_tree_path,
keep=["filtered_source.phy", "source.phy"])
if user_path is not None and user_path != "":
# Copy it into the start tree folder
log.info("Using user supplied topology at %s", user_path)
topology_path = os.path.join(self.cfg.start_tree_path, 'user_topology.phy')
self.cfg.processor.dupfile(user_path, topology_path)
else:
log.debug(
"didn't find tree at %s, making a new one" % tree_path)
topology_path = self.cfg.processor.make_topology(
self.filtered_alignment_path, self.cfg.datatype, self.cfg.cmdline_extras)
# Now estimate branch lengths
tree_path = self.cfg.processor.make_branch_lengths(
self.filtered_alignment_path,
topology_path,
self.cfg.datatype,
self.cfg.cmdline_extras)
self.tree_path = tree_path
log.info("Starting tree with branch lengths is here: %s", self.tree_path)
def make_tree(self, user_path):
# Begin by making a filtered alignment, containing ONLY those columns
# that are defined in the subsets
subset_with_everything = subset_ops.merge_subsets(
the_config.user_subsets)
self.filtered_alignment = SubsetAlignment(self.alignment,
subset_with_everything)
self.filtered_alignment_path = os.path.join(the_config.start_tree_path,
'filtered_source.phy')
self.filtered_alignment.write(self.filtered_alignment_path)
# Check the full subset against the alignment
subset_ops.check_against_alignment(subset_with_everything,
self.alignment, the_config)
# We start by copying the alignment
self.alignment_path = os.path.join(the_config.start_tree_path,
'source.phy')
# Now check for the tree
tree_path = the_config.processor.make_tree_path(
self.filtered_alignment_path)
if self.need_new_tree(tree_path):
log.debug("Estimating new starting tree, no old tree found")
# If we have a user tree, then use that, otherwise, create a topology
util.clean_out_folder(the_config.start_tree_path,
keep=["filtered_source.phy", "source.phy"])
if user_path is not None and user_path != "":
# Copy it into the start tree folder
log.info("Using user supplied topology at %s" % user_path)
topology_path = os.path.join(the_config.start_tree_path,
'user_topology.phy')
util.dupfile(user_path, topology_path)
need_bl = True
elif the_config.no_ml_tree == True:
log.debug("didn't find tree at %s, making a new one" %
tree_path)
topology_path = the_config.processor.make_topology(
self.filtered_alignment_path, the_config.datatype,
the_config.cmdline_extras)
need_bl = True
elif the_config.no_ml_tree == False:
log.debug(
"didn't find tree at %s, making an ML tree with RAxML" %
tree_path)
tree_scheme = scheme.create_scheme(
the_config, "tree_scheme",
range(len(the_config.user_subsets)))
topology_path = raxml.make_ml_topology(
self.filtered_alignment_path, the_config.datatype,
the_config.cmdline_extras, tree_scheme, self.threads)
# here we copy the ML tree topology so it can be used with PhyML too
# TODO: this is a hack, and it would be better to decide on a universal
# name for the different types of tree we might have.
phyml_tree = os.path.join(
os.path.dirname(topology_path),
"filtered_source.phy_phyml_tree.txt")
copyfile(topology_path, phyml_tree)
need_bl = False
if need_bl == True:
# Now estimate branch lengths
tree_path = the_config.processor.make_branch_lengths(
self.filtered_alignment_path, topology_path,
the_config.datatype, the_config.cmdline_extras)
self.tree_path = tree_path
log.debug("Starting tree with branch lengths is here: %s" %
self.tree_path)
def make_tree(self, user_path):
# Begin by making a filtered alignment, containing ONLY those columns
# that are defined in the subsets
subset_with_everything = subset_ops.merge_subsets(the_config.user_subsets)
self.filtered_alignment = SubsetAlignment(
self.alignment, subset_with_everything)
self.filtered_alignment_path = os.path.join(
the_config.start_tree_path, 'filtered_source.phy')
self.filtered_alignment.write(self.filtered_alignment_path)
# Check the full subset against the alignment
subset_ops.check_against_alignment(subset_with_everything, self.alignment, the_config)
# We start by copying the alignment
self.alignment_path = os.path.join(
the_config.start_tree_path, 'source.phy')
# Now check for the tree
tree_path = the_config.processor.make_tree_path(
self.filtered_alignment_path)
if self.need_new_tree(tree_path):
log.debug("Estimating new starting tree, no old tree found")
# If we have a user tree, then use that, otherwise, create a topology
util.clean_out_folder(the_config.start_tree_path,
keep=["filtered_source.phy", "source.phy"])
if user_path is not None and user_path != "":
# Copy it into the start tree folder
log.info("Using user supplied topology at %s" % user_path)
topology_path = os.path.join(the_config.start_tree_path, 'user_topology.phy')
util.dupfile(user_path, topology_path)
need_bl = True
elif the_config.no_ml_tree == True:
log.debug(
"didn't find tree at %s, making a new one" % tree_path)
topology_path = the_config.processor.make_topology(
self.filtered_alignment_path, the_config.datatype, the_config.cmdline_extras)
need_bl = True
elif the_config.no_ml_tree == False:
log.debug(
"didn't find tree at %s, making an ML tree with RAxML" % tree_path)
tree_scheme = scheme.create_scheme(
the_config, "tree_scheme", range(len(the_config.user_subsets)))
topology_path = raxml.make_ml_topology(
self.filtered_alignment_path, the_config.datatype, the_config.cmdline_extras, tree_scheme, self.threads)
# here we copy the ML tree topology so it can be used with PhyML too
# TODO: this is a hack, and it would be better to decide on a universal
# name for the different types of tree we might have.
phyml_tree = os.path.join(os.path.dirname(topology_path), "filtered_source.phy_phyml_tree.txt")
copyfile(topology_path, phyml_tree)
need_bl = False
if need_bl == True:
# Now estimate branch lengths
tree_path = the_config.processor.make_branch_lengths(
self.filtered_alignment_path,
topology_path,
the_config.datatype,
the_config.cmdline_extras)
self.tree_path = tree_path
log.debug("Starting tree with branch lengths is here: %s" %
self.tree_path)