def __init__(self, conv_cfg):
NexsonConverter.__init__(self, conv_cfg)
self._from_phylografter = conv_cfg.get('_from_phylografter', True)
if self._from_phylografter:
self._workaround_phylografter_rel_bug = True # pg uses "property" instead of "rel"
self._add_tree_xsi_type = True
self._coercing_literals = True # phylografter uses "true" for isLeaf
else:
self._workaround_phylografter_rel_bug = False
self._add_tree_xsi_type = False
def __init__(self, conv_cfg):
NexsonConverter.__init__(self, conv_cfg)
self.input_format = conv_cfg.input_format
self.use_default_root_atts = conv_cfg.get('use_default_root_atts', True)
self.otu_label = conv_cfg.get('otu_label', 'ot:originalLabel')
if self.otu_label.startswith('^'):
self.otu_label = self.otu_label[1:]
self._migrating_from_bf = _is_badgerfish_version(self.input_format)
# TreeBase and phylografter trees often lack the tree xsi:type
self._adding_tree_xsi_type = True
# we have started using ot:ottTaxonName, ot:originalLabel or ot:ottId
self._creating_otu_label = True
def __init__(self, conv_cfg):
NexsonConverter.__init__(self, conv_cfg)
self.suppress_label_if_ott_taxon = getattr(conv_cfg, 'suppress_label_if_ott_taxon', True)
def __init__(self, conv_cfg):
NexsonConverter.__init__(self, conv_cfg)
def __init__(self, conv_cfg):
NexsonConverter.__init__(self, conv_cfg)
self.output_format = conv_cfg.output_format
self._badgerfish_style_conversion = _is_badgerfish_version(conv_cfg.output_format)
def __init__(self, conv_cfg):
NexsonConverter.__init__(self, conv_cfg)
self.remove_old_structs = getattr(conv_cfg, 'remove_old_structs', True)
def __init__(self, conv_cfg):
NexsonConverter.__init__(self, conv_cfg)
self.remove_old_structs = getattr(conv_cfg, 'remove_old_structs', True)
