def _serialize_to_link(link_, identifier=DEFAULT_IDENTIFIER):
identifier = utils._check_identifier(identifier)
try:
if isinstance(link_, dict):
link_dict = copy.deepcopy(link_)
utils._remove_common_edge_fields(link_dict)
defined_fields = [ \
link_['from_node'], \
link_['from_orn'], \
link_['to_node'], \
link_['to_orn'], \
link_['alignment'] \
]
fields = ["L"]
fields.append(str(link_['from_node']))
fields.append(str(link_['from_orn']))
fields.append(str(link_['to_node']))
fields.append(str(link_['to_orn']))
if fv.is_gfa1_cigar(link_['alignment']):
fields.append(str(link_['alignment']))
else:
fields.append("*")
if not link_['eid'] in (None, '*'):
fields.append("ID:Z:" + str(link_['eid']))
fields.extend(utils._serialize_opt_fields(link_dict))
else:
defined_fields = [ \
link_.from_node, \
link_.from_orn, \
link_.to_node, \
link_.to_orn, \
link_.alignment \
]
fields = ["L"]
fields.append(str(link_.from_node))
fields.append(str(link_.from_orn))
fields.append(str(link_.to_node))
fields.append(str(link_.to_orn))
if fv.is_gfa1_cigar(link_.alignment):
fields.append(str(link_.alignment))
else:
fields.append("*")
if not link_.eid in (None, '*'):
fields.append("ID:Z:" + str(link_.eid))
fields.extend(utils._serialize_opt_fields(link_.opt_fields))
if not utils._are_fields_defined(defined_fields) or \
not utils._check_fields(fields[1:], LINK_FIELDS):
raise GFA1SerializationError()
return str.join("\t", fields)
except (KeyError, AttributeError, GFA1SerializationError) as e:
serializer_logger.debug(utils._format_exception(identifier, e))
return ""
def _serialize_to_fragment(fragment_, identifier=DEFAULT_IDENTIFIER):
identifier = utils._check_identifier(identifier)
try:
if isinstance(fragment_, dict):
fragment_dict = copy.deepcopy(fragment_)
utils._remove_common_edge_fields(fragment_dict)
defined_fields = [\
fragment_['from_node'], \
fragment_['to_node'], \
fragment_['to_orn'], \
fragment_['from_positions'][0], \
fragment_['from_positions'][1], \
fragment_['to_positions'][0], \
fragment_['to_positions'][1], \
fragment_['alignment'] \
]
fields = ["F"]
fields.append(str(fragment_['from_node']))
fields.append(str(fragment_['to_node']) + str(fragment_['to_orn']))
fields.append(str(fragment_['from_positions'][0]))
fields.append(str(fragment_['from_positions'][1]))
fields.append(str(fragment_['to_positions'][0]))
fields.append(str(fragment_['to_positions'][1]))
fields.append(str(fragment_['alignment']))
fields.extend(utils._serialize_opt_fields(fragment_dict))
else:
defined_fields = [\
fragment_.from_node, \
fragment_.to_node, \
fragment_.to_orn, \
fragment_.from_positions[0], \
fragment_.from_positions[1], \
fragment_.to_positions[0], \
fragment_.to_positions[1], \
fragment_.alignment \
]
fields = ["F"]
fields.append(str(fragment_.from_node))
fields.append(str(fragment_.to_node) + str(fragment_.to_orn))
fields.append(str(fragment_.from_positions[0]))
fields.append(str(fragment_.from_positions[1]))
fields.append(str(fragment_.to_positions[0]))
fields.append(str(fragment_.to_positions[1]))
fields.append(str(fragment_.alignment))
fields.extend(utils._serialize_opt_fields(fragment_.opt_fields))
if not utils. _are_fields_defined(defined_fields) or \
not utils._check_fields(fields[1:], FRAGMENT_FIELDS):
raise GFA2SerializationError("Required Fragment elements " \
+ "missing or invalid.")
return str.join("\t", fields)
except (KeyError, AttributeError, GFA2SerializationError) as e:
serializer_logger.debug(utils._format_exception(identifier, e))
return ""
def _serialize_to_gap(gap_, identifier=DEFAULT_IDENTIFIER):
identifier = utils._check_identifier(identifier)
try:
if isinstance(gap_, dict):
gap_dict = copy.deepcopy(gap_)
utils._remove_common_edge_fields(gap_dict)
defined_fields = [\
gap_['eid'], \
gap_['from_node'], \
gap_['from_orn'], \
gap_['to_node'], \
gap_['to_orn'], \
gap_['distance'], \
gap_['variance'] \
]
fields = ["G"]
fields.append(str(gap_['eid']))
fields.append(str(gap_['from_node']) + str(gap_['from_orn']))
fields.append(str(gap_['to_node']) + str(gap_['to_orn']))
fields.append(str(gap_['distance']))
fields.append(str(gap_['variance']))
fields.extend(utils._serialize_opt_fields(gap_dict))
return str.join("\t", fields)
else:
defined_fields = [\
gap_.eid, \
gap_.from_node, \
gap_.from_orn, \
gap_.to_node, \
gap_.to_orn, \
gap_.distance, \
gap_.variance \
]
fields = ["G"]
fields.append(str(gap_.eid))
fields.append(str(gap_.from_node) + str(gap_.from_orn))
fields.append(str(gap_.to_node) + str(gap_.to_orn))
fields.append(str(gap_.distance))
fields.append(str(gap_.variance))
fields.extend(utils._serialize_opt_fields(gap_.opt_fields))
if not utils. _are_fields_defined(defined_fields) or \
not utils._check_fields(fields[1:], GAP_FIELDS):
raise GFA2SerializationError("Required Gap elements " \
+ "missing or invalid.")
return str.join("\t", fields)
except (AttributeError, KeyError, GFA2SerializationError) as e:
serializer_logger.debug(utils._format_exception(identifier, e))
return ""
def _serialize_to_containment(containment_, identifier=DEFAULT_IDENTIFIER):
identifier = utils._check_identifier(identifier)
try:
if isinstance(containment_, dict):
containment_dict = copy.deepcopy(containment_)
utils._remove_common_edge_fields(containment_dict)
containment_dict.pop('pos')
defined_fields = [ \
containment_['from_node'], \
containment_['from_orn'], \
containment_['to_node'], \
containment_['to_orn'], \
containment_['alignment'], \
containment_['pos'].value
]
fields = ["C"]
fields.append(str(containment_['from_node']))
fields.append(str(containment_['from_orn']))
fields.append(str(containment_['to_node']))
fields.append(str(containment_['to_orn']))
fields.append(str(containment_['pos'].value))
if fv.is_gfa1_cigar(containment_['alignment']):
fields.append(str(containment_['alignment']))
else:
fields.append("*")
if not containment_['eid'] in (None, '*'):
fields.append("ID:Z:" + str(containment_['eid']))
fields.extend(utils._serialize_opt_fields(containment_dict))
else:
defined_fields = [ \
containment_.from_node, \
containment_.from_orn, \
containment_.to_node, \
containment_.to_orn, \
containment_.alignment, \
containment_.opt_fields['pos'].value \
]
fields = ["C"]
opt_fields = copy.deepcopy(containment_.opt_fields)
opt_fields.pop('pos')
fields.append(str(containment_.from_node))
fields.append(str(containment_.from_orn))
fields.append(str(containment_.to_node))
fields.append(str(containment_.to_orn))
fields.append(str(containment_.opt_fields['pos'].value))
if fv.is_gfa1_cigar(containment_.alignment):
fields.append(str(containment_.alignment))
else:
fields.append("*")
if not containment_.eid in (None, '*'):
fields.append("ID:Z:" + str(containment_.eid))
fields.extend(utils._serialize_opt_fields(opt_fields))
if not utils._are_fields_defined(defined_fields) or \
not utils._check_fields(fields[1:], CONTAINMENT_FIELDS):
raise GFA1SerializationError()
return str.join("\t", fields)
except (KeyError, AttributeError, GFA1SerializationError) as e:
serializer_logger.debug(utils._format_exception(identifier, e))
return ""