def applicable(cls, target=None, coord=None):
if not coord or coord.sequence is None:
return
if target.msaview_classname != 'data.msa':
return
if target.sequence_information.get_entry('uniprot-id', coord.sequence):
return cls(target, coord)
if UniprotID.extract_id(target.ids[coord.sequence]):
return cls(target, coord)
def applicable(cls, target=None, coord=None):
if target.msaview_classname != 'data.msa':
return
if not target:
return
if target.sequence_information.has_category('uniprot-id'):
return cls(target, coord)
for id in target.ids:
if UniprotID.extract_id(id):
return cls(target, coord)
def run(self):
sequence_index = self.coord.sequence
id = self.target.sequence_information.setdefault('uniprot-id')[sequence_index]
if not id:
id = UniprotID.from_msa_sequence(self.target, sequence_index)
self.target.sequence_information.add_entries(id)
url = 'http://pfam.sanger.ac.uk/protein?output=xml&entry='
xml = urllib2.urlopen(url + id.sequence_id)
root = etree.parse(xml, NamespaceIgnorantXMLTreeBuilder()).getroot()
features = parse_pfam_protein_etree(root, self.target, sequence_index, id.sequence_id)
if features is None:
raise ValueError('the Pfam sequence does not match/contain the MSA sequence')
self.target.features.add_features(features)
def applicable(cls, target, coord=None):
if not coord or coord.sequence is None:
return
if target.msaview_classname != 'data.msa':
return
entry = target.sequence_information.get_entry('uniprot-id', coord.sequence)
if not entry:
entry = UniprotID.from_msa_sequence(target, coord.sequence)
if not entry.sequence_id:
return
a = cls(target, coord)
a.path = list(cls.path)
a.path[-1] %= entry.sequence_id
return a
def run(self):
sequence_index = self.coord.sequence
etree_category = self.target.sequence_information.setdefault('uniprot-etree')
etree_entry = etree_category[sequence_index]
if not etree_entry:
id_category = self.target.sequence_information.setdefault('uniprot-id')
id_entry = id_category[sequence_index]
if not id_entry:
id_entry = UniprotID.from_msa_sequence(self.target, self.coord.sequence)
self.target.sequence_information.add_entries(id_entry)
etree_entry = dbfetch_uniprot_xml_for_sequence(self.target, sequence_index)
self.target.sequence_information.add_entries(etree_entry)
structures_entry = PDBStructures.from_uniprot_etree(etree_entry)
self.target.sequence_information.setdefault('pdb-ids')
self.target.sequence_information.add_entries(structures_entry)
def applicable(cls, target, coord=None):
if not coord or coord.sequence is None:
return
if target.msaview_classname != 'data.msa':
return
etree_entry = target.sequence_information.get_entry('uniprot-etree', coord.sequence)
if etree_entry:
if etree_entry.root is None:
return
return cls(target, coord)
id_entry = target.sequence_information.get_entry('uniprot-id', coord.sequence)
if not id_entry:
id_entry = UniprotID.from_msa_sequence(target, coord.sequence)
if not id_entry.sequence_id:
return
return cls(target, coord)
