def test_sequence_conversion(self):
pseq = PX.Sequence(
type="protein",
# id_ref=None,
# id_source=None,
symbol="ADHX",
accession=PX.Accession("P81431", source="UniProtKB"),
name="Alcohol dehydrogenase class-3",
# location=None,
mol_seq=PX.MolSeq(
"TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD"),
uri=None,
annotations=[
PX.Annotation(ref="EC:1.1.1.1"),
PX.Annotation(ref="GO:0004022")
],
domain_architecture=PX.DomainArchitecture(
length=50,
domains=[
PX.ProteinDomain(*args) for args in (
# value, start, end, confidence
("FOO", 0, 5, 7.0e-26),
("BAR", 8, 13, 7.2e-117),
("A-OK", 21, 34, 2.4e-06),
("WD40", 40, 50, 0.3))
],
))
srec = pseq.to_seqrecord()
# TODO: check seqrec-specific traits (see args)
# Seq(letters, alphabet), id, name, description, features
pseq2 = PX.Sequence.from_seqrecord(srec)
def test_sequence_conversion(self):
pseq = PX.Sequence(
type='protein',
# id_ref=None,
# id_source=None,
symbol='ADHX',
accession=PX.Accession('P81431', source='UniProtKB'),
name='Alcohol dehydrogenase class-3',
# location=None,
mol_seq=PX.MolSeq(
'TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD'),
uri=None,
annotations=[
PX.Annotation(ref='EC:1.1.1.1'),
PX.Annotation(ref='GO:0004022')
],
domain_architecture=PX.DomainArchitecture(
length=50,
domains=[
PX.ProteinDomain(*args) for args in (
# value, start, end, confidence
('FOO', 0, 5, 7.0e-26),
('BAR', 8, 13, 7.2e-117),
('A-OK', 21, 34, 2.4e-06),
('WD40', 40, 50, 0.3))
],
))
srec = pseq.to_seqrecord()
# TODO: check seqrec-specific traits (see args)
# Seq(letters, alphabet), id, name, description, features
pseq2 = PX.Sequence.from_seqrecord(srec)
def annotation(self, elem):
return PX.Annotation(
desc=_collapse_wspace(_get_child_text(elem, 'desc')),
confidence=_get_child_as(elem, 'confidence', self.confidence),
properties=_get_children_as(elem, 'property', self.property),
uri=_get_child_as(elem, 'uri', self.uri),
**elem.attrib)
def annotation(self, elem):
"""Create annotation object."""
return PX.Annotation(
desc=_collapse_wspace(_get_child_text(elem, "desc")),
confidence=_get_child_as(elem, "confidence", self.confidence),
properties=_get_children_as(elem, "property", self.property),
uri=_get_child_as(elem, "uri", self.uri),
**elem.attrib)
def main():
##################### get parser ###############################
parser = get_parser()
######## Print parser help if arguments missed #################
if len(sys.argv) == 1:
parser.print_help()
sys.exit(1)
########### Manage workflow accorded to Args ##################
Arguments = parser.parse_args()
# parser = etree.XMLParser(remove_blank_text=True)
# xmlfile = Arguments.xml
# tree = etree.ElementTree()
# tree =etree.parse(xmlfile,parser)
# print tree
# root = tree.getroot()
# print root
# test = root.xpath("phylogeny")
# print test
# for var in test :
# toto = var.findall("clade")[0]
# print toto.text
# print var
tree = Phylo.read("jpp2.xml", 'phyloxml')
for clade in tree.find_clades(name=True):
clade.other = [
PhyloXML.Other(tag="annotation",
namespace="",
children=[
PhyloXML.Other('desc', value='youpi'),
PhyloXML.Other('uri', value='http://lol.com')
])
]
clade.annotation = PhyloXML.Annotation(desc="youpi",
uri="http://lol.com")
Phylo.write(tree, "jpp.xml", 'phyloxml')
