def test_condense_xml_entry(self):
#read in rawuniprotentry.xml
for entry in self.root:
refparse.condense_xml_entry(entry)
self.assertNotEqual(self.entry.find(UP+'accession'), None)
self.assertTrue(self.entry.find(UP+'accession').text not in [None, ''])
self.assertNotEqual(self.entry.find(UP+'name'), None)
self.assertTrue(self.entry.find(UP+'name').text not in [None, ''])
self.assertNotEqual(self.entry.find(UP+'protein').find(UP+'recommendedName').find(UP+'fullName'), None)
self.assertTrue(self.entry.find(UP+'protein').find(UP+'recommendedName').find(UP+'fullName').text not in [None, ''])
self.assertNotEqual(self.entry.find(UP+'organism'), None)
self.assertNotEqual(self.entry.find(UP+'proteinExistence'), None)
self.assertNotEqual(self.entry.find(UP+'proteinExistence').find(UP+'depth'), None)
self.assertNotEqual(self.entry.find(UP+'sequence'), None)
self.assertTrue(self.entry.find(UP+'sequence').text not in [None, ''])
except Exception, e:
print >> sys.stderr, "failed: %s" % e
exit(2)
#Reference XML/FASTA
ensembl, uniprot = None, None
if options.reference_xml != None:
try:
refXml = os.path.abspath(options.reference_xml)
refXml = open(refXml, 'r')
p = et.XMLParser(
remove_blank_text=True) #required for pretty additions
uniprot = et.parse(refXml, p)
uniprot_root = uniprot.getroot()
for entry in uniprot_root:
refparse.condense_xml_entry(entry)
except Exception, e:
print >> sys.stderr, "Parsing and/or condensing reference xml failed: %s" % e
exit(2)
else:
print >> sys.stderr, "failed: no UniProt reference protein database specified"
#Read the Ensembl fasta into an XML structure
if options.protein_fasta != None:
try:
refFasta = os.path.abspath(options.protein_fasta)
refFasta = open(refFasta, 'r')
ensembl_root = et.Element(UP + 'uniprot', nsmap=NAMESPACE_MAP)
ensembl = et.ElementTree(ensembl_root)
refparse.read_fasta_to_xml(
ensembl_root, refFasta) #TODO: singluarize the entry here
protein_fasta = open(protein_fasta, 'r')
protein_fasta = refparse.read_protein_fasta(protein_fasta)
except Exception, e:
print >> sys.stderr, "failed: %s" % e
exit(2)
#Reference XML/FASTA
if options.reference_xml != None:
try:
refXml = os.path.abspath(options.reference_xml)
refXml = open(refXml, 'r')
p = et.XMLParser(remove_blank_text=True) #required for pretty additions
db = et.parse(refXml, p)
root = db.getroot()
for entry in root:
refparse.condense_xml_entry(entry)
except Exception, e:
print >> sys.stderr, "Parsing and/or condensing reference xml failed: %s" % e
exit(2)
elif options.protein_fasta != None:
try:
refFasta = os.path.abspath(options.protein_fasta)
refFasta = open(refFasta, 'r')
root = et.Element(UP+'uniprot', nsmap=NAMESPACE_MAP)
db = et.ElementTree(root)
refparse.read_fasta_to_xml(root, refFasta)
except Exception, e:
print >> sys.stderr, "Parsing reference fasta failed: %s" %e
exit(2)
else:
print >> sys.stderr, "failed: no reference database specified"
