"LKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLV"
for alignment in ClustalIterator(StringIO(aln_example2 + aln_example1)):
print("Alignment with %i records of length %i" \
% (len(alignment),
alignment.get_alignment_length()))
print("Checking empty file...")
assert 0 == len(list(ClustalIterator(StringIO(""))))
print("Checking write/read...")
alignments = list(ClustalIterator(StringIO(aln_example1))) \
+ list(ClustalIterator(StringIO(aln_example2)))*2
handle = StringIO()
ClustalWriter(handle).write_file(alignments)
handle.seek(0)
for i, a in enumerate(ClustalIterator(handle)):
assert a.get_alignment_length() == alignments[i].get_alignment_length()
handle.seek(0)
print("Testing write/read when there is only one sequence...")
alignment = alignment[0:1]
handle = StringIO()
ClustalWriter(handle).write_file([alignment])
handle.seek(0)
for i, a in enumerate(ClustalIterator(handle)):
assert a.get_alignment_length() == alignment.get_alignment_length()
assert len(a) == 1
aln_example3 = \
"""CLUSTAL 2.0.9 multiple sequence alignment
print("Evil multiline non-interlaced example failed as expected")
handle.close()
handle = StringIO(phylip_text5a)
list5 = list(PhylipIterator(handle))
handle.close()
assert len(list5) == 1
assert len(list4[0]) == 5
print("Concatenation")
handle = StringIO(phylip_text4 + "\n" + phylip_text4)
assert len(list(PhylipIterator(handle))) == 2
handle = StringIO(phylip_text3 + "\n" + phylip_text4 + "\n\n\n" + phylip_text)
assert len(list(PhylipIterator(handle))) == 3
print("OK")
print("Checking write/read")
handle = StringIO()
PhylipWriter(handle).write_file(list5)
handle.seek(0)
list6 = list(PhylipIterator(handle))
assert len(list5) == len(list6)
for a1, a2 in zip(list5, list6):
assert len(a1) == len(a2)
for r1, r2 in zip(a1, a2):
assert r1.id == r2.id
assert str(r1.seq) == str(r2.seq)
print("Done")
elif isinstance(value, (int, float, basestring)):
attr = {"name": key, "value": str(value)}
self.xml_generator.startElement("property",
AttributesImpl(attr))
self.xml_generator.endElement("property")
if __name__ == "__main__":
print("Running quick self test")
from SAP.Bio import SeqIO
import sys
with open("Tests/SeqXML/protein_example.xml", "r") as fileHandle:
records = list(SeqIO.parse(fileHandle, "seqxml"))
from SAP.Bio._py3k import StringIO
stringHandle = StringIO()
SeqIO.write(records, stringHandle, "seqxml")
SeqIO.write(records, sys.stdout, "seqxml")
print("")
stringHandle.seek(0)
records = list(SeqIO.parse(stringHandle, "seqxml"))
SeqIO.write(records, sys.stdout, "seqxml")
print("")
def __str__(self):
from SAP.Bio._py3k import StringIO
handle = StringIO()
save(self, handle)
handle.seek(0)
return handle.read()
self.xml_generator.endElement("property")
elif isinstance(value, (int, float, basestring)):
attr = {"name": key, "value": str(value)}
self.xml_generator.startElement(
"property", AttributesImpl(attr))
self.xml_generator.endElement("property")
if __name__ == "__main__":
print("Running quick self test")
from SAP.Bio import SeqIO
import sys
with open("Tests/SeqXML/protein_example.xml", "r") as fileHandle:
records = list(SeqIO.parse(fileHandle, "seqxml"))
from SAP.Bio._py3k import StringIO
stringHandle = StringIO()
SeqIO.write(records, stringHandle, "seqxml")
SeqIO.write(records, sys.stdout, "seqxml")
print("")
stringHandle.seek(0)
records = list(SeqIO.parse(stringHandle, "seqxml"))
SeqIO.write(records, sys.stdout, "seqxml")
print("")
def __str__(self):
from SAP.Bio._py3k import StringIO
handle = StringIO()
save(self, handle)
handle.seek(0)
return handle.read()
