def clustal_to_phylip(src,dest=None):
import os
from Bio.AlignIO.ClustalIO import ClustalIterator
from Bio.AlignIO.PhylipIO import PhylipWriter
if dest==None:
dest = src
head,tail = os.path.split(dest)
_dest = os.path.join(head,"."+tail)
with open(src) as i:
alignments = list(ClustalIterator(i))
with open(_dest,"w") as f:
writer = PhylipWriter(f)
writer.write_file(alignments)
os.rename(_dest,dest)
return dest
def __init__(self, input, output=None):
self._itemp=None
self.output = output
if isinstance(input, str):
assert(os.path.exists(input))
self.input = input
elif isinstance(input, list):
from tempfile import NamedTemporaryFile
from Bio.AlignIO.PhylipIO import PhylipWriter
self._itemp = NamedTemporaryFile()
self.input = self._itemp.name
writer = PhylipWriter(self._itemp)
writer.write_alignment(input)
self._itemp.flush()
else:
raise Exception("Unknown input type",input)
def test_write_read(self):
handle = StringIO(phylip_text5a)
list5 = list(PhylipIterator(handle))
handle.close()
handle = StringIO()
PhylipWriter(handle).write_file(list5)
handle.seek(0)
list6 = list(PhylipIterator(handle))
self.assertEqual(len(list5), len(list6))
for a1, a2 in zip(list5, list6):
self.assertEqual(len(a1), len(a2))
for r1, r2 in zip(a1, a2):
self.assertEqual(r1.id, r2.id)
self.assertEqual(str(r1.seq), str(r2.seq))
def test_write_read(self):
path = "Phylip/six.dat"
with open(path) as handle:
list5 = list(PhylipIterator(handle))
handle = StringIO()
PhylipWriter(handle).write_file(list5)
handle.seek(0)
list6 = list(PhylipIterator(handle))
self.assertEqual(len(list5), len(list6))
for a1, a2 in zip(list5, list6):
self.assertEqual(len(a1), len(a2))
for r1, r2 in zip(a1, a2):
self.assertEqual(r1.id, r2.id)
self.assertEqual(r1.seq, r2.seq)
