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phylip.py
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import os
import subprocess
import numpy
from hpf.utilities import QueueParser
from tempfile import NamedTemporaryFile
from hpf.runtime import runtime
def interleave(file):
from StringIO import StringIO
modified = False
with open(file) as handle:
runtime().debug("interleave")
lines = handle.readlines()
if not lines[0].strip().split()[-1] == 'I':
lines[0] = lines[0].replace("\n"," I\n")
modified = True
if modified:
for line in lines[1:]:
line = line.replace(" \n","\n")
line = line.replace("X","-")
line = line.replace("Z","-")
if modified:
with open(file,"w") as handle:
map(handle.write,lines)
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
class DnadistOptions(object):
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 stdin(self):
from StringIO import StringIO
input = StringIO()
print >>input, "%s" % self.input
print >>input, "P"
print >>input, "P"
#print >>input, "2"
print >>input, "Y"
return input.getvalue()
def __del__(self):
for temp in [self._itemp]:
if temp:
temp.close()
class Dnadist(object):
def __init__(self, options):
self.options = options
def run(self):
temp = NamedTemporaryFile()
temp.write(self.options.stdin())
temp.flush()
cmd = "dnadist <%s >/dev/null" % (temp.name)
print cmd
subprocess.check_call(cmd, shell=True)
temp.close()
if self.options.output:
os.rename("outfile",self.options.output)
self.options.__del__()
with open(self.options.output if self.options.output else "outfile") as array:
return DistParser(array).parse().dict()
class ProtdistOptions(object):
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 stdin(self):
from StringIO import StringIO
input = StringIO()
print >>input, "%s" % self.input
print >>input, "P"
print >>input, "P"
#print >>input, "2"
print >>input, "Y"
return input.getvalue()
def __del__(self):
for temp in [self._itemp]:
if temp:
temp.close()
class Protdist(object):
def __init__(self, options):
self.options = options
def run(self):
temp = NamedTemporaryFile()
temp.write(self.options.stdin())
temp.flush()
cmd = "protdist <%s >/dev/null" % (temp.name)
print cmd
subprocess.check_call(cmd, shell=True)
temp.close()
if self.options.output:
os.rename("outfile",self.options.output)
self.options.__del__()
with open(self.options.output if self.options.output else "outfile") as array:
return DistParser(array).parse().dict()
class DistParser(QueueParser):
"""Parses Protdist outfiles into a float array with a dictionary for matching names to rows/columns"""
def __init__(self,handle):
QueueParser.__init__(self,handle)
self.n = int(self._get().strip())
self.array = numpy.zeros((self.n,self.n))
self.names = {}
self.i = 0
def next(self):
if self._finished():
raise StopIteration()
name = self._peek().split()[0]
self.names[self.i] = name
j = 0
while(j<self.n):
line = self._get()
for part in line.strip().split():
try:
value = float(part)
self.array[self.i,j] = value
j+=1
except ValueError:
assert(part==name)
self.i += 1
return (self.names[self.i-1],self.array[self.i-1])
def parse(self):
for res in self:
pass
return self
def dict(self):
d = {}
for i in self.names:
name1 = self.names[i]
for j in self.names:
name2 = self.names[j]
d[(name1,name2)] = self.array[i,j]
return d
class ProtparsOptions(object):
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 stdin(self):
from StringIO import StringIO
input = StringIO()
print >>input, "%s" % self.input
print >>input, "Y"
return input.getvalue()
def __del__(self):
for temp in [self._itemp]:
if temp:
temp.close()
class Protpars(object):
def __init__(self, options):
self.options = options
def run(self):
temp = NamedTemporaryFile()
temp.write(self.options.stdin())
temp.flush()
cmd = "protpars <%s >/dev/null" % (temp.name)
print cmd
subprocess.check_call(cmd, shell=True)
temp.close()
if self.options.output:
os.rename("outtree",self.options.output)
os.remove("outfile")
self.options.__del__()
class ConsenseOptions(object):
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 stdin(self):
from StringIO import StringIO
input = StringIO()
print >>input, "%s" % self.input
print >>input, "Y"
return input.getvalue()
def __del__(self):
for temp in [self._itemp]:
if temp:
temp.close()
class Consense(object):
def __init__(self, options):
self.options = options
def run(self):
temp = NamedTemporaryFile()
temp.write(self.options.stdin())
temp.flush()
cmd = "consense <%s >/dev/null" % (temp.name)
print cmd
subprocess.check_call(cmd, shell=True)
temp.close()
if self.options.output:
os.rename("outtree",self.options.output)
os.remove("outfile")
self.options.__del__()