def run_alignment(self, clean=True, consensus=True):
# dialign requires ENV variable be set for dialign_dir
mafft = which("mafft")
# create results file
fd, aln = tempfile.mkstemp(suffix='.mafft')
os.close(fd)
aln_stdout = open(aln, 'w')
# dialign makes an extra file for fasta output
#fasta = "{}.{}".format(aln, 'fa')
# run MUSCLE on the temp file
cmd = [mafft, "--auto", self.input]
# just pass all ENV params
proc = subprocess.Popen(cmd,
stderr=subprocess.PIPE,
stdout=aln_stdout
)
stderr = proc.communicate()
aln_stdout.close()
self.alignment = AlignIO.read(open(aln, 'rU'), "fasta", \
alphabet=Gapped(IUPAC.unambiguous_dna, "-"))
# build a dumb consensus
if consensus:
self.alignment_summary, self.alignment_consensus = \
self._alignment_summary(self.alignment)
# cleanup temp files
if clean:
self._clean(aln)
def run_alignment(self, clean=True, consensus=True):
# dialign requires ENV variable be set for dialign_dir
daln = which("dialign2-2")
daln = os.path.join(os.path.split(daln)[0], 'dialign2_dir')
os.environ["DIALIGN2_DIR"] = "/Users/bcf/Bin/dialign2_dir/"
# create results file
fd, aln = tempfile.mkstemp(suffix='.dialign')
os.close(fd)
# dialign makes an extra file for fasta output
fasta = "{}.{}".format(aln, 'fa')
# run MUSCLE on the temp file
cmd = ["dialign2-2", "-fa", "-fn", aln, "-n", self.input]
# just pass all ENV params
proc = subprocess.Popen(cmd,
stderr=subprocess.PIPE,
stdout=subprocess.PIPE,
env=os.environ
)
stdout, stderr = proc.communicate()
self.alignment = AlignIO.read(open(fasta, 'rU'), "fasta", \
alphabet=Gapped(IUPAC.unambiguous_dna, "-"))
# build a dumb consensus
if consensus:
self.alignment_summary, self.alignment_consensus = \
self._alignment_summary(self.alignment)
# cleanup temp files
if clean:
self._clean([aln, fasta])
def run_alignment(self, clean=True, consensus=True):
# dialign requires ENV variable be set for dialign_dir
daln = which("dialign2-2")
daln = os.path.join(os.path.split(daln)[0], 'dialign2_dir')
os.environ["DIALIGN2_DIR"] = "/Users/bcf/Bin/dialign2_dir/"
# create results file
fd, aln = tempfile.mkstemp(suffix='.dialign')
os.close(fd)
# dialign makes an extra file for fasta output
fasta = "{}.{}".format(aln, 'fa')
# run MUSCLE on the temp file
cmd = ["dialign2-2", "-fa", "-fn", aln, "-n", self.input]
# just pass all ENV params
proc = subprocess.Popen(cmd,
stderr=subprocess.PIPE,
stdout=subprocess.PIPE,
env=os.environ)
stdout, stderr = proc.communicate()
self.alignment = AlignIO.read(open(fasta, 'rU'), "fasta", \
alphabet=Gapped(IUPAC.unambiguous_dna, "-"))
# build a dumb consensus
if consensus:
self.alignment_summary, self.alignment_consensus = \
self._alignment_summary(self.alignment)
# cleanup temp files
if clean:
self._clean([aln, fasta])
def run_alignment(self, clean=True):
""" muscle """
# dialign requires ENV variable be set for dialign_dir
muscle = which("muscle")
# create results file
fd, aln = tempfile.mkstemp(suffix='.muscle')
os.close(fd)
# run MUSCLE on the temp file
cmd = [muscle, "-in", self.input, "-out", aln]
proc = subprocess.Popen(cmd,
stderr=subprocess.PIPE,
stdout=subprocess.PIPE)
stdout, stderr = proc.communicate()
self.alignment = AlignIO.read(open(aln, 'rU'), \
"fasta", alphabet=Gapped(IUPAC.unambiguous_dna, "-"))
# cleanup temp files
if clean:
self._clean(aln)
def run_alignment(self, clean=True):
""" muscle """
# dialign requires ENV variable be set for dialign_dir
muscle = which("muscle")
# create results file
fd, aln = tempfile.mkstemp(suffix='.muscle')
os.close(fd)
# run MUSCLE on the temp file
cmd = [muscle, "-in", self.input, "-out", aln]
proc = subprocess.Popen(cmd,
stderr=subprocess.PIPE,
stdout=subprocess.PIPE
)
stdout, stderr = proc.communicate()
self.alignment = AlignIO.read(open(aln, 'rU'), \
"fasta", alphabet=Gapped(IUPAC.unambiguous_dna, "-"))
# cleanup temp files
if clean:
self._clean(aln)
def run_alignment(self, clean=True):
mafft = which("mafft")
# create results file
fd, aln = tempfile.mkstemp(suffix='.mafft')
os.close(fd)
aln_stdout = open(aln, 'w')
# run MAFFT on the temp file
cmd = [mafft, "--adjustdirection", "--maxiterate", "1000", self.input]
# just pass all ENV params
proc = subprocess.Popen(cmd,
stderr=subprocess.PIPE,
stdout=aln_stdout
)
stderr = proc.communicate()
aln_stdout.close()
self.alignment = AlignIO.read(open(aln, 'rU'), "fasta", \
alphabet=Gapped(IUPAC.unambiguous_dna, "-"))
if clean:
self._clean(aln)
