def loadPair( self, seq1, seq2 ):
temp_mali = Mali.Mali()
temp_mali.addSequence( "seq1", 0, len(seq1), seq1 )
temp_mali.addSequence( "seq2", 0, len(seq2), seq2 )
try:
self.mResult = self.mBaseml.Run( temp_mali,
tree = "(seq1,seq2);",
dump = self.mDump,
test = self.mTest )
except WrapperCodeML.UsageError:
self.mResult = None
def Run(self, mali, tree=None, dump=0, test=False, options={}):
self.mTempdir = tempfile.mkdtemp()
self.mFilenameInput = "input"
self.mFilenameOutput = "output"
if test:
print "# temporary directory is %s" % self.mTempdir
mali.writeToFile(open(self.mTempdir + "/" + self.mFilenameInput, "w"),
format="fasta")
statement = " ".join((self.mExecutable, "-in %s" % self.mFilenameInput,
"-out %s" % self.mFilenameOutput))
s = subprocess.Popen(statement,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
cwd=self.mTempdir,
close_fds=True)
(out, err) = s.communicate()
if s.returncode != 0:
raise UsageError, "Error in running %s \n%s\n%s\nTemporary directory in %s" % (
self.mExecutable, err, out, self.mTempdir)
if dump:
print "# stdout output of %s:\n%s\n######################################" % (
self.mExecutable, out)
result = Mali.Mali()
result.readFromFile(open(
"%s/%s" % (self.mTempdir, self.mFilenameOutput), "r"),
format="fasta")
if not test:
shutil.rmtree(self.mTempdir)
return result
def create( self, infile ):
"""create profile library from file."""
self.mOutfileDatabase = open( self.mFilenameProfiles, "wb" )
outfile_index = open( self.mFilenameIndex, "w" )
ninput, noutput = 0, 0
while mali.readFromFile( sys.stdin, format="profile" ):
ninput += 1
m = Mali.convertMali2Alignlib( mali )
p = alignlib.makeProfile( m )
p.prepare()
self.add( mali.getName(), p )
noutput += 1
return ninput, noutput
def verify( self, infile ):
"""verify data in database against original data."""
if not self.mIndex: self.__loadIndex()
ninput, nfound, nnotfound, ndifferent = 0,0,0,0
while mali.readFromFile( sys.stdin, format="profile" ):
ninput += 1
m = Mali.convertMali2Alignlib( mali )
p1 = alignlib.makeProfile( m )
p1.prepare()
p2 = self.getProfile( mali.getName() )
if p1.getLength() != p2.getLength() or \
str(p1) != str(p2):
ndifferent += 1
continue
nfound += 1
return ninput, nfound, nnotfound, ndifferent
parser.add_option("-w", "--weightor", dest="weightor", type="choice",
choices=("none", "Henikoff", "HenikoffKimmen" ),
help="sequence weightor to choose." )
parser.set_defaults( prefix = "profiles",
action = "create",
weightor = None,
source = None,
)
(options, args) = Experiment.Start( parser )
#--------------------------------------------------------
# main part of script
mali = Mali.Mali()
if options.action in ("create", "merge", "extract" ):
mode = "w"
else:
mode = "r"
plib = ProfileLibrary( options.prefix, mode )
plib.setWeightor( options.weightor )
if options.action == "verify":
ninput, nfound, nnotfound, ndifferent = plib.verify(sys.stdin)
if options.loglevel >= 1:
options.stdlog.write( "# verify: ninput=%i, nfound=%i, nnotfound=%i, ndifferent=%i\n" % (ninput, nfound, nnotfound, ndifferent))
elif options.action == "create":
