def run(self, fname="codeml-input.txt"):
""" """
# CHECK FOR NECESSARY FILES (PHYLIP and NEWICK)
if os.path.isfile(self.seqfile) is False:
raise Exception(""" seqfile does not exist! """)
if os.path.isfile(self.treefile) is False:
raise Exception(""" treefile does not exist! """)
# Write out the control file
self.write(fname)
# Run a subprocess for codeml
run_subprocess("codeml", fname)
def run(self, fname="codeml-input.txt"):
""" """
# CHECK FOR NECESSARY FILES (PHYLIP and NEWICK)
if os.path.isfile(self.seqfile) is False:
raise Exception(""" seqfile does not exist! """)
if os.path.isfile(self.treefile) is False:
raise Exception(""" treefile does not exist! """)
# Write out the control file
self.write(fname)
# Run a subprocess for codeml
run_subprocess("codeml", fname)
def run(fname_prefix, dtype="aa", rm_tmp=True, *args, **kwargs):
""" Simple wrapper for running PhyML within Python.
Options
-------
b :
"""
# Create a temporary fasta file from homologs as input to PhyML.
# Build command array and run it.
phy_fname = "%s.phy" % fname_prefix
stats_fname = "%s.phy_phyml_stats.txt" % fname_prefix # Default name for output from phyml
tree_fname = "%s.phy_phyml_tree.txt" % fname_prefix # default name for output tree file
# Construct arguments for subprocess
stuff = ("-i", phy_fname, "-d", dtype)
stuff += args
run_subprocess("phyml", *stuff, **kwargs)
# Read the tree file and add to homologset.
with open(tree_fname, "r") as f:
tree = f.read()
# Read the stats file.
with open(stats_fname, "r") as f:
stats_string = f.read()
# Return stats.
stats = parse_phyml_stats(stats_string)
# Remove alignment files if you want to just keep homologs.
if rm_tmp:
os.remove(phy_fname)
return tree, stats
def run(fname_prefix, dtype="aa", rm_tmp=True, *args, **kwargs):
""" Simple wrapper for running PhyML within Python.
Options
-------
b :
"""
# Create a temporary fasta file from homologs as input to PhyML.
# Build command array and run it.
phy_fname = "%s.phy" % fname_prefix
stats_fname = "%s.phy_phyml_stats.txt" % fname_prefix # Default name for output from phyml
tree_fname = "%s.phy_phyml_tree.txt" % fname_prefix # default name for output tree file
# Construct arguments for subprocess
stuff = ("-i", phy_fname, "-d", dtype)
stuff += args
run_subprocess("phyml", *stuff, **kwargs)
# Read the tree file and add to homologset.
with open(tree_fname, "r") as f:
tree = f.read()
# Read the stats file.
with open(stats_fname, "r") as f:
stats_string = f.read()
# Return stats.
stats = parse_phyml_stats(stats_string)
# Remove alignment files if you want to just keep homologs.
if rm_tmp:
os.remove(phy_fname)
return tree, stats