def run(self, pamlsrc, output_folder, model='M1'):
"""Run PAML using ETE.
The default model is M1 as it is best for orthology inference in
our case. You can use models `M2`, `M0`, `M3`.
Ensure that you have the correct path to your codeml binary. It should
be in the paml `/bin`.
:param pamlsrc: Path to the codemly binary.
:param output_folder: The name of the output folder.
:param model: The model to be used. (Default value = 'M1')
"""
# Import the newick tree
tree = EvolTree('temptree.nw')
# Import the alignment
tree.link_to_alignment(self.alignmentfile)
tree.workdir = self.workdir
# Set the binpath of the codeml binary
tree.execpath = pamlsrc
# Run the model M1, M2, M3, or M0
model_path = model + '.' + output_folder
tree.run_model(model_path)
self.ete3paml_log.info('Codeml is generating data in %s.' % model_path)
def main(self):
"""The main function for running the test."""
print("Running model %s paml on input." % str(self.defaultmodel))
tree = EvolTree(self.tree) # Import the newick tree
tree.link_to_alignment(self.alignment) # Import the alignment
tree.workdir = self.workdir # Set the working directory
tree.execpath = self.pamlpath # Set the binpath of the codeml binary
tree.run_model(self.defaultmodel) # Run the codeml model
def ete3paml(gene, paml_path, workdir='data/paml-output/', model='M1'):
""" Use ETE3's integration with PAML"""
# Import the species tree to compare species that are present in alignment
# file
t = Tree('data/initial-data/species_tree.nw', format=1)
orgsfile = pd.read_csv('data/initial-data/organisms.csv', header=None)
# Create a list name/variable and use list()
orgs = list(orgsfile[0])
organismslist = formatlist(orgs)
# Import alignment file as string
alignment_file = open(
'data/clustal-output/' + gene + '_Aligned/' + gene +
'_aligned_cds_nucl.fasta', 'r')
alignment_str = alignment_file.read()
alignment_file.close()
# Keep the branches in the species tree for species in the alignment file
# Some species may not be present in the alignment file
branches2keep = []
for organism in organismslist:
if organism in alignment_str:
#print('Yup.')
branches2keep.append(organism)
else:
pass
#print('Nope.') Make an error code in the log
# Input a list of branches to keep on the base tree
speciestree = t.prune(branches2keep, preserve_branch_length=True)
# Import the newick tree
tree = EvolTree(speciestree)
# Import the alignment
tree.link_to_alignment('data/clustal-output/' + gene + '_Aligned/' + gene +
'_aligned_cds_nucl.fasta')
tree.workdir = workdir
# Set the binpath of the codeml binary
tree.execpath = paml_path
# Run the codeml model
tree.run_model(model + '.' + gene)
