def test_consensus(self):
# create a list of trees and make a consensus
phylogenies = [self.phylo for i in range(100)]
with open('distribution.tre', 'w') as file:
Phylo.write(phylogenies, file, 'newick')
ptools.consensus(outdir='.', min_freq=0.5,
is_rooted=True, trees_splits_encoded=False)
self.assertTrue(os.path.isfile('consensus.tre'))
def run(wd=os.getcwd(), logger=logging.getLogger('')):
# PRINT STAGE
logger.info("Stage 4: Phylogeny generation")
# DIRS
alignment_dir = os.path.join(wd, '3_alignment')
phylogeny_dir = os.path.join(wd, '4_phylogeny')
outfile = os.path.join(phylogeny_dir, 'distribution.tre')
outfile_unconstrained = os.path.join(phylogeny_dir,
'distribution_unconstrained.tre')
temp_dir = os.path.join(wd, 'tempfiles')
# CHECK DEPS
if not ptools.raxml:
raise MissingDepError('raxml')
# INPUT
with open(os.path.join(temp_dir, "paradict.p"), "rb") as file:
paradict = pickle.load(file)
with open(os.path.join(temp_dir, "genedict.p"), "rb") as file:
genedict = pickle.load(file)
with open(os.path.join(temp_dir, "allrankids.p"), "rb") as file:
allrankids = pickle.load(file)
# PARAMETERS
nphylos = int(paradict["nphylos"])
maxtrys = int(paradict["maxtrys"])
rttstat = float(paradict["rttstat"])
constraint = int(paradict["constraint"])
ptools.logger = logger
# READ ALIGMENTS
clusters = sorted(os.listdir(alignment_dir))
clusters = [e for e in clusters if not re.search("^\.|^log\.txt$", e)]
logger.info("Reading in alignments ....")
alignment_store = ptools.AlignmentStore(clusters=clusters,
genedict=genedict,
allrankids=allrankids,
indir=alignment_dir, logger=logger)
# GENERATE TREE DIST
logger.info("Generating [{0}] phylogenies ....".format(nphylos))
generator = ptools.Generator(alignment_store=alignment_store,
rttstat=rttstat, outdir=phylogeny_dir,
maxtrys=maxtrys, logger=logger, wd=temp_dir)
if 1 == constraint:
generator.constraint = False
for i in range(ptools.countNPhylos(nphylos, outfile)):
logger.info(".... Iteration [{0}]".format(i + 1))
success = False
while not success:
success = generator.run()
with open(outfile, "a") as file:
counter = Phylo.write(generator.phylogenies[-1], file, 'newick')
# GENERATE CONSENSUS
logger.info('Generating consensus ....')
success = ptools.consensus(phylogeny_dir, min_freq=0.5, is_rooted=True,
trees_splits_encoded=False)
if not success:
logger.info('.... can`t generate consensus, too few names in all trees.')
# RUN UNCONSTRAINED
if 3 == constraint:
logger.info('Repeating unconstrained ....')
generator.phylogenies = []
generator.constraint = False
for i in range(ptools.countNPhylos(nphylos, outfile_unconstrained)):
logger.info(".... Iteration [{0}]".format(i + 1))
success = False
while not success:
success = generator.run()
with open(outfile_unconstrained, "a") as file:
counter = Phylo.write(generator.phylogenies[-1], file, 'newick')
# FINISH MESSAGE
logger.info('Stage finished. Generated [{0}] phylogenies.'.
format(counter))
def run(wd=os.getcwd(), logger=logging.getLogger('')):
# PRINT STAGE
logger.info("Stage 4: Phylogeny generation")
# DIRS
alignment_dir = os.path.join(wd, '3_alignment')
phylogeny_dir = os.path.join(wd, '4_phylogeny')
outfile = os.path.join(phylogeny_dir, 'distribution.tre')
outfile_unconstrained = os.path.join(phylogeny_dir,
'distribution_unconstrained.tre')
temp_dir = os.path.join(wd, 'tempfiles')
# CHECK DEPS
if not ptools.raxml:
raise MissingDepError('raxml')
# INPUT
with open(os.path.join(temp_dir, "paradict.p"), "rb") as file:
paradict = pickle.load(file)
with open(os.path.join(temp_dir, "genedict.p"), "rb") as file:
genedict = pickle.load(file)
with open(os.path.join(temp_dir, "allrankids.p"), "rb") as file:
allrankids = pickle.load(file)
# PARAMETERS
nphylos = int(paradict["nphylos"])
maxtrys = int(paradict["maxtrys"])
rttstat = float(paradict["rttstat"])
constraint = int(paradict["constraint"])
ptools.logger = logger
# READ ALIGMENTS
clusters = sorted(os.listdir(alignment_dir))
clusters = [e for e in clusters if not re.search("^\.|^log\.txt$", e)]
logger.info("Reading in alignments ....")
alignment_store = ptools.AlignmentStore(clusters=clusters,
genedict=genedict,
allrankids=allrankids,
indir=alignment_dir, logger=logger)
# GENERATE TREE DIST
logger.info("Generating [{0}] phylogenies ....".format(nphylos))
counter = 0
generator = ptools.Generator(alignment_store=alignment_store,
rttstat=rttstat, outdir=phylogeny_dir,
maxtrys=maxtrys, logger=logger, wd=temp_dir)
if 1 == constraint:
generator.constraint = False
for i in range(ptools.countNPhylos(nphylos, outfile)):
logger.info(".... Iteration [{0}]".format(i + 1))
success = False
while not success:
success = generator.run()
with open(outfile, "a") as file:
counter += Phylo.write(generator.phylogenies[-1], file, 'newick')
# GENERATE CONSENSUS
logger.info('Generating consensus ....')
success = ptools.consensus(phylogeny_dir, min_freq=0.5, is_rooted=True,
trees_splits_encoded=False)
if not success:
logger.info('.... can`t generate consensus, too few names in all trees.')
# RUN UNCONSTRAINED
if 3 == constraint:
logger.info('Repeating unconstrained ....')
generator.phylogenies = []
generator.constraint = False
for i in range(ptools.countNPhylos(nphylos, outfile_unconstrained)):
logger.info(".... Iteration [{0}]".format(i + 1))
success = False
while not success:
success = generator.run()
with open(outfile_unconstrained, "a") as file:
counter += Phylo.write(generator.phylogenies[-1], file, 'newick')
# FINISH MESSAGE
logger.info('Stage finished. Generated [{0}] phylogenies.'.
format(counter))