def main():
args = get_args()
# read in phylip files
alns = {}
for f in glob.glob(os.path.join(args.input, '*.phy*')):
alns[os.path.splitext(os.path.basename(f))[0]] = open(f, 'rU').read()
# replicate our options for passing to map()
opts = [args.phyml for i in range(len(alns))]
# compute genetrees
if args.run == 'genetrees' or args.run == 'both':
sys.stdout.write("Running genetrees...\n\n")
params = zip(alns.items(), opts)
genetrees = mmap(genetree_worker, params)
# write genetrees to output file
outf = open(os.path.join(args.output, 'genetrees.tre'), 'w')
for tree in genetrees:
outf.write("%s\n" % (tree[2]))
outf.close()
# compute bootreps on genetrees from above
if args.run == 'both':
sys.stdout.write("Running boostraps of genetrees...\n")
# get models for each locus based on genetrees in-memory
models = dict([[tree[0], tree[1]] for tree in genetrees])
boostrap_all_loci(args, models, alns)
# compute bootreps on genetrees from a file
if args.run == 'bootstraps':
sys.stdout.write("Running boostraps...\n")
# get models for each locus based on genetrees in genetree file
models = get_models_from_genetrees(args.genetrees)
boostrap_all_loci(args, models, alns)
def main():
args = get_args()
# read in phylip files
alns = {}
for f in glob.glob(os.path.join(args.input, '*.phy*')):
alns[os.path.splitext(os.path.basename(f))[0]] = open(f, 'rU').read()
# replicate our options for passing to map()
opts = [args.phyml for i in range(len(alns))]
# compute genetrees
if args.run == 'genetrees' or args.run == 'both':
sys.stdout.write("Running genetrees...\n\n")
params = zip(alns.items(), opts)
genetrees = mmap(genetree_worker, params)
# write genetrees to output file
outf = open(os.path.join(args.output, 'genetrees.tre'), 'w')
for tree in genetrees:
outf.write("%s\n" % (tree[2]))
outf.close()
# compute bootreps on genetrees from above
if args.run == 'both':
sys.stdout.write("Running bootstraps of genetrees...\n")
# get models for each locus based on genetrees in-memory
models = dict([[tree[0], tree[1]] for tree in genetrees])
boostrap_all_loci(args, models, alns)
# compute bootreps on genetrees from a file
if args.run == 'bootstraps':
sys.stdout.write("Running boostraps...\n")
# get models for each locus based on genetrees in genetree file
models = get_models_from_genetrees(args.genetrees)
boostrap_all_loci(args, models, alns)
def boostrap_all_loci(args, models, alns):
"""Compute trees from bootstrap replicates of a dataset"""
oneliners = [phylip_to_oneliner(phylip, locus, models[locus]) for locus, phylip in alns.iteritems()]
# for every rep in boostraps, map loci onto worker that will
# bootstrap, run phyml, and return bootstrap trees
params = generate_bootreps(args.bootreps, args.phyml, oneliners)
bootreps = mmap(bootstrap_worker, params)
# write
outname = "%s-bootreps.tree" % (args.bootreps)
outf = open(os.path.join(args.output, outname), "w")
for bootrep in bootreps:
for tree in bootrep:
outf.write("%s\n" % (tree))
def boostrap_all_loci(args, models, alns):
"""Compute trees from bootstrap replicates of a dataset"""
oneliners = [phylip_to_oneliner(phylip, locus, models[locus]) \
for locus, phylip in alns.iteritems()]
# for every rep in boostraps, map loci onto worker that will
# bootstrap, run phyml, and return bootstrap trees
params = generate_bootreps(args.bootreps, args.phyml, oneliners)
bootreps = mmap(bootstrap_worker, params)
# write
outname = "%s-bootreps.tree" % (args.bootreps)
outf = open(os.path.join(args.output, outname), 'w')
for bootrep in bootreps:
for tree in bootrep:
outf.write("%s\n" % (tree))
def main():
args = get_args()
# iterate over files reading contents into a list that we'll pass to sate
loci = get_fasta_dict(args)
opts = [[args.sate, args.cfg] for i in range(len(loci))]
params = zip(loci.items(), opts)
sys.stdout.write('Aligning')
# pass to map or Pool.map or mpimap
alignments = mmap(worker, params)
for data in alignments:
name, aln = data
out_file = os.path.join(args.output, name) + '.aln'
out = open(out_file, 'w')
out.write(aln)
out.close()
def main():
args = get_args()
# iterate over files reading contents into a list that we'll pass to sate
loci = get_fasta_dict(args)
opts = [[args.sate, args.cfg] for i in range(len(loci))]
params = zip(loci.items(), opts)
sys.stdout.write("Aligning")
# pass to map or Pool.map or mpimap
alignments = mmap(worker, params)
for data in alignments:
name, aln = data
out_file = os.path.join(args.output, name) + ".aln"
out = open(out_file, "w")
out.write(aln)
out.close()
