def test3(self):
outdir = 'test/tmp/test_vistrans/Vis_test3/'
make_clean_dir(outdir)
stree = treelib.parse_newick(stree_newick)
tree = treelib.read_tree(treefile3)
brecon = phylo.read_brecon(breconfile3, tree, stree)
phylo.add_implied_spec_nodes_brecon(tree, brecon)
phylo.write_brecon(open(outdir + 'brecon', 'w'), brecon)
transsvg.draw_tree(tree, brecon, stree, filename=outdir + "tree.svg")
def test3(self):
outdir = 'test/tmp/test_vistrans/Vis_test3/'
make_clean_dir(outdir)
stree = treelib.parse_newick(stree_newick)
tree = treelib.read_tree(treefile3)
brecon = phylo.read_brecon(breconfile3, tree, stree)
phylo.add_implied_spec_nodes_brecon(tree, brecon)
phylo.write_brecon(open(outdir + 'brecon', 'w'), brecon)
transsvg.draw_tree(tree, brecon, stree, filename=outdir + "tree.svg")
def process_files(*args):
conn = tinys3.Connection(os.environ.get('AWS_ACCESS_KEY'), os.environ.get('AWS_SECRET_ACCESS_KEY'),
default_bucket=os.environ.get('S3_BUCKET_NAME'))
filename = args[0]
url = "http://s3.amazonaws.com/{}/{}".format(os.environ.get('S3_BUCKET_NAME'), filename)
urllib.urlretrieve(url, filename)
raw_name = os.path.splitext(filename)[0]
Reconcile(args)
freqSummation(args)
with open("{}freqFile.txt".format(raw_name)) as f:
lines = f.readlines()
score_list = ast.literal_eval(lines[0])
total_freq = float(lines[1][:-2])
total_recon = float(lines[3])
total_cost = float(lines[2][:-2])
scoring = args[4]
if scoring == "Frequency":
score_method = "Frequency"
elif scoring == "xscape":
score_method = "Xscape Scoring"
else:
score_method = "Unit Scoring"
results_list = []
for x, score in enumerate(score_list):
tree = treelib1.read_tree("{}.tree".format(raw_name))
stree = treelib1.read_tree("{}{}.stree".format(raw_name, x))
brecon = phylo.read_brecon("{}{}.mowgli.brecon".format(raw_name, x), tree, stree)
output = "{}{}.svg".format(raw_name, x)
phylo.add_implied_spec_nodes_brecon(tree, brecon)
transsvg.draw_tree(tree, brecon, stree, filename=output)
conn.upload(output, open(output, 'rb'), content_type='image/svg+xml')
percent = 100.0 * score / total_freq
running_tot_score = sum(score_list[:x])
running_tot = min(100.0 * running_tot_score / total_freq, 100)
results_list.append((score, percent, running_tot))
return {'results_list': results_list, 'raw_name': raw_name, 'dup': args[1], 'trans': args[2], 'loss': args[3],
'total_cost': total_cost, 'score_method': score_method, 'total_freq': total_freq,
'total_recon': total_recon}
#gene2species = phylo.read_gene2species(conf.smap)
stree = treelib1.read_tree(conf.stree)
tree = treelib1.read_tree(conf.tree)
if conf.names:
snames = dict(util.read_delim(conf.names))
else:
snames = None
if conf.brecon:
brecon = phylo.read_brecon(conf.brecon, tree, stree)
elif conf.recon:
recon, events = phylo.read_recon_events(conf.recon, tree, stree)
brecon = phylo.recon_events2brecon(recon, events)
else:
gene2species = phylo.read_gene2species(conf.smap)
recon = phylo.reconcile(tree, stree, gene2species)
events = phylo.label_events(tree, recon)
brecon = phylo.recon_events2brecon(recon, events)
phylo.add_implied_spec_nodes_brecon(tree, brecon)
transsvg.draw_tree(tree, brecon, stree, filename=conf.output,
snames=snames)
#=============================================================================
# parse options
conf, args = o.parse_args()
#gene2species = phylo.read_gene2species(conf.smap)
stree = treelib1.read_tree(conf.stree)
tree = treelib1.read_tree(conf.tree)
if conf.names:
snames = dict(util.read_delim(conf.names))
else:
snames = None
if conf.brecon:
brecon = phylo.read_brecon(conf.brecon, tree, stree)
elif conf.recon:
recon, events = phylo.read_recon_events(conf.recon, tree, stree)
brecon = phylo.recon_events2brecon(recon, events)
else:
gene2species = phylo.read_gene2species(conf.smap)
recon = phylo.reconcile(tree, stree, gene2species)
events = phylo.label_events(tree, recon)
brecon = phylo.recon_events2brecon(recon, events)
phylo.add_implied_spec_nodes_brecon(tree, brecon)
transsvg.draw_tree(tree, brecon, stree, filename=conf.output, snames=snames)
