def parse_arguments():
parser = argparse.ArgumentParser(description='redraw trees only')
parser.add_argument("--env",
action="store",
dest="path_env",
required=True)
parser.add_argument("--project",
action="store",
dest="path_project",
required=True)
parser.add_argument("--config", nargs='+', dest="configs", required=True)
# parse arguments
params = parser.parse_args()
# read environment configuration
envs = utils.read_json_config(params.path_env)
# get config json files
config_jsons = utils.handle_config_args(params.path_project,
params.configs)
return params, envs, config_jsons
def parse_arguments():
parser = argparse.ArgumentParser(description='run simulation')
parser.add_argument("--env",
action="store",
dest="path_env",
required=True)
parser.add_argument("--project",
action="store",
dest="path_project",
required=True)
parser.add_argument("--config", nargs='+', dest="configs", required=True)
parser.add_argument("--quiet", action="store_true", dest="quiet")
parser.add_argument("--simulate-tree-only",
action="store_true",
default=False,
dest="simulate_tree_only")
# parse arguments
params = parser.parse_args()
# read environment configuration
envs = utils.read_json_config(params.path_env)
# get config json files
config_jsons = utils.handle_config_args(params.path_project,
params.configs)
return params, envs, config_jsons
def get_simulation_output_path(path_project, config_filename):
# read simulation configuration
config = utils.read_json_config(os.path.join(path_project,
config_filename))
path_simulation_output = os.path.join(
path_project, config[const.CONFIG_PATH_RELATIVE_OUTPUT])
return path_simulation_output
def run(path_matlab, path_project, config_filename, simulate_tree_only, quiet):
"run function"
# read simulation configuration
config = utils.read_json_config(os.path.join(path_project,
config_filename))
# get seed from simulation.xml
seed = get_seed_from_simulation_xml(
os.path.join(
path_project,
config.get(const.CONFIG_PROGRAM_FILE, const.FILE_SIMULATION_XML)))
# run stochastic lineage tree simulation
simulate_lineage_tree(path_matlab, path_project, config_filename)
path_simulation_output = os.path.join(
path_project, config[const.CONFIG_PATH_RELATIVE_OUTPUT])
# take simulation tree and make ascii plot
generate_tree_ascii_plot(
os.path.join(path_simulation_output, const.FILE_SIMULATION_NEWICK))
# run genotyping simulation (wga proportion, dropout, coverage)
# output mutation table
run_genotyping_simulation(
config.get(const.CONFIG_SIMULATION_BIALLELIC, 'False'), path_project,
path_simulation_output, seed)
# user wants to generate tree only
if simulate_tree_only:
return
methods = []
# if biallelic=true
if config.get(const.CONFIG_SIMULATION_BIALLELIC, 'False'):
methods = handle_biallelic(path_project, path_simulation_output)
else:
methods = handle_monoallelic(path_project, path_simulation_output)
for path_reconstruction_output, calling in methods:
# reconstruct using TMC based on mutation table generated from simulation
reconstruct_TMC(
calling, path_reconstruction_output, 'root',
config.get(const.CONFIG_RECONSTRUCT_SCORING_METHOD, 'uri10'),
config.get(const.CONFIG_RECONSTRUCT_CHOOSING_METHOD, 'mms'), quiet)
# take reconstructed tree and make ascii plot
generate_tree_ascii_plot(
os.path.join(path_reconstruction_output,
const.FILE_RECONSTRUCTED_NEWICK))
# highlight tree differences and save to png
highlight_tree_differences_to_png(
envs[const.ENV_MATLAB_KEY],
os.path.join(path_simulation_output, const.FILE_SIMULATION_NEWICK),
os.path.join(path_reconstruction_output,
const.FILE_RECONSTRUCTED_NEWICK),
os.path.join(path_reconstruction_output, const.FILE_SISTERS_COUNT),
os.path.join(path_reconstruction_output, const.FILE_DIFF_METRICS))
# compare simulation tree and reconstructed tree
compare(
os.path.join(path_simulation_output, const.FILE_SIMULATION_NEWICK),
os.path.join(path_reconstruction_output,
const.FILE_RECONSTRUCTED_NEWICK),
os.path.join(path_reconstruction_output,
const.FILE_COMPARISON_METRICS_RAW))
# report the final comparison metrics in a pretty format
report(
os.path.join(path_reconstruction_output,
const.FILE_COMPARISON_METRICS_RAW),
os.path.join(path_reconstruction_output,
const.FILE_COMPARISON_METRICS_PRETTY), quiet)
def make_html(report_title, path_project, config_jsons,
exclude_mutation_table):
templ = """
<html>
<head>
<title>{{reportTitle}}</title>
<link rel="stylesheet" type="text/css" href="http://fonts.googleapis.com/css?family=Open+Sans" />
<style>
table {
font-family: "Open Sans";
font-size: 14px;
}
.tree-img {
width: 650px;
}
.metrics-table {
min-width: 390px;
}
.overall-score {
font-family: "Open Sans";
font-size: 120px;
text-align: center;
width: 40%;
}
</style>
</head>
<body>
{% for item in items %}
<h1>{{item.config.contents.title}} ({{item.config.filename}})</h1>
<hr/>
<h2>Parameters</h2>
<table>
<tr>
<td style="width:230px">Simulation Seed:</td>
<td>{{item.simulation.seed}}</td>
</tr>
<tr>
<td>Simulation Time:</td>
<td>{{item.simulation.time}}</td>
</tr>
<tr>
<td>Number of Microsatellite Loci:</td>
<td>{{item.simulation.numOfLoci}}
</tr>
<tr>
<td>Mutation:</td>
<td>{{item.config.contents.addMutations}}{% if item.config.contents.mutationSpeed %} / Speed {{item.config.contents.mutationSpeed}} {% endif %}</td>
</tr>
<tr>
<td>Allelic Dropouts:</td>
<td>{{item.config.contents.addAllelicDropOuts}}</td>
</tr>
<tr>
<td>Noises:</td>
<td>{{item.config.contents.addNoises}}</td>
</tr>
<tr>
<td>Early Stop Population:</td>
<td>{{item.config.contents.earlyStopPopulation}}</td>
</tr>
<tr>
<td>Scoring Method:</td>
<td>{% if item.config.contents.scoringMethod %}{{item.config.contents.scoringMethod}}{% else %}probably uri10?{% endif %}</td>
</table>
<h2>Mutation Table</h2>
{{item.simulation.mutationTable}}
<p style="page-break-after: always;"> </p>
<table>
<tr>
<td>
<img src="{{item.simulation.img}}" class="tree-img"/>
</td>
<td>
<img src="{{item.reconstructed.img}}" class="tree-img"/>
</td>
</tr>
</table>
<table cellpadding="0" cellspacing="0" border="0" style="width:100%" width="100%">
<tr>
<td>{{item.metrics.compare1}}</td>
<td class="overall-score">{{item.metrics.compare2}}</td>
</tr>
</table>
<p style="page-break-after: always;"> </p>
<table>
<tr>
<td>
<pre>{{item.simulation.ascii}}</pre>
</td>
<td style="padding-left:30px;">
<pre>{{item.reconstructed.ascii}}</pre>
</td>
</tr>
</table>
<p style="page-break-after: always;"> </p>
{% endfor %}
</body>
</html>
"""
items = []
for config_json in config_jsons:
if not config_json:
continue
if not os.path.exists(os.path.join(path_project, config_json)):
raise Exception("Unable to find {}".format(config_json))
# read simulation configuration
config = utils.read_json_config(os.path.join(path_project,
config_json))
path_output = os.path.join(path_project,
config[const.CONFIG_PATH_RELATIVE_OUTPUT])
# path_diff_metrics = os.path.join(path_output, const.FILE_DIFF_METRICS)
# diff_metrics = get_diff_metrics(path_diff_metrics)
# overall_score = '{0:2.1f}%'.format((diff_metrics['total'] - (
# diff_metrics['diff'] + diff_metrics['missing'])) / diff_metrics['total'] * 100.0)
if exclude_mutation_table:
mutation_table = "excluded"
else:
mutation_table = convert_mutation_table_to_html(
path_output, const.FILE_MUTATION_TABLE)
df_metrics, metrics_html = convert_metrics_to_html(
path_output, const.FILE_COMPARISON_METRICS_RAW)
sim_xdoc = read_simulation_xml(
os.path.join(path_project, const.FILE_SIMULATION_XML))
sim_seed, sim_time = get_sim_seed_time(sim_xdoc)
num_of_ms_loci = get_num_of_ms_loci(sim_xdoc)
item = {
"config": {
"filename": config_json,
"contents": config
},
"simulation": {
"time":
sim_time,
"seed":
sim_seed,
"numOfLoci":
num_of_ms_loci,
"mutationTable":
mutation_table,
"img":
"{}/{}.png".format(config[const.CONFIG_PATH_RELATIVE_OUTPUT],
const.FILE_SIMULATION_NEWICK)
},
"reconstructed": {
"img":
"{}/{}.png".format(config[const.CONFIG_PATH_RELATIVE_OUTPUT],
const.FILE_RECONSTRUCTED_NEWICK)
},
"metrics": {
"compare1": metrics_html,
"compare2": df_metrics.loc['Triples_toYuleAvg'][0]
}
}
item["simulation"]["ascii"] = get_ascii_plot(
os.path.join(path_output, const.FILE_SIMULATION_NEWICK))
item["reconstructed"]["ascii"] = get_ascii_plot(
os.path.join(path_output, const.FILE_RECONSTRUCTED_NEWICK))
items.append(item)
template = Template(templ)
html = template.render(reportTitle=report_title, items=items)
with open(os.path.join(path_project, const.FILE_REPORT_HTML),
'wt') as fout:
fout.write(html)
fout.write('\n')