#!/usr/bin/env python
"""Tool to draw pedigrees defined in a file."""
import argparse
import logging
import sys
import matplotlib as mpl
import matplotlib.pyplot as plt
from dae.common_reports.family_report import FamiliesReport
from dae.configuration.gpf_config_parser import FrozenBox
from dae.pedigrees.drawing import OffsetLayoutDrawer, PDFLayoutDrawer
from dae.pedigrees.families_data import FamiliesData
from dae.pedigrees.layout import Layout
from dae.pedigrees.loader import FamiliesLoader
from dae.person_sets import PersonSetCollection
mpl.use("PS")
plt.ioff()
logger = logging.getLogger("draw_pedigree")
[docs]def build_families_report(families: FamiliesData) -> FamiliesReport:
"""Build a family report based on affected status."""
status_collection_config = {
"id": "status",
"name": "Affected status",
"domain": [
{
"id": "affected",
"name": "affected",
"values": ["affected"],
"color": "#e35252",
},
{
"id": "unaffected",
"name": "unaffected",
"values": ["unaffected"],
"color": "#ffffff",
},
],
"default": {
"id": "unspecified",
"name": "unspecified",
"color": "#aaaaaa",
},
"sources": [{"from": "pedigree", "column": "status"}],
}
status_collection_config = FrozenBox(
status_collection_config,
)
status_collection = PersonSetCollection.from_families(
status_collection_config, families,
)
return FamiliesReport.from_families_data(
families, [status_collection], draw_all_families=False)
[docs]def draw_pedigree(layout, title, show_family=True, tags=None):
layout_drawer = OffsetLayoutDrawer(
layout, show_family=show_family,
)
figure = layout_drawer.draw(title=title, tags=tags)
return figure
[docs]def build_family_layout(family):
# layout = Layout.from_family_layout(family)
# if layout is None:
return Layout.from_family(family)
[docs]def draw_families_report(families):
"""Draw families from families report."""
families_report = build_families_report(families)
assert len(families_report.families_counters) == 1
family_counters = list(families_report.families_counters.values())[0]
logger.info("total number family types: %s", len(family_counters.counters))
for family_counter in family_counters.counters.values():
family_id = family_counter.family
family = families[family_id]
layout = build_family_layout(family)
logger.info(
"drawing %s; list of families in this category: %s",
family, ",".join(family_counter.families))
if len(family_counter.families) > 5:
count = len(family_counter.families)
title = f"Number of families: {count}"
else:
title = ", ".join(family_counter.families)
figure = draw_pedigree(layout, title=title, tags=family.tag_labels)
yield figure
[docs]def draw_families(families):
"""Draw families."""
for family_id, family in families.items():
layout = build_family_layout(family)
figure = draw_pedigree(layout, title=family_id, tags=family.tag_labels)
yield figure
[docs]def main(argv=None):
"""Run the CLI for draw_pedigree tool."""
if argv is None:
argv = sys.argv[1:]
parser = argparse.ArgumentParser(
description="Produce a pedigree drawing in PDF format "
"from a pedigree file with layout coordinates.",
conflict_handler="resolve",
formatter_class=argparse.RawDescriptionHelpFormatter,
)
parser.add_argument("--verbose", "-V", action="count", default=0)
FamiliesLoader.cli_arguments(parser)
parser.add_argument(
"--output",
"-o",
metavar="o",
help="the output filename file",
default="output.pdf",
)
parser.add_argument(
"--mode",
type=str,
default="report",
dest="mode",
help="mode of drawing; supported modes are `families` and `report`; "
"defaults: `report`",
)
argv = parser.parse_args(argv)
if argv.verbose == 1:
logging.basicConfig(level=logging.WARNING)
elif argv.verbose == 2:
logging.basicConfig(level=logging.INFO)
elif argv.verbose >= 3:
logging.basicConfig(level=logging.DEBUG)
else:
logging.basicConfig(level=logging.WARNING)
logging.getLogger("matplotlib").setLevel(logging.WARNING)
filenames, params = FamiliesLoader.parse_cli_arguments(argv)
filename = filenames[0]
families_loader = FamiliesLoader(filename, **params)
families = families_loader.load()
mode = argv.mode
assert mode in ("families", "report")
logger.warning("using mode: %s", mode)
if mode == "report":
generator = draw_families_report(families)
else:
generator = draw_families(families)
with PDFLayoutDrawer(argv.output) as pdf_drawer:
for fig in generator:
pdf_drawer.savefig(fig)
plt.close(fig)
if __name__ == "__main__":
main()