From b4ed18af1808b4f02369d5a7688e0e38b04de351 Mon Sep 17 00:00:00 2001
From: unknown <david.hoksza@gmail.com>
Date: Wed, 30 Oct 2019 12:20:29 +0100
Subject: [PATCH] updated command line parameters; correct naming of output
file; updated mrm scripts
---
talent/graph_utils.py | 3 ++-
talent/layout_merge.py | 2 +-
talent/utils/transfer.py | 40 +++++++++++++++++++++++----------
talent_gui.py | 1 +
tests/mrm/scripts/report_ins.py | 2 +-
tests/mrm/scripts/run_insert.sh | 7 ++++--
6 files changed, 38 insertions(+), 17 deletions(-)
diff --git a/talent/graph_utils.py b/talent/graph_utils.py
index 522745a..22102a6 100644
--- a/talent/graph_utils.py
+++ b/talent/graph_utils.py
@@ -665,7 +665,8 @@ def get_all_reaction_ids(g) -> List[str]:
def get_all_species_ids(g, filterFunctions = []) -> List[str]:
return get_filtered_nodes(g, {'type': be.TYPE.SPECIES}, filterFunctions)
-def get_first_species(g: nx.MultiGraph) -> be.Species:
+
+def get_first_species(g: nx.MultiGraph) -> 'be.Species':
for id in g.nodes():
entity = get_node_data(id, g)
if entity.is_species():
diff --git a/talent/layout_merge.py b/talent/layout_merge.py
index ab9477a..eed74df 100644
--- a/talent/layout_merge.py
+++ b/talent/layout_merge.py
@@ -14,7 +14,7 @@ from . import layout as lt
from . import settings
from . import bioentity as be
-import forcelayout as fl
+# import forcelayout as fl
class CompartmentCCNodeSpecies(NamedTuple):
diff --git a/talent/utils/transfer.py b/talent/utils/transfer.py
index d1355ad..33197c8 100644
--- a/talent/utils/transfer.py
+++ b/talent/utils/transfer.py
@@ -152,7 +152,8 @@ def process_db(tmps_path, fmt, split_by_cmprtmnt, ddup, cc_before_ddup) -> List[
cnt_cmprtments += 1
gc = gu.extract_comparment(gu.removeOneComponents(g), cmprtmentName)
gc_rg = gu.get_reaction_graph(gc)
- tmps += process(gc, gc_rg, ddup, cc_before_ddup, cmprtmentName)
+ name = "{}-{}".format(common.extract_target_from_fn(fn), cmprtmentName)
+ tmps += process(gc, gc_rg, ddup, cc_before_ddup, name)
else:
cnt_cmprtments += 1
g_rg = gu.get_reaction_graph(gu.removeOneComponents(g))
@@ -208,8 +209,11 @@ def load_mapping(name, ged_params, cache_path):
return pickle.load(open(file_name, "rb")) if os.path.isfile(file_name) else None
-def get_tgt_tmp_name(tgt, tmp):
- return "{}--from--{}".format(tgt.get_name(), tmp.get_name())
+def get_tgt_tmp_name(tgt: ReactionGraph or str, tmp: ReactionGraph or str):
+ tgt_name = tgt.get_name() if isinstance(tgt, ReactionGraph) else tgt
+ tmp_name = tmp.get_name() if isinstance(tmp, ReactionGraph) else tmp
+ return "{}--from--{}".format(tgt_name, tmp_name)
+
def obtain_ed(tgt, tmp, costs, cache_path, ed_settings={}, load_map=True, store_map=True, min_mapped_ratio=0):
if (len(tmp.get_reaction_graph())/len(tgt.get_reaction_graph()) < min_mapped_ratio):
@@ -333,7 +337,7 @@ def map_transfer_store(tgt:ReactionGraph, tmps: List[ReactionGraph], cache_path:
for mtr in mtrs:
tmp = mtr.tmp
bc = mtr.bc
- fname = "{}/{}-tmp_order_{}-tgt-ddup_{}_tmp-ddup_{}.pkl".format(output_path, common.sanitize_string(get_tgt_tmp_name(tgt, tmp)), i,
+ fname = "{}{}-tmp_order_{}-tgt-ddup_{}_tmp-ddup_{}.pkl".format(output_path, common.sanitize_string(get_tgt_tmp_name(tgt, tmp)), i,
tgt.is_ddup(), tmp.is_ddup())
i += 1
rv_fnames.append(fname)
@@ -358,10 +362,10 @@ def group_gs_by_compartment(gs: List[nx.MultiGraph]) -> Dict[str, List[nx.MultiG
def transfer(tgt_name, tgt_fname, tgt_fmt, split_by_cmprtmnt, tmps_path, tmp_fmt,
- output_path,
+ output_path, separate_cmprtmnt,
ddup_tgt=False,
ddup_tmp=False, cache_path=None, tgt_sbml_source=None, tmp_cc_before_ddup=True,
- separate_cmprtmnt=True):
+ ):
"""
:param tgt_name:
@@ -399,6 +403,7 @@ def transfer(tgt_name, tgt_fname, tgt_fmt, split_by_cmprtmnt, tmps_path, tmp_fmt
# Extract best mapping from each transfer result list
g_ress = [mtrs[0].bc.g for mtrs in mtrss]
+ # tmps_ress = [mtrs[0].tmp for mtrs in mtrss]
# Each graph is shifted to the beginning of the coordinate frame because we then need to reposition them relative to each other
for g_res in g_ress:
@@ -410,11 +415,14 @@ def transfer(tgt_name, tgt_fname, tgt_fmt, split_by_cmprtmnt, tmps_path, tmp_fmt
g_tgt_complete: nx.MultiGraph = gu.load_graph(tgt_fname, tgt_fmt)
g_res = ltm.merge_compartments(cmp_gs=cmp_gs, g_tgt=g_tgt_complete)
bc = BeautificationChain(g_res)
- fname = "{}/{}.pkl".format(output_path, "test", i)
+
+ # tmp_name = "".join([tmp_res.get_name() for tmp_res in tmps_ress if tmp_res is not None]) #single-species components do not have a template
+ tmp_name = "multiple"
+ fname = "{}{}-tgt-ddup_{}_tmp-ddup_{}.pkl".format(output_path, common.sanitize_string(get_tgt_tmp_name(tgt_name, tmp_name)), ddup_tgt, ddup_tmp)
bc.save(fname)
- export.export(input_path=fname, format="svg", minerva_instance=settings.minerva_instance, output_path=fname + ".svg")
- export.export(input_path=fname, format="celldesigner", minerva_instance=settings.minerva_instance, output_path=fname + ".xml")
- export.export(input_path=fname, format="sbgn", minerva_instance=settings.minerva_instance, output_path=fname + ".sbgn")
+ # export.export(input_path=fname, format="svg", minerva_instance=settings.minerva_instance, output_path=fname + ".svg")
+ # export.export(input_path=fname, format="celldesigner", minerva_instance=settings.minerva_instance, output_path=fname + ".xml")
+ # export.export(input_path=fname, format="sbgn", minerva_instance=settings.minerva_instance, output_path=fname + ".sbgn")
@@ -482,10 +490,16 @@ if __name__ == '__main__':
required=False,
type=common.str2bool,
default=True)
+ parser.add_argument("-sep-cmp", "--separate-compartments",
+ required=False,
+ type=common.str2bool,
+ help="The target is split by compartments into multiple connected components, each of which is laid out separately, possibly using different templates, and the result is then assembled into a single resulting layout",
+ default = True)
parser.add_argument("-split-cmp", "--split-by-compartments",
required=False,
type=common.str2bool,
- default=True)
+ help="Splits target into compartments and each of them having a separate layout (this option is not considered if --sep-cmp=True)",
+ default=False)
parser.add_argument("-tmp-split-by-cc-before-ddup", "--tmp-split-by-cc-before-ddup",
required=False,
type=common.str2bool,
@@ -508,5 +522,7 @@ if __name__ == '__main__':
tgt_name=name, tgt_fname=args.target, tgt_fmt=args.target_format, ddup_tgt=args.ddup_tgt,
tmps_path=args.template_path, tmp_fmt=args.template_format, ddup_tmp=args.ddup_tmp,
output_path=args.output,
- split_by_cmprtmnt=args.split_by_compartments, tmp_cc_before_ddup=args.tmp_split_by_cc_before_ddup,
+ separate_cmprtmnt=args.separate_compartments,
+ split_by_cmprtmnt=args.split_by_compartments,
+ tmp_cc_before_ddup=args.tmp_split_by_cc_before_ddup,
cache_path=args.cache)
\ No newline at end of file
diff --git a/talent_gui.py b/talent_gui.py
index 14245a0..fd1c207 100644
--- a/talent_gui.py
+++ b/talent_gui.py
@@ -262,6 +262,7 @@ class InputWidget(QGroupBox):
transfer.transfer(tgt_name="{}".format(tgt_name), tgt_fname=tgt_path, tgt_fmt=tgt_type,
tmps_path=tmp_path, tmp_fmt=tmp_type,
output_path=output_path,
+ separate_cmprtmnt=True,
split_by_cmprtmnt=False,
ddup_tgt=False, ddup_tmp=False,
cache_path=None, tmp_cc_before_ddup=False)
diff --git a/tests/mrm/scripts/report_ins.py b/tests/mrm/scripts/report_ins.py
index b9f7437..b78d770 100644
--- a/tests/mrm/scripts/report_ins.py
+++ b/tests/mrm/scripts/report_ins.py
@@ -17,7 +17,7 @@ def main(dir_name: str):
for f_path in glob.glob("{}/*.svg".format(dir_name)):
f_name = os.path.basename(f_path)
- tmp_name = re.match(r'.*from--(.*)-c.*', f_name).group(1)
+ tmp_name = re.match(r'.*---(.*)---.*', f_name).group(1)
tmp_path = "{}/{}.svg".format(tmptgt_path, tmp_name)
f.write('<div class="group">'
'<div class="group-header">{}</div>'
diff --git a/tests/mrm/scripts/run_insert.sh b/tests/mrm/scripts/run_insert.sh
index 8b95d84..95c42c0 100644
--- a/tests/mrm/scripts/run_insert.sh
+++ b/tests/mrm/scripts/run_insert.sh
@@ -19,14 +19,17 @@ for dir in `ls -d ${TEST_ROOT}/sbml/*`; do
for template_path in `ls -1 ${dir}/${target}_*`; do
template=${template_path##*/}
+ template=${template/.sbml/}
echo "Laying out target " $target "against template " $template
- echo ${PYTHON} ${TALENT_UTILS}/transfer.py -tgt ${target_path} -tmp ${template_path} -o ${out_dir} -ddup-tmp false -ddup-tgt false -s settings_insert.json -cache cache
- ${PYTHON} ${TALENT_UTILS}/transfer.py -tgt ${target_path} -tmp ${template_path} -o ${out_dir} -ddup-tmp false -ddup-tgt false -s settings_insert.json -cache cache
+ echo ${PYTHON} ${TALENT_UTILS}/transfer.py -tgt ${target_path} -tmp ${template_path} -o ${out_dir}${target}---${template}--- -ddup-tmp false -ddup-tgt false -s settings_insert.json -cache cache
+ ${PYTHON} ${TALENT_UTILS}/transfer.py -tgt ${target_path} -tmp ${template_path} -o ${out_dir}/${target}---${template}--- -ddup-tmp false -ddup-tgt false -s settings_insert.json -cache cache
# ${PYTHON} ${TALENT_UTILS}/transfer.py -tgt ${target_path} -tmp ${template_path} -o ${out_dir} -ddup-tmp true -ddup-tgt true -s settings_insert.json -cache cache
done
for pkl in `ls -1 ${out_dir}/*.pkl`; do
echo "Exporting " $pkl
+ echo "${PYTHON} ${TALENT_UTILS}/export.py -i $pkl -f svg > ${pkl}.svg"
+
${PYTHON} ${TALENT_UTILS}/export.py -i $pkl -f svg > ${pkl}.svg
done
--
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