From 33eee184f0861daf86c45961401b2353786d0d1f Mon Sep 17 00:00:00 2001
From: Sylvain Soliman <Sylvain.Soliman@inria.fr>
Date: Sun, 12 Feb 2023 15:42:53 +0100
Subject: [PATCH] Allow to fix input/KO/KI values via a CSV file
---
casq/celldesigner2qual.py | 9 ++++++++-
casq/write.py | 40 ++++++++++++++++++++++++++++-----------
2 files changed, 37 insertions(+), 12 deletions(-)
diff --git a/casq/celldesigner2qual.py b/casq/celldesigner2qual.py
index 6cbbaa1..6caad2c 100755
--- a/casq/celldesigner2qual.py
+++ b/casq/celldesigner2qual.py
@@ -76,6 +76,13 @@ def main():
size is smaller than S.
A negative S leads to keep only the biggest(s) connected component(s)""",
)
+ parser.add_argument(
+ "-f",
+ "--fixed",
+ type=argparse.FileType(),
+ help="""A CSV file containing input values or knock-ins/knock-outs,
+ one per line, with name in the first column and the value in the second."""
+ )
if sys.version_info >= (3, 8, 0):
parser.add_argument(
"-u",
@@ -162,7 +169,7 @@ def main():
args.outfile, info, args.granularity, args.input, False, args.colourConstant
)
else:
- write_qual(args.outfile, info, width, height, remove=args.remove, sif=args.sif)
+ write_qual(args.outfile, info, width, height, remove=args.remove, sif=args.sif, fixed=args.fixed)
if args.csv and args.outfile != sys.stdout:
write_csv(args.outfile, info)
diff --git a/casq/write.py b/casq/write.py
index 59e4a66..e132204 100644
--- a/casq/write.py
+++ b/casq/write.py
@@ -19,7 +19,7 @@ along with this program. If not, see <https://www.gnu.org/licenses/>.
import csv
import xml.etree.ElementTree as etree
from itertools import chain, repeat
-from typing import List, Optional, Tuple # noqa: F401
+from typing import IO, List, Optional, Tuple # noqa: F401
from loguru import logger # type: ignore
@@ -34,7 +34,13 @@ NEGATIVE = ("INHIBITION", "NEGATIVE_INFLUENCE", "UNKNOWN_INHIBITION")
def write_qual(
- filename: str, info, width: str, height: str, remove: int = 0, sif: bool = False
+ filename: str,
+ info,
+ width: str,
+ height: str,
+ remove: int = 0,
+ sif: bool = False,
+ fixed: IO = None,
):
# pylint: disable=too-many-arguments, too-many-locals
"""Write the SBML qual with layout file for our model."""
@@ -66,11 +72,20 @@ def write_qual(
qlist = etree.SubElement(model, "qual:listOfQualitativeSpecies")
tlist = etree.SubElement(model, "qual:listOfTransitions")
graph = nx.DiGraph()
+ initial = {}
+ if fixed:
+ # dialect = csv.Sniffer().sniff(fixed.read(1024))
+ # fixed.seek(0)
+ for row in csv.reader(fixed):
+ if row[0] in info:
+ info[row[0]]["transitions"] = []
+ initial[row[0]] = row[1]
+
add_transitions(tlist, info, graph)
remove_connected_components(tlist, info, graph, remove)
if sif:
write_sif(filename, info, graph)
- add_qual_species(layout, qlist, info)
+ add_qual_species(layout, qlist, info, initial)
etree.ElementTree(root).write(filename, encoding="utf-8", xml_declaration=True)
@@ -130,7 +145,7 @@ def write_sif(sbml_filename: str, info, graph: nx.DiGraph):
)
-def add_qual_species(layout: etree.Element, qlist: etree.Element, info):
+def add_qual_species(layout: etree.Element, qlist: etree.Element, info, initial):
"""Create layout sub-elements and species."""
llist = etree.SubElement(layout, "layout:listOfAdditionalGraphicalObjects")
for species, data in info.items():
@@ -152,16 +167,19 @@ def add_qual_species(layout: etree.Element, qlist: etree.Element, info):
constant = "false"
else:
constant = "true"
+ attribs = {
+ "qual:maxLevel": "1",
+ "qual:compartment": "comp1",
+ "qual:name": data["name"],
+ "qual:constant": constant,
+ "qual:id": species,
+ }
+ if species in initial:
+ attribs["qual:initialLevel"] = initial[species]
qspecies = etree.SubElement(
qlist,
"qual:qualitativeSpecies",
- {
- "qual:maxLevel": "1",
- "qual:compartment": "comp1",
- "qual:name": data["name"],
- "qual:constant": constant,
- "qual:id": species,
- },
+ attribs,
)
add_annotation(qspecies, data["annotations"])
--
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