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cannin/config.json

Last active September 6, 2023 11:40
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Use syblars (https://github.com/iVis-at-Bilkent/syblars) to Generate Layout and Render SBGNML to PNG using Python
Raw
config.json
{"layoutOptions": {
"name": "fcose",
"randomize": true,
"padding": 30
},
"imageOptions": {
"format": "png",
"background": "transparent",
"width": 1280,
"height": 1280,
"color": "bluescale"
}
}
Raw
glycolysis.sbgn
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<sbgn xmlns="http://sbgn.org/libsbgn/0.3">
<map version="http://identifiers.org/combine.specifications/sbgn.pd.level-1.version-1.3" id="map1">
<glyph id="glyph9" class="macromolecule">
<label text="hexokinase"/>
<bbox y="40.0" x="170.0" h="60.0" w="120.0"/>
</glyph>
<glyph id="glyph0" class="simple chemical">
<label text="glucose"/>
<bbox y="140.0" x="90.0" h="60.0" w="60.0"/>
</glyph>
<glyph id="glyph6" class="simple chemical">
<label text="ATP"/>
<clone/>
<bbox y="230.0" x="140.0" h="60.0" w="60.0"/>
</glyph>
<glyph id="glyph8" class="process">
<bbox y="160.0" x="220.0" h="20.0" w="20.0"/>
<port id="glyph8.1" y="170.0" x="210.0"/>
<port id="glyph8.2" y="170.0" x="250.0"/>
</glyph>
<glyph id="glyph7" class="simple chemical">
<label text="ADP"/>
<clone/>
<bbox y="230.0" x="270.0" h="60.0" w="60.0"/>
</glyph>
<glyph id="glyph12" class="simple chemical">
<label text="ADP"/>
<clone/>
<bbox y="230.0" x="700.0" h="60.0" w="60.0"/>
</glyph>
<glyph id="glyph13" class="simple chemical">
<label text="ATP"/>
<clone/>
<bbox y="230.0" x="570.0" h="60.0" w="60.0"/>
</glyph>
<glyph id="glyph1" class="simple chemical">
<label text="glucose&#xA;6P"/>
<bbox y="140.0" x="320.0" h="60.0" w="60.0"/>
</glyph>
<glyph id="glyph2" class="simple chemical">
<label text="fructose&#xA;6P"/>
<bbox y="140.0" x="520.0" h="60.0" w="60.0"/>
</glyph>
<glyph id="glyph15" class="macromolecule">
<label text="triose-P&#xA;isomerase"/>
<bbox y="140.0" x="1080.0" h="60.0" w="120.0"/>
</glyph>
<glyph id="glyph3" class="simple chemical">
<label text="fructose&#xA;1,6P"/>
<bbox y="140.0" x="730.0" h="60.0" w="60.0"/>
</glyph>
<glyph id="glyph17" class="macromolecule">
<label text="glucose-6P&#xA;isomerase"/>
<bbox y="40.0" x="380.0" h="60.0" w="120.0"/>
</glyph>
<glyph id="glyph10" class="process">
<bbox y="160.0" x="430.0" h="20.0" w="20.0"/>
<port id="glyph10.1" y="170.0" x="420.0"/>
<port id="glyph10.2" y="170.0" x="460.0"/>
</glyph>
<glyph id="glyph19" class="macromolecule">
<label text="phospho&#xA;fructokinase"/>
<bbox y="40.0" x="600.0" h="60.0" w="120.0"/>
</glyph>
<glyph id="glyph11" class="process">
<bbox y="160.0" x="650.0" h="20.0" w="20.0"/>
<port id="glyph11.2" y="170.0" x="680.0"/>
<port id="glyph11.1" y="170.0" x="640.0"/>
</glyph>
<glyph id="glyph18" class="macromolecule">
<label text="adolase"/>
<bbox y="40.0" x="820.0" h="60.0" w="120.0"/>
</glyph>
<glyph id="glyph16" class="process">
<bbox y="160.0" x="870.0" h="20.0" w="20.0"/>
<port id="glyph16.1" y="170.0" x="860.0"/>
<port id="glyph16.2" y="170.0" x="900.0"/>
</glyph>
<glyph id="glyph22" class="macromolecule">
<label text="GAPDH"/>
<bbox y="350.0" x="1080.0" h="60.0" w="120.0"/>
</glyph>
<glyph id="glyph4" class="simple chemical">
<label text="GA-3P"/>
<bbox y="240.0" x="960.0" h="60.0" w="60.0"/>
</glyph>
<glyph id="glyph23" class="simple chemical">
<label text="Pi"/>
<bbox y="280.0" x="880.0" h="60.0" w="60.0"/>
</glyph>
<glyph id="glyph24" class="simple chemical">
<label text="NAD"/>
<bbox y="280.0" x="1050.0" h="60.0" w="60.0"/>
</glyph>
<glyph id="glyph25" class="simple chemical">
<label text="H+"/>
<bbox y="420.0" x="1050.0" h="60.0" w="60.0"/>
</glyph>
<glyph id="glyph20" orientation="vertical" class="process">
<bbox y="370.0" x="980.0" h="20.0" w="20.0"/>
<port id="glyph20.1" y="360.0" x="990.0"/>
<port id="glyph20.2" y="400.0" x="990.0"/>
</glyph>
<glyph id="glyph26" class="simple chemical">
<label text="NADH"/>
<bbox y="490.0" x="1050.0" h="60.0" w="60.0"/>
</glyph>
<glyph id="glyph35" class="macromolecule">
<label text="PGK1"/>
<bbox y="540.0" x="820.0" h="60.0" w="120.0"/>
</glyph>
<glyph id="glyph36" class="macromolecule">
<label text="PG mutase"/>
<bbox y="540.0" x="580.0" h="60.0" w="120.0"/>
</glyph>
<glyph id="glyph37" class="macromolecule">
<label text="enolase"/>
<bbox y="540.0" x="350.0" h="60.0" w="120.0"/>
</glyph>
<glyph id="glyph38" class="macromolecule">
<label text="pyruvate&#xA;kinase"/>
<bbox y="540.0" x="100.0" h="60.0" w="120.0"/>
</glyph>
<glyph id="glyph21" class="simple chemical">
<label text="1,3 BPG"/>
<bbox y="460.0" x="960.0" h="60.0" w="60.0"/>
</glyph>
<glyph id="glyph42" class="simple chemical">
<label text="ADP"/>
<clone/>
<bbox y="390.0" x="910.0" h="60.0" w="60.0"/>
</glyph>
<glyph id="glyph41" class="simple chemical">
<label text="ATP"/>
<clone/>
<bbox y="390.0" x="780.0" h="60.0" w="60.0"/>
</glyph>
<glyph id="glyph31" class="process">
<bbox y="480.0" x="870.0" h="20.0" w="20.0"/>
<port id="glyph31.2" y="490.0" x="900.0"/>
<port id="glyph31.1" y="490.0" x="860.0"/>
</glyph>
<glyph id="glyph27" class="simple chemical">
<label text="3 PG"/>
<bbox y="460.0" x="720.0" h="60.0" w="60.0"/>
</glyph>
<glyph id="glyph32" class="process">
<bbox y="480.0" x="630.0" h="20.0" w="20.0"/>
<port id="glyph32.2" y="490.0" x="660.0"/>
<port id="glyph32.1" y="490.0" x="620.0"/>
</glyph>
<glyph id="glyph28" class="simple chemical">
<label text="2 PG"/>
<bbox y="460.0" x="490.0" h="60.0" w="60.0"/>
</glyph>
<glyph id="glyph43" class="simple chemical">
<label text="H2O"/>
<bbox y="390.0" x="320.0" h="60.0" w="60.0"/>
</glyph>
<glyph id="glyph33" class="process">
<bbox y="480.0" x="400.0" h="20.0" w="20.0"/>
<port id="glyph33.2" y="490.0" x="430.0"/>
<port id="glyph33.1" y="490.0" x="390.0"/>
</glyph>
<glyph id="glyph29" class="simple chemical">
<label text="PEP"/>
<bbox y="460.0" x="270.0" h="60.0" w="60.0"/>
</glyph>
<glyph id="glyph39" class="simple chemical">
<label text="ADP"/>
<clone/>
<bbox y="390.0" x="210.0" h="60.0" w="60.0"/>
</glyph>
<glyph id="glyph40" class="simple chemical">
<label text="ATP"/>
<clone/>
<bbox y="390.0" x="60.0" h="60.0" w="60.0"/>
</glyph>
<glyph id="glyph34" class="process">
<bbox y="480.0" x="150.0" h="20.0" w="20.0"/>
<port id="glyph34.2" y="490.0" x="180.0"/>
<port id="glyph34.1" y="490.0" x="140.0"/>
</glyph>
<glyph id="glyph30" class="simple chemical">
<label text="pyruvate"/>
<bbox y="460.0" x="30.0" h="60.0" w="60.0"/>
</glyph>
<glyph id="glyph14" orientation="vertical" class="process">
<bbox y="160.0" x="980.0" h="20.0" w="20.0"/>
<port id="glyph14.2" y="190.0" x="990.0"/>
<port id="glyph14.1" y="150.0" x="990.0"/>
</glyph>
<glyph id="glyph5" class="simple chemical">
<label text="DHA-P"/>
<bbox y="40.0" x="960.0" h="60.0" w="60.0"/>
</glyph>
<arc target="glyph8" source="glyph9" class="catalysis" id="a01">
<start y="100.0" x="230.0"/>
<end y="160.0" x="230.0"/>
</arc>
<arc target="glyph8.1" source="glyph0" class="consumption" id="a02">
<start y="170.0" x="150.0"/>
<end y="170.0" x="210.0"/>
</arc>
<arc target="glyph1" source="glyph8.2" class="production" id="a03">
<start y="170.0" x="250.0"/>
<end y="170.0" x="320.0"/>
</arc>
<arc target="glyph8.1" source="glyph6" class="consumption" id="a04">
<start y="232.58565" x="182.18416"/>
<end y="170.0" x="210.0"/>
</arc>
<arc target="glyph7" source="glyph8.2" class="production" id="a05">
<start y="170.0" x="250.0"/>
<end y="236.31943" x="281.5818"/>
</arc>
<arc target="glyph12" source="glyph11.2" class="production" id="a06">
<start y="170.0" x="680.0"/>
<end y="236.31943" x="711.5818"/>
</arc>
<arc target="glyph11.1" source="glyph13" class="consumption" id="a07">
<start y="232.58565" x="612.18414"/>
<end y="170.0" x="640.0"/>
</arc>
<arc target="glyph10.1" source="glyph1" class="consumption" id="a08">
<start y="170.0" x="380.0"/>
<end y="170.0" x="420.0"/>
</arc>
<arc target="glyph2" source="glyph10.2" class="production" id="a09">
<start y="170.0" x="460.0"/>
<end y="170.0" x="520.0"/>
</arc>
<arc target="glyph11.1" source="glyph2" class="consumption" id="a10">
<start y="170.0" x="580.0"/>
<end y="170.0" x="640.0"/>
</arc>
<arc target="glyph3" source="glyph11.2" class="production" id="a11">
<start y="170.0" x="680.0"/>
<end y="170.0" x="730.0"/>
</arc>
<arc target="glyph4" source="glyph14.2" class="production" id="a12">
<start y="190.0" x="990.0"/>
<end y="240.0" x="990.0"/>
</arc>
<arc target="glyph14" source="glyph15" class="catalysis" id="a13">
<start y="170.0" x="1080.0"/>
<end y="170.0" x="1000.0"/>
</arc>
<arc target="glyph16.1" source="glyph3" class="consumption" id="a14">
<start y="170.0" x="790.0"/>
<end y="170.0" x="860.0"/>
</arc>
<arc target="glyph5" source="glyph16.2" class="production" id="a15">
<start y="170.0" x="900.0"/>
<end y="90.18018" x="967.8018"/>
</arc>
<arc target="glyph4" source="glyph16.2" class="production" id="a16">
<start y="170.0" x="900.0"/>
<end y="249.81981" x="967.8018"/>
</arc>
<arc target="glyph10" source="glyph17" class="catalysis" id="a17">
<start y="100.0" x="440.0"/>
<end y="160.0" x="440.0"/>
</arc>
<arc target="glyph11" source="glyph19" class="catalysis" id="a18">
<start y="100.0" x="660.0"/>
<end y="160.0" x="660.0"/>
</arc>
<arc target="glyph16" source="glyph18" class="catalysis" id="a19">
<start y="100.0" x="880.0"/>
<end y="160.0" x="880.0"/>
</arc>
<arc target="glyph20" source="glyph22" class="catalysis" id="a20">
<start y="380.0" x="1080.0"/>
<end y="380.0" x="1000.0"/>
</arc>
<arc target="glyph20.1" source="glyph4" class="consumption" id="a21">
<start y="300.0" x="990.0"/>
<end y="360.0" x="990.0"/>
</arc>
<arc target="glyph21" source="glyph20.2" class="production" id="a22">
<start y="400.0" x="990.0"/>
<end y="460.0" x="990.0"/>
</arc>
<arc target="glyph20.1" source="glyph23" class="consumption" id="a23">
<start y="325.89996" x="935.43994"/>
<end y="360.0" x="990.0"/>
</arc>
<arc target="glyph20.1" source="glyph24" class="consumption" id="a24">
<start y="324.56927" x="1053.7753"/>
<end y="360.0" x="990.0"/>
</arc>
<arc target="glyph25" source="glyph20.2" class="production" id="a25">
<start y="400.0" x="990.0"/>
<end y="431.5818" x="1056.3195"/>
</arc>
<arc target="glyph26" source="glyph20.2" class="production" id="a26">
<start y="400.0" x="990.0"/>
<end y="494.76465" x="1063.7772"/>
</arc>
<arc target="glyph31" source="glyph35" class="catalysis" id="a27">
<start y="540.0" x="880.0"/>
<end y="500.0" x="880.0"/>
</arc>
<arc target="glyph32" source="glyph36" class="catalysis" id="a28">
<start y="540.0" x="640.0"/>
<end y="500.0" x="640.0"/>
</arc>
<arc target="glyph33" source="glyph37" class="catalysis" id="a29">
<start y="540.0" x="410.0"/>
<end y="500.0" x="410.0"/>
</arc>
<arc target="glyph34" source="glyph38" class="catalysis" id="a30">
<start y="540.0" x="160.0"/>
<end y="500.0" x="160.0"/>
</arc>
<arc target="glyph31.2" source="glyph21" class="consumption" id="a31">
<start y="490.0" x="960.0"/>
<end y="490.0" x="900.0"/>
</arc>
<arc target="glyph31.2" source="glyph42" class="consumption" id="a32">
<start y="446.0473" x="925.11584"/>
<end y="490.0" x="900.0"/>
</arc>
<arc target="glyph41" source="glyph31.1" class="production" id="a33">
<start y="490.0" x="860.0"/>
<end y="441.2132" x="831.2132"/>
</arc>
<arc target="glyph27" source="glyph31.1" class="production" id="a34">
<start y="490.0" x="860.0"/>
<end y="490.0" x="780.0"/>
</arc>
<arc target="glyph32.2" source="glyph27" class="consumption" id="a35">
<start y="490.0" x="720.0"/>
<end y="490.0" x="660.0"/>
</arc>
<arc target="glyph28" source="glyph32.1" class="production" id="a36">
<start y="490.0" x="620.0"/>
<end y="490.0" x="550.0"/>
</arc>
<arc target="glyph33.2" source="glyph28" class="consumption" id="a37">
<start y="490.0" x="490.0"/>
<end y="490.0" x="430.0"/>
</arc>
<arc target="glyph43" source="glyph33.1" class="production" id="a38">
<start y="490.0" x="390.0"/>
<end y="442.7777" x="369.52374"/>
</arc>
<arc target="glyph29" source="glyph33.1" class="production" id="a39">
<start y="490.0" x="390.0"/>
<end y="490.0" x="330.0"/>
</arc>
<arc target="glyph34.2" source="glyph29" class="consumption" id="a40">
<start y="490.0" x="270.0"/>
<end y="490.0" x="180.0"/>
</arc>
<arc target="glyph34.2" source="glyph39" class="consumption" id="a41">
<start y="442.7777" x="220.47626"/>
<end y="490.0" x="180.0"/>
</arc>
<arc target="glyph40" source="glyph34.1" class="production" id="a42">
<start y="490.0" x="140.0"/>
<end y="441.2132" x="111.2132"/>
</arc>
<arc target="glyph30" source="glyph34.1" class="production" id="a43">
<start y="490.0" x="140.0"/>
<end y="490.0" x="90.0"/>
</arc>
<arc target="glyph5" source="glyph14.1" class="production" id="a44">
<start y="150.0" x="990.0"/>
<end y="100.0" x="990.0"/>
</arc>
</map>
</sbgn>
Raw
syblars_example.py
import requests
import base64
import json
import io
from PIL import Image
sbgn_path = "glycolysis.sbgn"
config_path = "config.json"
url = 'http://syblars.cs.bilkent.edu.tr/sbgnml?edges=true'
with open(sbgn_path, 'r') as f:
data_sbgn = f.read()
with open(config_path, 'r') as f:
options = f.read()
data = data_sbgn + options
with open("debug.txt", "w") as f:
f.write(data)
headers = {"Content-Type": "text/plain"}
res = requests.post(url, headers=headers, data=data)
print(res.status_code)
tmp = json.loads(res.text)
data_base64 = tmp['image']
data_layout = tmp['layout']
im = Image.open(io.BytesIO(base64.b64decode(data_base64.split(',')[1])))
im.save("syblars.png")
Raw
syblars_pc.py
import requests
import base64
import json
import io
import re
from PIL import Image
def slugify(s):
s = s.lower().strip()
s = re.sub(r'[^\w\s-]', '-', s)
s = re.sub(r'[\s_-]+', '-', s)
s = re.sub(r'^-+|-+$', '', s)
return s
# GMT file from https://www.pathwaycommons.org/archives/PC2/v12/
pc_gmt_file = "PathwayCommons12.kegg.hgnc.gmt"
config_path = "config.json"
syblars_url = 'http://syblars.cs.bilkent.edu.tr/sbgnml?edges=true'
pc_gmt = open(pc_gmt_file, 'r')
lines = pc_gmt.readlines()
for i in range(10, 84):
tmp = lines[i].split('\t', 1)
pathway_id = tmp[0]
#pathway_id
if not pathway_id.startswith("http"):
continue
print(f'I: {str(i)}; Pathway: {pathway_id}')
output_file_slug = slugify(pathway_id)
sbgn_path = f'{output_file_slug}.sbgn'
png_path = f'{output_file_slug}.png'
#sbgn_path = "glycolysis.sbgn"
pc_url = f'https://www.pathwaycommons.org/pc2/get?uri={pathway_id}&format=SBGN'
r = requests.get(pc_url, allow_redirects=True)
s = r.content
open(sbgn_path, 'wb').write(s)
with open(sbgn_path, 'r') as f:
data_sbgn = f.read()
with open(config_path, 'r') as f:
options = f.read()
data = data_sbgn + options
with open("debug.txt", "w") as f:
f.write(data)
headers = {"Content-Type": "text/plain"}
res = requests.post(syblars_url, headers=headers, data=data)
print(res.status_code)
tmp = json.loads(res.text)
data_base64 = tmp['image']
im = Image.open(io.BytesIO(base64.b64decode(data_base64.split(',')[1])))
im.save(png_path)
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