def create_graph(filename,
layout="dot",
use_singularity=False,
color_for_disabled_converter='red'):
"""
:param filename: should end in .png or .svg or .dot
If extension is .dot, only the dot file is created.
This is useful if you have issues installing graphviz.
If so, under Linux you could use our singularity container
see github.com/cokelaer/graphviz4all
"""
from bioconvert.core.registry import Registry
rr = Registry()
try:
if filename.endswith(".dot") or use_singularity is True:
raise Exception()
from pygraphviz import AGraph
dg = AGraph(directed=True)
for a, b, s in rr.get_all_conversions():
dg.add_edge(a,
b,
color='black' if s else color_for_disabled_converter)
dg.layout(layout)
dg.draw(filename)
except Exception as e:
_log.error(e)
dot = """
strict digraph{
node [label="\\N"];
"""
nodes = set([
item for items in rr.get_all_conversions() for item in items[0:1]
])
for node in nodes:
dot += "\"{}\";\n".format(node)
for a, b, s in rr.get_all_conversions():
dot += "\"{}\" -> \"{}\";\n".format(a, b)
dot += "}\n"
from easydev import TempFile
from bioconvert import shell
dotfile = TempFile(suffix=".dot")
with open(dotfile.name, "w") as fout:
fout.write(dot)
dotpath = ""
if use_singularity:
from bioconvert.core.downloader import download_singularity_image
singfile = download_singularity_image(
"graphviz.simg", "shub://cokelaer/graphviz4all:v1",
"4288088d91c848e5e3a327282a1ab3d1")
dotpath = "singularity run {} ".format(singfile)
on_rtd = environ.get('READTHEDOCS', None) == 'True'
if on_rtd:
dotpath = ""
ext = filename.rsplit(".", 1)[1]
cmd = "{}dot -T{} {} -o {}".format(dotpath, ext, dotfile.name,
filename)
try:
shell(cmd)
except:
import os
os.system(cmd)
def create_graph(filename,
layout="dot",
use_singularity=False,
color_for_disabled_converter='red'):
"""
:param filename: should end in .png or .svg or .dot
If extension is .dot, only the dot file is created.
This is useful if you have issues installing graphviz.
If so, under Linux you could use our singularity container
see github.com/cokelaer/graphviz4all
"""
from bioconvert.core.registry import Registry
rr = Registry()
try:
if filename.endswith(".dot") or use_singularity is True:
raise Exception()
from pygraphviz import AGraph
dg = AGraph(directed=True)
url = "https://bioconvert.readthedocs.io/en/master/formats.html#{}"
for a, b, s in rr.get_all_conversions():
if len(a) == 1 and len(b) == 1:
dg.add_node(a[0],
shape="rectangle",
style="filled",
url=url.format(a[0].upper()))
dg.add_node(b[0],
shape="rectangle",
style="filled",
url=url.format(b[0].upper()))
dg.add_edge(
a[0],
b[0],
color='black' if s else color_for_disabled_converter)
else:
and_node = "_".join(a) + "_and_" + "_".join(b)
dg.add_node(and_node,
label="",
fillcolor="black",
width=.1,
height=.1,
styled="filled",
fixedsize=True,
shape="circle")
for this in a:
dg.add_edge(
this,
and_node,
color="black" if s else color_for_disabled_converter)
for this in b:
dg.add_edge(
and_node,
this,
color="black" if s else color_for_disabled_converter)
for name in dg.nodes():
if dg.degree(name) < 5:
dg.get_node(name).attr["fillcolor"] = "white"
elif dg.degree(name) < 10:
# yellow
dg.get_node(name).attr["fillcolor"] = "yellow"
elif dg.degree(name) < 20:
# orange
dg.get_node(name).attr["fillcolor"] = "orange"
else:
# red
dg.get_node(name).attr["fillcolor"] = "red"
dg.layout(layout)
dg.draw(filename)
dg.write("conversion.dot")
print(list(dg.get_node("FASTQ").attr.values()))
except Exception as e:
_log.error(e)
dot = """
strict digraph{
node [label="\\N"];
"""
nodes = set([
item for items in rr.get_all_conversions() for item in items[0:1]
])
for node in nodes:
dot += "\"{}\";\n".format(node)
for a, b, s in rr.get_all_conversions():
dot += "\"{}\" -> \"{}\";\n".format(a, b)
dot += "}\n"
from easydev import TempFile
from bioconvert import shell
dotfile = TempFile(suffix=".dot")
with open(dotfile.name, "w") as fout:
fout.write(dot)
dotpath = ""
if use_singularity:
from bioconvert.core.downloader import download_singularity_image
singfile = download_singularity_image(
"graphviz.simg", "shub://cokelaer/graphviz4all:v1",
"4288088d91c848e5e3a327282a1ab3d1")
dotpath = "singularity run {} ".format(singfile)
on_rtd = environ.get('READTHEDOCS', None) == 'True'
if on_rtd:
dotpath = ""
ext = filename.rsplit(".", 1)[1]
cmd = "{}dot -T{} {} -o {}".format(dotpath, ext, dotfile.name,
filename)
print(dotfile.name)
try:
shell(cmd)
except:
import os
os.system(cmd)