def test_read_and_write_KGML_files(self):
""" Read KGML from, and write KGML to, local files.
Check we read/write the correct number of elements.
"""
for p in self.data:
# Test opening file
with open(p.infilename, 'rU') as f:
pathway = read(f)
# Do we have the correct number of elements of each type
self.assertEqual((len(pathway.entries),
len(pathway.orthologs),
len(pathway.compounds),
len(pathway.maps)),
p.element_counts)
# Test writing file
with open(p.outfilename, 'w') as f:
f.write(pathway.get_KGML())
# Can we read the file we wrote?
with open(p.outfilename, 'rU') as f:
pathway = read(f)
# Do we have the correct number of elements of each type
self.assertEqual((len(pathway.entries),
len(pathway.orthologs),
len(pathway.compounds),
len(pathway.maps)),
p.element_counts)
def test_read_and_write_KGML_files(self):
""" Read KGML from, and write KGML to, local files.
Check we read/write the correct number of elements.
"""
for p in self.data:
# Test opening file
with open(p.infilename, 'rU') as f:
pathway = read(f)
# Do we have the correct number of elements of each type
self.assertEqual((len(pathway.entries),
len(pathway.orthologs),
len(pathway.compounds),
len(pathway.maps)),
p.element_counts)
# Test writing file
with open(p.outfilename, 'w') as f:
f.write(pathway.get_KGML())
# Can we read the file we wrote?
with open(p.outfilename, 'rU') as f:
pathway = read(f)
# Do we have the correct number of elements of each type
self.assertEqual((len(pathway.entries),
len(pathway.orthologs),
len(pathway.compounds),
len(pathway.maps)),
p.element_counts)
def test_render_KGML_modify(self):
""" Rendering of KGML to PDF, with modification.
"""
# We test rendering of the original and roundtrip KGML for KO01100,
# modifying line width for the lipid pathway
p = self.data[0]
for filename, ext in [(p.infilename, "_mod_original.pdf"), (p.outfilename, "_mod_roundtrip.pdf")]:
with open(filename) as f:
pathway = read(f)
mod_rs = [e for e in pathway.orthologs if len(set(e.name.split()).intersection(self.ko_ids))]
for r in mod_rs:
for g in r.graphics:
g.width = 10
kgml_map = KGMLCanvas(pathway)
kgml_map.draw(os.path.splitext(filename)[0] + ext)
# We test rendering of the original and roundtrip KGML for KO3070,
# modifying the reaction colours for each ortholog entry
p = self.data[1]
for filename, ext in [(p.infilename, "_mod_original.pdf"), (p.outfilename, "_mod_roundtrip.pdf")]:
with open(filename) as f:
pathway = read(f)
orthologs = [e for e in pathway.orthologs]
# Use Biopython's ColorSpiral to generate colours
cs = ColorSpiral(a=2, b=0.2, v_init=0.85, v_final=0.5, jitter=0.03)
colors = cs.get_colors(len(orthologs))
for o, c in zip(orthologs, colors):
for g in o.graphics:
g.bgcolor = c
kgml_map = KGMLCanvas(pathway)
pathway.image = p.pathway_image
kgml_map.import_imagemap = p.show_pathway_image
kgml_map.draw(os.path.splitext(filename)[0] + ext)
def test_render_KGML_modify(self):
""" Rendering of KGML to PDF, with modification.
"""
# We test rendering of the original and roundtrip KGML for KO01100,
# modifying line width for the lipid pathway
p = self.data[0]
for filename, ext in [(p.infilename, '_mod_original.pdf'),
(p.outfilename, '_mod_roundtrip.pdf')]:
with open(filename) as f:
pathway = read(f)
mod_rs = [
e for e in pathway.orthologs
if len(set(e.name.split()).intersection(self.ko_ids))
]
for r in mod_rs:
for g in r.graphics:
g.width = 10
kgml_map = KGMLCanvas(pathway)
kgml_map.draw(os.path.splitext(filename)[0] + ext)
# We test rendering of the original and roundtrip KGML for KO3070,
# modifying the reaction colours for each ortholog entry
p = self.data[1]
for filename, ext in [(p.infilename, '_mod_original.pdf'),
(p.outfilename, '_mod_roundtrip.pdf')]:
with open(filename) as f:
pathway = read(f)
orthologs = [e for e in pathway.orthologs]
# Use Biopython's ColorSpiral to generate colours
cs = ColorSpiral(a=2,
b=0.2,
v_init=0.85,
v_final=0.5,
jitter=0.03)
colors = cs.get_colors(len(orthologs))
for o, c in zip(orthologs, colors):
for g in o.graphics:
g.bgcolor = c
kgml_map = KGMLCanvas(pathway)
pathway.image = p.pathway_image
kgml_map.import_imagemap = p.show_pathway_image
kgml_map.draw(os.path.splitext(filename)[0] + ext)
def test_render_KGML_basic(self):
""" Basic rendering of KGML: write to PDF without modification.
"""
# We test rendering of both the original KEGG KGML and the
# roundtrip KGML written by this module, using only local files.
for p in self.data:
for filename, ext in [(p.infilename, "_original.pdf"), (p.outfilename, "_roundtrip.pdf")]:
with open(filename, "rU") as f:
pathway = read(f)
pathway.image = p.pathway_image
kgml_map = KGMLCanvas(pathway)
kgml_map.import_imagemap = p.show_pathway_image
kgml_map.draw(os.path.splitext(filename)[0] + ext)
def test_render_KGML_basic(self):
""" Basic rendering of KGML: write to PDF without modification.
"""
# We test rendering of both the original KEGG KGML and the
# roundtrip KGML written by this module, using only local files.
for p in self.data:
for filename, ext in [(p.infilename, '_original.pdf'),
(p.outfilename, '_roundtrip.pdf')]:
with open(filename, 'rU') as f:
pathway = read(f)
pathway.image = p.pathway_image
kgml_map = KGMLCanvas(pathway)
kgml_map.import_imagemap = p.show_pathway_image
kgml_map.draw(os.path.splitext(filename)[0] + ext)
def retrieve_KEGG_pathway(map_id):
""" Returns a KEGGPathway object, downloaded from KEGG, for the passed
KEGG map ID
"""
return read(retrieve_kgml_stream(map_id))
def retrieve_KEGG_pathway(map_id):
""" Returns a KEGGPathway object, downloaded from KEGG, for the passed
KEGG map ID
"""
return read(retrieve_kgml_stream(map_id))