def test_write_arguments(self):
"""Check how the write methods respond to output format arguments."""
gdd = Diagram('Test Diagram')
gdd.drawing = None # Hack - need the ReportLab drawing object to be created.
filename = os.path.join("Graphics", "error.txt")
# We (now) allow valid formats in any case.
for output in ["XXX", "xxx", None, 123, 5.9]:
with self.assertRaises(ValueError):
gdd.write(filename, output)
with self.assertRaises(ValueError):
gdd.write_to_string(output)
def test_write_arguments(self):
"""Check how the write methods respond to output format arguments."""
gdd = Diagram("Test Diagram")
gdd.drawing = None # Hack - need the ReportLab drawing object to be created.
filename = os.path.join("Graphics", "error.txt")
# We (now) allow valid formats in any case.
for output in ["XXX", "xxx", None, 123, 5.9]:
with self.assertRaises(ValueError):
gdd.write(filename, output)
with self.assertRaises(ValueError):
gdd.write_to_string(output)
def test_write_arguments(self) :
"""Check how the write methods respond to output format arguments."""
gdd = Diagram('Test Diagram')
filename = os.path.join("Graphics","error.txt")
#We (now) allow valid formats in any case.
for output in ["XXX","xxx",None,123,5.9] :
try :
gdd.write(filename, output)
assert False, \
"Should have rejected %s as an output format" % output
except ValueError, e :
#Good!
pass
try :
gdd.write_to_string(output)
assert False, \
"Should have rejected %s as an output format" % output
except ValueError, e :
#Good!
pass
def test_write_arguments(self):
"""Check how the write methods respond to output format arguments."""
gdd = Diagram('Test Diagram')
filename = os.path.join("Graphics", "error.txt")
#We (now) allow valid formats in any case.
for output in ["XXX", "xxx", None, 123, 5.9]:
try:
gdd.write(filename, output)
assert False, \
"Should have rejected %s as an output format" % output
except ValueError, e:
#Good!
pass
try:
gdd.write_to_string(output)
assert False, \
"Should have rejected %s as an output format" % output
except ValueError, e:
#Good!
pass
def test_partial_diagram(self):
"""construct and draw SVG and PDF for just part of a SeqRecord."""
genbank_entry = self.record
start = 6500
end = 8750
gdd = Diagram(
'Test Diagram',
# For the circular diagram we don't want a closed cirle:
circular=False,
)
# Add a track of features,
gdt_features = gdd.new_track(1,
greytrack=True,
name="CDS Features",
scale_largetick_interval=1000,
scale_smalltick_interval=100,
scale_format="SInt",
greytrack_labels=False,
height=0.5)
# We'll just use one feature set for these features,
gds_features = gdt_features.new_set()
for feature in genbank_entry.features:
if feature.type != "CDS":
# We're going to ignore these.
continue
if feature.location.end.position < start:
# Out of frame (too far left)
continue
if feature.location.start.position > end:
# Out of frame (too far right)
continue
# This URL should work in SVG output from recent versions
# of ReportLab. You need ReportLab 2.4 or later
try:
url = "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi" +\
"?db=protein&id=%s" % feature.qualifiers["protein_id"][0]
except KeyError:
url = None
# Note that I am using strings for color names, instead
# of passing in color objects. This should also work!
if len(gds_features) % 2 == 0:
color = "white" # for testing the automatic black border!
else:
color = "red"
# Checking it can cope with the old UK spelling colour.
# Also show the labels perpendicular to the track.
gds_features.add_feature(feature,
colour=color,
url=url,
sigil="ARROW",
label_position=None,
label_size=8,
label_angle=90,
label=True)
# And draw it...
gdd.draw(format='linear',
orientation='landscape',
tracklines=False,
pagesize=(10 * cm, 6 * cm),
fragments=1,
start=start,
end=end)
output_filename = os.path.join('Graphics', 'GD_region_linear.pdf')
gdd.write(output_filename, 'PDF')
# Also check the write_to_string (bytes string) method matches,
# (Note the possible confusion over new lines on Windows)
assert open(output_filename, "rb").read().replace(b"\r\n", b"\n") \
== gdd.write_to_string('PDF').replace(b"\r\n", b"\n")
output_filename = os.path.join('Graphics', 'GD_region_linear.svg')
gdd.write(output_filename, 'SVG')
# Circular with a particular start/end is a bit odd, but by setting
# circular=False (above) a sweep of 90% is used (a wedge is left out)
gdd.draw(format='circular',
tracklines=False,
pagesize=(10 * cm, 10 * cm),
start=start,
end=end)
output_filename = os.path.join('Graphics', 'GD_region_circular.pdf')
gdd.write(output_filename, 'PDF')
output_filename = os.path.join('Graphics', 'GD_region_circular.svg')
gdd.write(output_filename, 'SVG')
def test_partial_diagram(self):
"""construct and draw SVG and PDF for just part of a SeqRecord."""
genbank_entry = self.record
start = 6500
end = 8750
gdd = Diagram('Test Diagram',
#For the circular diagram we don't want a closed cirle:
circular=False,
)
#Add a track of features,
gdt_features = gdd.new_track(1, greytrack=True,
name="CDS Features",
scale_largetick_interval=1000,
scale_smalltick_interval=100,
scale_format = "SInt",
greytrack_labels=False,
height=0.5)
#We'll just use one feature set for these features,
gds_features = gdt_features.new_set()
for feature in genbank_entry.features:
if feature.type != "CDS":
#We're going to ignore these.
continue
if feature.location.end.position < start:
#Out of frame (too far left)
continue
if feature.location.start.position > end:
#Out of frame (too far right)
continue
#This URL should work in SVG output from recent versions
#of ReportLab. You need ReportLab 2.4 or later
try :
url = "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi"+\
"?db=protein&id=%s" % feature.qualifiers["protein_id"][0]
except KeyError :
url = None
#Note that I am using strings for color names, instead
#of passing in color objects. This should also work!
if len(gds_features) % 2 == 0:
color = "white" # for testing the automatic black border!
else:
color = "red"
#Checking it can cope with the old UK spelling colour.
#Also show the labels perpendicular to the track.
gds_features.add_feature(feature, colour=color,
url = url,
sigil="ARROW",
label_position = None,
label_size = 8,
label_angle = 90,
label=True)
#And draw it...
gdd.draw(format='linear', orientation='landscape',
tracklines=False, pagesize=(10*cm,6*cm), fragments=1,
start=start, end=end)
output_filename = os.path.join('Graphics', 'GD_region_linear.pdf')
gdd.write(output_filename, 'PDF')
#Also check the write_to_string method matches,
#(Note the possible confusion over new lines on Windows)
assert open(output_filename).read().replace("\r\n","\n") \
== gdd.write_to_string('PDF').replace("\r\n","\n")
output_filename = os.path.join('Graphics', 'GD_region_linear.svg')
gdd.write(output_filename, 'SVG')
#Circular with a particular start/end is a bit odd, but by setting
#circular=False (above) a sweep of 90% is used (a wedge is left out)
gdd.draw(format='circular',
tracklines=False, pagesize=(10*cm,10*cm),
start=start, end=end)
output_filename = os.path.join('Graphics', 'GD_region_circular.pdf')
gdd.write(output_filename, 'PDF')
output_filename = os.path.join('Graphics', 'GD_region_circular.svg')
gdd.write(output_filename, 'SVG')
