def __call__(self, track, slice = None ):
edir = EXPORTDIR
method = "utr_extension"
blocks = ResultBlocks()
filepath = "%(edir)s/%(method)s/%(track)s.readextension_%(region)s_%(direction)s.%(slice)s.png"
block = \
'''
.. figure:: %(filename)s
:height: 300
'''
# append spaces for file extension
block = "\n".join( [ x + " " * 200 for x in block.split("\n") ] )
for region, direction in itertools.product( ("downstream", "upstream"),
("sense", "antisense", "anysense" )):
filename = filepath % locals()
if os.path.exists( filename ):
blocks.append( ResultBlock( text = block % locals(),
title = "%(track)s %(region)s %(direction)s" % locals() ) )
# else:
# blocks.append( ResultBlock( "",
# title = "%(track)s %(region)s %(direction)s" % locals() ) )
return odict( (("rst", "\n".join(Utils.layoutBlocks( blocks, layout="columns-3" ))),))
def __call__(self, track, slice=None):
# note there are spaces behind the %(image)s directive to accomodate
# for path substitution
block = '''
.. figure:: %(image)s
:height: 300
'''
blocks = ResultBlocks()
tracks = sorted([x.asFile() for x in TRACKS])
for track in tracks:
files = glob.glob(
os.path.join(EXPORTDIR, "fastqc", "%s*_fastqc" % track))
for x, fn in enumerate(sorted(files)):
y = x + 1
image = os.path.abspath(
os.path.join(fn, "Images", "%s.png" % slice))
if not os.path.exists(image):
continue
blocks.append(
ResultBlock(text=block % locals(),
title=os.path.basename(fn)))
return odict(
(("rst", "\n".join(Utils.layoutBlocks(blocks,
layout="columns-2"))), ))
