def test_fileformat_ps(self):
''' test we can pick ps output format
'''
temp = tempfile.NamedTemporaryFile(suffix='.ps')
ext, surf = fileformat(temp.name, 50, 100)
self.assertEqual(ext, 'ps')
self.assertEqual(type(surf), cairo.PSSurface)
def test_fileformat_svg(self):
''' test we can pick svg output format
'''
temp = tempfile.NamedTemporaryFile(suffix='.svg')
ext, surf = fileformat(temp.name, 50, 100)
self.assertEqual(ext, 'svg')
self.assertEqual(type(surf), cairo.SVGSurface)
def test_fileformat_png(self):
''' test we can pick png output format
'''
temp = tempfile.NamedTemporaryFile(suffix='.png')
ext, surf = fileformat(temp.name, 50, 100)
self.assertEqual(ext, 'png')
self.assertEqual(type(surf), cairo.ImageSurface)
# check that we've set the height and width correctly
self.assertEqual(surf.get_height(), 100)
self.assertEqual(surf.get_width(), 50)
def covplot(seqfiles, chrom, start, end, fastafile, out=None):
'''
'''
if type(seqfiles) is not list:
seqfiles = [seqfiles]
chrom = str(chrom)
with pysam.FastaFile(fastafile) as handle:
reference = handle.fetch(start=start, end=end, region=chrom)
ref = reference
axis_offset = 75
cov_height = 200
height = len(seqfiles) * cov_height + (len(seqfiles) -
1) * 50 + axis_offset
out_type, surface = fileformat(out,
width=(end - start) * 10,
height=height)
context = cairo.Context(surface)
plot_axis(context, start, end, axis_offset - 10)
plot_grid(context, start, end, axis_offset, height)
for seqfile in seqfiles:
seq = pysam.AlignmentFile(seqfile, 'rb')
coords = OrderedDict({0: -1e9})
reps = (parse_read(x, coords, ref, start)
for x in seq.fetch(chrom, start, end))
plot_coverage(context, get_coverage(reps), axis_offset, start,
(end - start) * 10, cov_height)
axis_offset += cov_height
if seqfiles.index(seqfile) < len(seqfiles) - 1:
insert_spacer(context, coords, start, end)
axis_offset += 50
context.save()
if out_type == 'png':
surface.write_to_png(out)
elif out_type is None:
return surface.write_to_png()
def test_fileformat_unknown(self):
''' test we raise error for unknown output format
'''
with self.assertRaises(AssertionError):
fileformat('a.zzz', 50, 100)
def seqplot(seqfiles,
chrom,
start,
end,
fastafile,
out=None,
by_strand=False,
merge_delta=0.05):
''' the plotting function
Args:
seqfiles: list of paths to sequence files
chrom: chromosome to fetch reads from
start: start nucleotide of plotting window.
end: end nucleotide of plotting window.
fastafile: path to reference FASTA file.
out: path to write image file to, or None to return bytes-encoded png
by_strand: whether to shade reads by strand
merge_delta: difference allowed between neighboring qualities before not merging
Returns:
None, or if out is None, returns image plot as bytes-encoded png
'''
if type(seqfiles) is not list:
seqfiles = [seqfiles]
chrom = str(chrom)
with pysam.FastaFile(fastafile) as handle:
reference = handle.fetch(start=start, end=end, region=chrom)
ref = reference
axis_offset = 75
height = get_height(seqfiles, chrom, start, end, axis_offset)
out_type, surface = fileformat(out,
width=(end - start) * 10,
height=height)
context = cairo.Context(surface)
depths = [axis_offset]
for seqfile in seqfiles:
seq = pysam.AlignmentFile(seqfile, 'r')
coords = OrderedDict({max(depths): -1e9})
reps = (parse_read(x, coords, ref, start)
for x in seq.fetch(chrom, start, end))
_plot(context, reps, start, end, axis_offset, height, reference,
by_strand, merge_delta)
reference = None # don't plot the reference in subsequent BAMs
if seqfiles.index(seqfile) < len(seqfiles) - 1:
insert_spacer(context, coords, start, end)
depths.append(max(coords))
context.save()
if out_type == 'png':
surface.write_to_png(out)
elif out_type is None:
return surface.get_data()
def seqplot(seqfiles, chrom, start, end, fastafile, out=None, by_strand=False, add_names=False, verbose=False):
''' the plotting function
Args:
seqfiles: list of paths to sequence files
chrom: chromosome to fetch reads from
start: start nucleotide of plotting window.
end: end nucleotide of plotting window.
fastafile: path to reference FASTA file.
out: path to write image file to, or None to return bytes-encoded png
by_strand: whether to shade reads by strand
add_names: whether to print the name of the reference and the reads next to the sequence
verbose: whether to print additional information to STDOUT
Returns:
None, or if out is None, returns image plot as bytes-encoded png
'''
if type(seqfiles) is not list:
seqfiles = [seqfiles]
if add_names:
extraspace = 150
else:
extraspace = 0
if verbose:
print("FILE = {}\nREGION = {}:{}-{}".format(fastafile, chrom, start, end))
chrom = str(chrom)
with pysam.FastaFile(fastafile) as handle:
reference = handle.fetch(chrom, start, end)
ref = reference
axis_offset = 75
height = get_height(seqfiles, chrom, start, end, axis_offset)
out_type, surface = fileformat(out, width=(end - start) * 10 + extraspace, height=height)
context = cairo.Context(surface)
depths = [axis_offset]
right_border = 0
for seqfile in seqfiles:
seq = pysam.AlignmentFile(seqfile, 'rb')
refname = seq.get_reference_name(0)
coords = OrderedDict({max(depths): -1e9})
reps = ( parse_read(x, coords, ref, start) for x in seq.fetch(chrom, start, end) )
right_border = _plot(context, reps, start, end, axis_offset, height, right_border, reference, by_strand, refname)
reference = None # don't plot the reference in subsequent BAMs
if seqfiles.index(seqfile) < len(seqfiles) - 1:
insert_spacer(context, coords, start, end)
depths.append(max(coords))
context.save()
if out_type == 'png':
surface.write_to_png(out)
elif out_type is None:
return surface.write_to_png()