def plot_i_tool(i, method, **kwargs):
a = pybedtools.BedTool(i)
result = getattr(a, method)(**kwargs)
fig = plt.figure(figsize=(8, 2))
ax = fig.add_subplot(111)
res_track = plotting.Track(result, color='r', alpha=0.5, ybase=0, visibility='squish')
a_track = plotting.Track(a, color='b', alpha=0.5, ybase=1.1, visibility='squish')
ax.add_collection(res_track)
ax.add_collection(a_track)
ax.set_yticks([res_track.midpoint, a_track.midpoint])
ax.set_yticklabels(['result', os.path.basename(a.fn)])
ax.axis('tight')
ax.set_title(' '.join([os.path.basename(k) for k in result._cmds]))
fig.subplots_adjust(top=0.8, bottom=0.15)
return ax
def plot_a_b_tool(a, b, method, **kwargs):
"""
Use for BEDTools programs that use -a and -b input arguments. Filenames
`a` and `b` are used for `method` of the BedTool class, and `kwargs` are
sent to that method.
The result is a plot of `a`, `b`, and the result, with the commandline
argument as the plot title.
"""
a = pybedtools.BedTool(a)
b = pybedtools.BedTool(b)
kwargs["b"] = b
result = getattr(a, method)(**kwargs)
fig = plt.figure(figsize=(8, 2))
ax = fig.add_subplot(111)
ybase = 0
yheight = 1
ylabels = []
yticks = []
for color, bt, label in zip(
colors,
[result, b, a],
["result", os.path.basename(b.fn),
os.path.basename(a.fn)],
):
ylabels.append(label)
track = plotting.Track(bt,
visibility="squish",
alpha=0.5,
ybase=ybase,
color=color)
yticks.append(track.midpoint)
ybase = track.ymax + 0.1
ax.add_collection(track)
ax.set_yticklabels(ylabels)
ax.set_yticks(yticks)
ax.set_title(" ".join([os.path.basename(i) for i in result._cmds]))
ax.axis("tight")
fig.subplots_adjust(top=0.8, bottom=0.15)
return ax
def plot_bedtool(filea, fileb=None, method=None, **kwargs):
"""
Use for BEDTools programs that use -a and -b input arguments. Filenames
`a` and `b` are used for `method` of the BedTool class, and `kwargs` are
sent to that method.
The result is a plot of `a`, `b`, and the result, with the commandline
argument as the plot title.
"""
a = pybedtools.BedTool(filea)
if fileb is not None:
b = pybedtools.BedTool(fileb)
kwargs['b'] = fileb
result = getattr(a, method)(**kwargs)
bfn = b.fn
bts = [result, b, a]
labels = ['result', os.path.basename(b.fn), os.path.basename(a.fn)]
else:
result = getattr(a, method)(**kwargs)
bfn = None
bts = [result, a]
labels = ['result', os.path.basename(a.fn)]
fig = plt.figure(figsize=(8, 3))
ax = fig.add_subplot(111)
ybase = 0
yheight = 1
ylabels = []
yticks = []
pad = 0.4
any_stranded = sum(sum(j.strand != '.' for j in i) for i in bts)
for color, bt, label in zip(colors, bts, labels):
if bt is None:
continue
ax.axhline(ybase, color='k', zorder=100)
ybase += pad
if any_stranded:
strands = ['+', '-', '.']
strand_labels = {
'+': '(+)',
'-': '(-)',
'.': '( )',
}
else:
strands = ['.']
strand_labels = {'.': ''}
for strand in strands:
sbt = bt.filter(lambda x: x.strand == strand)
ylabels.append(label + ' ' + strand_labels[strand])
track = plotting.Track(
sbt, visibility='squish', alpha=0.5, ybase=ybase, color=color, stranded=False)
yticks.append(track.midpoint)
ybase = track.ymax + pad
ax.axhline(ybase, color='0.7', linewidth=0.3)
if strand != '.':
ybase += pad
ax.add_collection(track)
ax.axhline(ybase, color='k', zorder=100)
ax.set_yticklabels(ylabels, fontdict=dict(name='Monospace'))
ax.set_yticks(yticks)
cmds = result._cmds
cmds[0] = 'bedtools ' + pybedtools.settings._prog_names[cmds[0]]
cleaned_cmds = fix_args(cmds)
ax.set_title(cleaned_cmds, fontdict=dict(name='Monospace'))
ax.axis('tight')
fig.subplots_adjust(top=0.8, bottom=0.15)
sns.despine(ax=ax, left=True, right=True, top=True)
plt.tick_params(axis='y', which='both', left='off')
ax.axis(ymin=0)
return ax, cleaned_cmds
b = pybedtools.example_filename('b.bed')
plot_a_b_tool(a, b, 'intersect', u=True)
plot_a_b_tool(a, b, 'intersect')
plot_a_b_tool(a, b, 'subtract')
plot_i_tool(a, 'merge')
# Check performance -- should be <2s for 15k features
t0 = time.time()
fig = plt.figure(figsize=(8, 2))
ax = fig.add_subplot(111)
big = pybedtools.example_bedtool('dm3-chr2L-5M.gff.gz')
gene_track = plotting.Track(big.filter(lambda x: x[2] == 'gene'),
color='k',
visibility='squish',
alpha=0.5,
label='genes')
exon_track = plotting.Track(big.filter(lambda x: x[2] == 'exon'),
color='r',
visibility='squish',
alpha=0.5,
ybase=gene_track.ymax,
label='exons')
ax.add_collection(gene_track)
ax.add_collection(exon_track)
ax.legend(loc='best')
ax.axis('tight')
print '%.2fs' % (time.time() - t0)
plot_a_b_tool(a, b, "intersect", u=True)
plot_a_b_tool(a, b, "intersect")
plot_a_b_tool(a, b, "subtract")
plot_i_tool(a, "merge")
# Check performance -- should be <2s for 15k features
t0 = time.time()
fig = plt.figure(figsize=(8, 2))
ax = fig.add_subplot(111)
big = pybedtools.example_bedtool("dm3-chr2L-5M.gff.gz")
gene_track = plotting.Track(
big.filter(lambda x: x[2] == "gene"),
color="k",
visibility="squish",
alpha=0.5,
label="genes",
)
exon_track = plotting.Track(
big.filter(lambda x: x[2] == "exon"),
color="r",
visibility="squish",
alpha=0.5,
ybase=gene_track.ymax,
label="exons",
)
ax.add_collection(gene_track)
ax.add_collection(exon_track)
ax.legend(loc="best")