def compare(fileUrl, chrom, start, end):
bbiStartTime = time.time()
with bbi.open(fileUrl) as file:
file.fetch(chrom, start, end)
bbiEndTime = time.time()
osStartTime = time.time()
subprocess.run([
'bin/bigWigToBedGraph', fileUrl, 'out/out.bedGraph',
'-chrom=%s' % chrom,
'-start=%s' % start,
'-end=%s' % end
],
stdout=subprocess.PIPE).stdout.decode('utf-8')
osEndTime = time.time()
return pd.Series({
'chrom': chrom,
'start': start,
'end': end,
'length': end - start,
'bbiStartTime': bbiStartTime,
'bbiEndTime': bbiEndTime,
'bbiTimeDiff': bbiEndTime - bbiStartTime,
'osStartTime': osStartTime,
'osEndTime': osEndTime,
'osTimeDiff': osEndTime - osStartTime
})
def read_bigbed(path, chrom, start=None, end=None, engine="auto"):
"""
Read intervals from a bigBed file.
Parameters
----------
path : str
Path or URL to a bigBed file
chrom : str
start, end : int, optional
Start and end coordinates. Defaults to 0 and chromosome length.
engine : {"auto", "pybbi", "pybigwig"}
Library to use for querying the bigBed file.
Returns
-------
DataFrame
"""
engine = engine.lower()
if engine == "auto":
if bbi is None and pyBigWig is None:
raise ImportError(
"read_bigbed requires either the pybbi or pyBigWig package"
)
elif bbi is not None:
engine = "pybbi"
else:
engine = "pybigwig"
if engine in ("pybbi", "bbi"):
if start is None:
start = 0
if end is None:
end = -1
with bbi.open(path) as f:
df = f.fetch_intervals(chrom, start=start, end=end)
elif engine == "pybigwig":
f = pyBigWig.open(path)
if start is None:
start = 0
if end is None:
end = f.chroms()[chrom]
ivals = f.entries(chrom, start, end)
df = pd.DataFrame(ivals, columns=["start", "end", "rest"])
df.insert(0, "chrom", chrom)
else:
raise ValueError(
"engine must be 'auto', 'pybbi' or 'pybigwig'; got {}".format(engine)
)
return df
def getCoverageFile(task, dataPath):
problem = task['problem']
coveragePath = os.path.join(dataPath, 'coverage.bedGraph')
coverageUrl = task['trackUrl']
with bbi.open(coverageUrl) as coverage:
try:
coverageInterval = coverage.fetch_intervals(problem['chrom'],
problem['chromStart'],
problem['chromEnd'],
iterator=True)
return fixAndSaveCoverage(coverageInterval, coveragePath, problem)
except KeyError:
return
def runTest(fileUrl, chrom, start, end, bins):
diff = end - start
if diff <= bins:
raise Exception
bbiStartTime = time.time()
with bbi.open(fileUrl) as file:
bbiOut = file.fetch(chrom, start, end, bins)
bbiEndTime = time.time()
bbiLen = len(bbiOut)
subprocessStartTime = time.time()
subprocessOut = subprocess.run(
['bin/bigWigSummary', fileUrl, chrom,
str(start),
str(end),
str(bins)],
stdout=subprocess.PIPE).stdout.decode('utf-8')
data = subprocessOut.split()
floatData = []
for i in data:
try:
floatData.append(float(i))
except ValueError:
continue
data = np.array(floatData).astype(np.double)
subprocessEndTime = time.time()
subprocessLen = len(data)
return {
'chrom': chrom,
'start': start,
'end': end,
'diff': diff,
'bins': bins,
'bbiStartTime': bbiStartTime,
'bbiEndTime': bbiEndTime,
'bbiTimeDiff': bbiEndTime - bbiStartTime,
'bbiLen': bbiLen,
'subprocessStartTime': subprocessStartTime,
'subprocessEndTime': subprocessEndTime,
'subprocessTimeDiff': subprocessEndTime - subprocessStartTime,
'subprocessLen': subprocessLen
}
def runTest(fileUrl, chrom, start, end, bins):
diff = end - start
if diff <= bins:
raise Exception
bbiStartTime = time.time()
bbiLen = 0
with bbi.open(fileUrl) as file:
bbiOut = file.fetch(chrom, start, end, bins)
bbiEndTime = time.time()
bbiLen = len(bbiOut)
osCommand = './bigWigSummary %s %s %s %s %s' % (fileUrl, chrom, start, end,
bins)
osStartTime = time.time()
osOut = subprocess.run(
['./bigWigSummary', fileUrl, chrom,
str(start),
str(end),
str(bins)],
stdout=subprocess.PIPE).stdout.decode('utf-8')
osEndTime = time.time()
osLen = len(osOut.split())
return {
'chrom': chrom,
'start': start,
'end': end,
'diff': diff,
'bins': bins,
'bbiStartTime': bbiStartTime,
'bbiEndTime': bbiEndTime,
'bbiTimeDiff': bbiEndTime - bbiStartTime,
'bbiLen': bbiLen,
'osStartTime': osStartTime,
'osEndTime': osEndTime,
'osTimeDiff': osEndTime - osStartTime,
'osLen': osLen
}
def __init__(self, file, **kwargs):
properties = BigWig.DEFAULT_PROPERTIES.copy()
properties.update({'file': file, **kwargs})
super().__init__(**properties)
import bbi
self.bw = bbi.open(self.properties['file'])
