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import subprocess
import pybedtools
def bigbed(
x,
genome,
output,
blockSize=256,
itemsPerSlot=512,
bedtype=None,
_as=None,
unc=False,
tab=False,
):
"""
Converts a BedTool object to a bigBed format and returns the new filename.
`x` is a BedTool object
`genome` is an assembly string
`output` is the name of the bigBed file to create.
Other args are passed to bedToBigBed. In particular, `bedtype` (which
becomes the "-type=" argument) is automatically handled for you if it is
kept as the default None.
Assumes that a recent version of bedToBigBed from UCSC is on the path.
"""
if isinstance(x, str):
x = pybedtools.BedTool(x)
if not isinstance(x.fn, str):
x = x.saveas()
chromsizes = pybedtools.chromsizes_to_file(pybedtools.chromsizes(genome))
if bedtype is None:
bedtype = "bed%s" % x.field_count()
cmds = [
"bedToBigBed",
x.fn,
chromsizes,
output,
"-blockSize=%s" % blockSize,
"-itemsPerSlot=%s" % itemsPerSlot,
"-type=%s" % bedtype,
]
if unc:
cmds.append("-unc")
if tab:
cmds.append("-tab")
if _as:
cmds.append("-as=%s" % _as)
p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
stdout, stderr = p.communicate()
if p.returncode:
raise ValueError(
"cmds: %s\nstderr:%s\nstdout:%s" % (" ".join(cmds), stderr, stdout)
)
return output
def bigbed_to_bed(fn, chrom=None, start=None, end=None, maxItems=None):
cmds = ["bigBedToBed", fn]
if chrom is not None:
cmds.extend(["-chrom", chrom])
if start is not None:
cmds.extend(["-start", start])
if end is not None:
cmds.extend(["-end", end])
if maxItems is not None:
cmds.extend(["-maxItems", maxItems])
outfn = pybedtools.BedTool._tmp()
cmds.append(outfn)
p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
stdout, stderr = p.communicate()
if p.returncode:
raise ValueError(
"cmds: %s\nstderr:%s\nstdout:%s" % (" ".join(cmds), stderr, stdout)
)
return pybedtools.BedTool(outfn)
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