'score']].drop_duplicates().sort_values(by=['chrom', 'start'])
elif strd == True:
bed['name'] = 'range_id_R' + (bed['index'] + 1).astype(str) + '_' + \
bed['chrom'].astype(str) + '_' + \
bed['start'].astype(str) + '_' + \
bed['end'].astype(str) + '_' + \
bed['strand'].astype(str)
bed = bed[['chrom', 'start', 'end', 'name', 'score',
'strand']].drop_duplicates().sort_values(by=['chrom', 'start'])
if not args.debug:
pass
else:
bed = bed.head(args.debug)
BedTool.from_dataframe(bed).saveas(args.outfile +
'.datamatrix/genomic_ranges.bed')
print()
print("Generating FASTA sequences for each entry")
if args.create_fastas == True:
Popen('mkdir -p ' + args.outfile + '.datamatrix/temp/fastas', shell=True)
entry_list = list(range(len(bed)))
if __name__ == '__main__':
p = Pool((args.ncores))
p.map(make_fasta, entry_list)
else:
for k in chromosomes.keys()
}
for k in chromosomes.keys():
print chrom_Intervals[k][0:10]
with open('humanBedInterval.bed', 'w') as f:
for k in chromosomes.keys():
f.write('\n'.join(
'%s\t%d\t%d' %
(k, chrom_Intervals[k][i], chrom_Intervals[k][i + 1] - 1)
for i in range(len(chrom_Intervals[k]) - 1)) + '\n')
a = BedTool('humanBedInterval.bed').sort()
b = BedTool('/mnt/disks/data-vcf/GSN79Tumor_normal.vcf')
print a.head()
print b.head()
a.coverage(b).saveas('VCFCoverage.bed') #,hist=True
#for k in chromosomes.keys():
positionHistogram = defaultdict(list)
with open('/mnt/disks/data-vcf/GSN79Tumor_normal.vcf', 'r') as f:
for line in f.readlines():
if line and line.startswith('#') == 0:
if line.split('\t')[0] not in positionHistogram.keys():
positionHistogram[line.split('\t')[0]] = []
positionHistogram[line.split('\t')[0]].append(
int(line.split('\t')[1]))
class Bed:
""" The Bed class is a wrapper to the pybedtools.BedTool class.
It handles the temporary file internally, and provides interface to several BedTool methods.
Attributes
----------
fn: string
The temporary filename sitting on disk that holds contents of this Bed() object.
istmp: bool
Flag for whether this Bed() object is temporary. If temporary, self.fn file will be deleted upon destruction.
__len__: int
Number of intervals contained in this Bed() object.
"""
def __init__(self, fn=None):
""" Initializer of Bed class.
Parameters
----------
fn: None, BedTool, string, tuple, list, generator
None: Empty Bed() object
BedTool: wraps input existing BedTool object.
string: filename, wraps the input file with name {fn}.
list/tuple/generator: loops over the input fn, writing as an temporary file, wraps it.
Init with this type will automatically set self.istmp=True
"""
self.istmp = False # flag, set to true to delete the bed file during destruction
if fn == None:
self.bedtool = BedTool()
elif isinstance(fn, BedTool):
self.bedtool = fn
elif isinstance(fn, str):
self.bedtool = BedTool(fn)
elif isinstance(fn, collections.Iterable):
tmpfn = write_tmp_bed(fn)
self.bedtool = BedTool(tmpfn)
self.istmp = True
else:
self.bedtool = None
raise NotImplementedError(
f'Initializing with type {type(fn)} is not implemented')
@property
def fn(self):
return self.bedtool.fn
def __len__(self):
if not self.fn:
return 0
with open(self.fn) as fn:
length = sum(1 for line in fn)
return length
def __str__(self):
return self.bedtool.__str__()
def __getitem__(self, key):
return self.bedtool.__getitem__(key)
def __iter__(self):
return self.bedtool.__iter__()
def __eq__(self, target):
if len(self) != len(target):
return False
elif len(self) == len(target) == 0:
return True
else:
return self.bedtool == target.bedtool
def _delete_tmp(self):
if self.istmp == True:
try:
os.unlink(self.fn)
except FileNotFoundError:
pass
def __del__(self):
self._delete_tmp()
del self.bedtool
def head(self):
""" Wrapper for BelTool.head() method, which prints the first few intervals. """
self.bedtool.head()
def copy(self):
""" Create a temporary copy of the Bed() object. """
newfn = tempfile.mkstemp(suffix='.bed', prefix='sirius_')[1]
shutil.copyfile(self.fn, newfn)
newBed = Bed(newfn)
newBed.istmp = True
return newBed
def extend(self, d):
""" Modify the intervals by extending each to left and right by {d} """
self.extend_asym(d, d)
def extend_asym(self, dl, dr):
""" Extend the range of each interval, by dl to left and dr to right """
# create a new file with extended range
def gen_iv_ext():
# we use a generator to
for iv in self.bedtool:
chrom, start, end, name, score, strand, _id, tp = iv.fields[:8]
yield (chrom, int(start) - dl, int(end) + dr, name, score,
strand, _id, tp)
newfn = write_tmp_bed(gen_iv_ext())
# delete the old tmp file
self._delete_tmp()
# switch to the new file
self.bedtool = BedTool(newfn)
# we are now using a tmp file
self.istmp = True
def gids(self):
""" Return a set of gnode ids from self.bedtool """
return set(iv[3] for iv in self.bedtool)
def intersect(self, b):
""" intersect method wrapps BedTool.intersect()
Parameters
----------
b: Bed
Target Bed() object to be intersected with
Returns
-------
c: Bed
Temporary Bed() object that contains all intervals in {self} which intersects with {b}.
"""
c = Bed()
c.bedtool = self.bedtool.intersect(b.bedtool, u=True)
c.istmp = True
return c
def window(self, b, window=1000):
""" window method wrapps BedTool.window()
Parameters
----------
b: Bed
Target Bed() object to be windowed with
window: int, default 1000
The window size
Returns
-------
c: Bed
Temporary Bed() object that contains all intervals in {self} which is within {window} from any interval in {b}.
"""
c = Bed()
c.bedtool = self.bedtool.window(b.bedtool, w=window, u=True)
c.istmp = True
return c
