Source code for outrigger.region
"""Define locations in the genome"""
STRANDS = '+', '-', '.'
[docs]class Region(object):
__slots__ = ('region', 'chrom', 'start', 'stop', 'strand')
def __init__(self, name=None, region=None, chrom=None, start=None,
stop=None, strand=None):
"""A location in the genome
Parameters
----------
name : str
A string of either of the two forms:
- chrom:start-stop:strand, e.g. "chr1:100-200:-"
- region:chrom:start-stop:strand, e.g. "exon:chr1:100-200:+"
Start must always be smaller than stop.
"""
if name is not None:
region = None
try:
region, chrom, startstop, strand = name.split(':')
except ValueError:
# There is no "region"
chrom, startstop, strand = name.split(':')
start, stop = map(int, startstop.split('-'))
if start > stop:
raise ValueError('Start ({0}) cannot be larger than stop'
' ({1})'.format(start, stop))
self.region = region
self.chrom = chrom
self.start = start
self.stop = stop
self.strand = strand
# Use non-private start, stop to save negative strand coordinates with
# negative numbers to make the calculation of "before" and "after" in
# the transcript easier
@property
def _start(self):
"""Relative start of the feature
If strand is negative, this is negative so relativity is easy"""
if self.strand == '-':
return -self.start
else:
return self.start
@property
def _stop(self):
"""Relative start of the feature
If strand is negative, this is negative so relativity is easy"""
if self.strand == '-':
return -self.stop
else:
return self.stop
@property
def name(self):
base = '{0}:{1}-{2}:{3}'.format(self.chrom, self.start,
self.stop, self.strand)
if self.region is not None:
base = self.region + ':' + base
return base
def __len__(self):
"""Length of region. Add 1 to include last base of stop"""
return self.stop - self.start + 1
def __repr__(self):
return 'outrigger.Region ({0})'.format(self.name)
def __str__(self):
return self.__repr__()
def __eq__(self, other):
if isinstance(other, Region):
return all(getattr(self, attr) == getattr(other, attr)
for attr in self.__slots__)
else:
return False
def __neq__(self, other):
return not self.__eq__(other)
[docs] def overlaps(self, other):
"""Returns true if any part of other region is contained in this one"""
if other.chrom == self.chrom:
if other.start > self.stop or other.stop < self.start:
return False
else:
return True
else:
return False
[docs] def to_zero_based(self):
"""Convert genome coordinates to 0-based
Assumes that this event is one-based.
"""
region = self.region
chrom = self.chrom
start = self.start - 1
stop = self.stop
strand = self.strand
base = '{chrom}:{start}-{stop}:{strand}'.format(
chrom=chrom, start=start, stop=stop, strand=strand)
if region is not None:
base = '{region}:{base}'.format(region=region, base=base)
return Region(base)
