from array import array
from collections import namedtuple
-_PY_VERSION = sys.version
+_PY_VERSION = sys.version_info
-if _PY_VERSION.startswith('2'):
+if _PY_VERSION[0] == 2:
from io import open
-
-if not _PY_VERSION.startswith('2'):
+else:
from functools import lru_cache
from bamnostic.utils import *
-def format_warnings(message, category, filename, lineno, file=None, line=None):
- return ' {}:{}: {}:{}'.format(filename, lineno, category.__name__, message)
-
-
warnings.formatwarning = format_warnings
# Helper compiled structs
@@ -227,19 +221,14 @@ Source code for bamnostic.bai
RefIdx = namedtuple('RefIdx', ('start_offset', 'end_offset', 'n_bins'))
-class Bin(object):
- __slots__ = ['bin_id', 'chunks']
-
- def __init__(self, *args):
- self.bin_id, self.chunks = args
-
-
class Chunk(object):
__slots__ = ['voffset_beg', 'voffset_end']
def __init__(self, handle):
self.voffset_beg, self.voffset_end = unpack_chunk(handle.read(16))
+ def __repr__(self):
+ return 'Chunk(voffset_beg={}, voffset_end={})'.format(self.voffset_beg, self.voffset_end)
class Ref(object):
__slots__ = ['bins', 'intervals', 'ref_id']
@@ -247,6 +236,9 @@ Source code for bamnostic.bai
def __init__(self, *args):
self.bins, self.intervals, self.ref_id = args
+ def __getitem__(self, key):
+ return self.bins[key]
+
class Unmapped(object):
__slots__ = ['unmapped_beg', 'unmapped_end', 'n_mapped', 'n_unmapped']
@@ -258,20 +250,20 @@ Source code for bamnostic.bai
self.n_unmapped = numap
-[docs]def reg2bin(beg, end):
+[docs]def reg2bin(rbeg, rend):
"""Finds the largest superset bin of region. Numeric values taken from hts-specs
Args:
- beg (int): inclusive beginning position of region
- end (int): exclusive end position of region
+ rbeg (int): inclusive beginning position of region
+ rend (int): exclusive end position of region
Returns:
(int): distinct bin ID for largest superset bin of region
"""
left_shift = 15
for i in range(14, 27, 3):
- if beg >> i == (end - 1) >> i:
- return int(((1 << left_shift) - 1) / 7 + (beg >> i))
+ if rbeg >> i == (rend - 1) >> i:
+ return int(((1 << left_shift) - 1) / 7 + (rbeg >> i))
left_shift -= 3
else:
return 0
@@ -281,8 +273,8 @@ Source code for bamnostic.bai
"""Generates bin ids which overlap the specified region.
Args:
- beg (int): inclusive beginning position of region
- end (int): exclusive end position of region
+ rbeg (int): inclusive beginning position of region
+ rend (int): exclusive end position of region
Yields:
(int): bin IDs for overlapping bins of region
@@ -357,7 +349,6 @@ Source code for bamnostic.bai
self._io = open(filename, 'rb')
else:
raise OSError('{} not found. Please change check your path or index your BAM file'.format(filename))
- self._io = open(filename, 'rb')
# Constant for linear index window size and unmapped bin id
self._LINEAR_INDEX_WINDOW = 16384
@@ -477,7 +468,7 @@ Source code for bamnostic.bai
# @functools.lru_cache(maxsize=256, typed=True)
# @lru_cache(6)
-[docs] @conditional_decorator(lambda func: lru_cache(maxsize=6)(func), _PY_VERSION.startswith('2'))
+[docs] @conditional_decorator(lambda func: lru_cache(maxsize=6)(func), _PY_VERSION[0] == 2)
def get_ref(self, ref_id=None, idx=False):
"""Interatively unpacks all the bins, linear intervals, and chunks for a given reference
@@ -567,12 +558,12 @@ Source code for bamnostic.bai
for binID in reg2bins(start, stop):
try:
- bin_chunks = self.current_ref.bins[binID]
+ bin_chunks = self.current_ref[binID]
except KeyError:
continue
for chunk in bin_chunks:
- if not linear_offset <= chunk.voffset_end:
+ if not chunk.voffset_beg <= linear_offset <= chunk.voffset_end:
continue
else:
return chunk.voffset_beg
@@ -632,7 +623,7 @@ Source code for bamnostic.bai
- © Copyright 2018, Marcus D. Sherman.
+ © Copyright 2018, Marcus D. Sherman
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