/usr/lib/python3/dist-packages/ngs/Reference.py is in python3-ngs 1.3.0-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
#
#
from ctypes import byref, c_int, c_uint64
from . import NGS
from .Refcount import Refcount
from .String import NGS_RawString, NGS_String, getNGSString, getNGSValue
from .Alignment import Alignment
from .AlignmentIterator import AlignmentIterator
from .PileupIterator import PileupIterator
# Represents a reference sequence
class Reference(Refcount):
def getCommonName(self):
"""
:returns: the common name of reference, e.g. "chr1"
"""
return getNGSString(self, NGS.lib_manager.PY_NGS_ReferenceGetCommonName)
def getCanonicalName(self):
'''
:returns: the accessioned name of reference, e.g. "NC_000001.11"
'''
return getNGSString(self, NGS.lib_manager.PY_NGS_ReferenceGetCanonicalName)
def getIsCircular(self):
return bool(getNGSValue(self, NGS.lib_manager.PY_NGS_ReferenceGetIsCircular, c_int))
def getLength(self):
return getNGSValue(self, NGS.lib_manager.PY_NGS_ReferenceGetLength, c_uint64)
def getReferenceBases(self, offset, length=-1):
"""
:param: offset is zero-based and non-negative
:param: length must be >= 0
:returns: sub-sequence bases for Reference
"""
ngs_str_err = NGS_RawString()
try:
ngs_str_ret = NGS_String()
try:
res = NGS.lib_manager.PY_NGS_ReferenceGetReferenceBases(self.ref, offset, length, byref(ngs_str_ret.ref), byref(ngs_str_err.ref))
return ngs_str_ret.getPyString()
finally:
ngs_str_ret.close()
finally:
ngs_str_err.close()
def getReferenceChunk(self, offset, length=-1):
"""
:param: offset is zero-based and non-negative
:param: length must be >= 0
:returns: largest contiguous chunk available of sub-sequence bases for Reference
NB - actual returned sequence may be shorter
than requested. to obtain all bases available
in chunk, use a negative "size" value
"""
ngs_str_err = NGS_RawString()
try:
ngs_str_ret = NGS_String()
try:
res = NGS.lib_manager.PY_NGS_ReferenceGetReferenceChunk(self.ref, offset, length, byref(ngs_str_ret.ref), byref(ngs_str_err.ref))
return ngs_str_ret.getPyString()
finally:
ngs_str_ret.close()
finally:
ngs_str_err.close()
# ----------------------------------------------------------------------
# ALIGNMENTS
def getAlignment(self, alignmentId):
"""
:returns: an individual Alignment
:throws: ErrorMsg if Alignment does not exist or is not part of this Reference
"""
ret = Alignment()
ngs_str_err = NGS_RawString()
try:
res = NGS.lib_manager.PY_NGS_ReferenceGetAlignment(self.ref, alignmentId.encode("UTF-8"), byref(ret.ref), byref(ngs_str_err.ref))
finally:
ngs_str_err.close()
return ret
def getAlignments(self, categories):
"""
:returns: an iterator of contained alignments
"""
ret = AlignmentIterator()
ngs_str_err = NGS_RawString()
try:
res = NGS.lib_manager.PY_NGS_ReferenceGetAlignments(self.ref, categories, byref(ret.ref), byref(ngs_str_err.ref))
finally:
ngs_str_err.close()
return ret
def getAlignmentSlice(self, start, length, categories=Alignment.all):
"""
:param: start is a signed 0-based offset from the start of the Reference
:param: length is the length of the slice.
:param: categories provides a means of filtering by AlignmentCategory
:returns: an iterator across a range of Alignments
"""
ret = AlignmentIterator()
ngs_str_err = NGS_RawString()
try:
res = NGS.lib_manager.PY_NGS_ReferenceGetAlignmentSlice(self.ref, start, length, categories, byref(ret.ref), byref(ngs_str_err.ref))
finally:
ngs_str_err.close()
return ret
def getFilteredAlignmentSlice(self, start, length, categories, filters, mappingQuality):
"""Behaves like "getAlignmentSlice" except that supported filters are applied to selection
:param: start is a signed 0-based offset from the start of the Reference
:param: length is the length of the slice.
:param: categories provides a means of filtering by AlignmentCategory
:param: filters is a set of filter bits defined in Alignment
:param: mappingQuality is a cutoff to be used according to bits in "filter"
:returns: an iterator across a range of Alignments
"""
ret = AlignmentIterator()
ngs_str_err = NGS_RawString()
try:
res = NGS.lib_manager.PY_NGS_ReferenceGetFilteredAlignmentSlice(self.ref, start, length, categories, filters, mappingQuality, byref(ret.ref), byref(ngs_str_err.ref))
finally:
ngs_str_err.close()
return ret
# ----------------------------------------------------------------------
# PILEUP
def getPileups(self, categories):
"""
:returns: an iterator of contained Pileups
"""
ret = PileupIterator()
ngs_str_err = NGS_RawString()
try:
res = NGS.lib_manager.PY_NGS_ReferenceGetPileups(self.ref, categories, byref(ret.ref), byref(ngs_str_err.ref))
finally:
ngs_str_err.close()
return ret
def getFilteredPileups(self, categories, filters, mappingQuality):
"""
:returns: an iterator of contained Pileups
"""
ret = PileupIterator()
ngs_str_err = NGS_RawString()
try:
res = NGS.lib_manager.PY_NGS_ReferenceGetFilteredPileups(self.ref, categories, filters, mappingQuality, byref(ret.ref), byref(ngs_str_err.ref))
finally:
ngs_str_err.close()
return ret
def getPileupSlice(self, start, length, categories=Alignment.all):
"""Creates a PileupIterator on a slice (window) of reference
:param: start is the signed starting position on reference
:param: length is the unsigned number of bases in the window
:param: categories provides a means of filtering by AlignmentCategory
:returns: an iterator of contained Pileups
"""
ret = PileupIterator()
ngs_str_err = NGS_RawString()
try:
res = NGS.lib_manager.PY_NGS_ReferenceGetPileupSlice(self.ref, start, length, categories, byref(ret.ref), byref(ngs_str_err.ref))
finally:
ngs_str_err.close()
return ret
def getFilteredPileupSlice(self, start, length, categories, filters, mappingQuality):
"""Creates a PileupIterator on a slice (window) of reference
:param: start is the signed starting position on reference
:param: length is the unsigned number of bases in the window
:param: categories provides a means of filtering by AlignmentCategory
:param: filters is a set of filter bits defined in Alignment
:param: mappingQuality is a cutoff to be used according to bits in "filter"
:returns: an iterator of contained Pileups
"""
ret = PileupIterator()
ngs_str_err = NGS_RawString()
try:
res = NGS.lib_manager.PY_NGS_ReferenceGetFilteredPileupSlice(self.ref, start, length, categories, filters, mappingQuality, byref(ret.ref), byref(ngs_str_err.ref))
finally:
ngs_str_err.close()
return ret
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