/usr/lib/python2.7/dist-packages/ngs/ReferenceSequence.py is in python-ngs 1.3.0-2.
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, create_string_buffer
from . import NGS
from .Refcount import Refcount
from .ErrorMsg import ErrorMsg
from .String import NGS_RawString, NGS_String, getNGSString, getNGSValue
# Represents a reference sequence standalone object
class ReferenceSequence(Refcount):
def getCanonicalName(self):
'''
:returns: the accessioned name of reference, e.g. "NC_000001.11"
'''
return getNGSString(self, NGS.lib_manager.PY_NGS_ReferenceSequenceGetCanonicalName)
def getIsCircular(self):
return bool(getNGSValue(self, NGS.lib_manager.PY_NGS_ReferenceSequenceGetIsCircular, c_int))
def getLength(self):
return getNGSValue(self, NGS.lib_manager.PY_NGS_ReferenceSequenceGetLength, 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_ReferenceSequenceGetReferenceBases(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_ReferenceSequenceGetReferenceChunk(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 openReferenceSequence(spec):
"""Create an object representing a named reference
:param: spec may be a path to an object or may be an id, accession, or URL
:throws: ErrorMsg if object cannot be located
:throws: ErrorMsg if object cannot be converted to a ReferenceSequence
:throws: ErrorMsg if an error occurs during construction
"""
ret = ReferenceSequence()
ERROR_BUFFER_SIZE = 4096
str_err = create_string_buffer(ERROR_BUFFER_SIZE)
from . import PY_RES_OK
res = NGS.lib_manager.PY_NGS_Engine_ReferenceSequenceMake(spec.encode(), byref(ret.ref), str_err, len(str_err))
if res != PY_RES_OK:
raise ErrorMsg(str_err.value)
return ret
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