/usr/lib/python2.7/dist-packages/ngs/String.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 c_void_p, c_size_t, c_char_p, string_at, byref, cast
from . import NGS
class NGS_String:
"""Refcounted object to work with StringItf objects imported from ngs-sdk
Provides read-only operaton getPyString: returns python str object constructed from StringItf
"""
def __init__(self):
self.init_members_with_null()
def __del__(self):
self.close()
def __enter__(self):
return self
def __exit__(self, t, value, traceback):
self.close()
def close(self):
if self.ref:
from .Refcount import RefcountRelease
RefcountRelease(self.ref)
self.init_members_with_null()
def init_members_with_null(self):
self.ref = c_void_p()
self.size = c_size_t()
self.data = c_char_p()
def getData(self):
if not self.ref:
pass # TODO: process error?
res = NGS.lib_manager.PY_NGS_StringGetData(self.ref, byref(self.data))
# TODO: process error?
return self.data.value
def getSize(self):
if not self.ref:
pass # TODO: process error?
res = NGS.lib_manager.PY_NGS_StringGetSize(self.ref, byref(self.size))
# TODO: process error?
return self.size.value
def getPyString(self):
ret = string_at(self.getData(), self.getSize()).decode()
if isinstance(ret, bytes):
ret = ret.decode(encoding='UTF-8')
return ret
class NGS_RawString:
"""object to work with raw string (char*) objects imported from ngs-sdk
Provides read-only operaton getPyString: returns python str object constructed from raw ngs-sdk string
This class is used for getting error string from ngs-sdk sicne its StringItf class doesn't provide
interface for NGS string duplication (creating a copy)
"""
def __init__(self):
self.init_members_with_null()
def __del__(self):
self.close()
def __enter__(self):
return self
def __exit__(self, t, value, traceback):
self.close()
def close(self):
if self.ref:
from .Refcount import RefcountRawStringRelease
RefcountRawStringRelease(self.ref)
self.init_members_with_null()
def init_members_with_null(self):
self.ref = c_void_p()
def ref_to_char_p(self):
return cast(self.ref, c_char_p)
def getData(self):
if not self.ref:
pass # TODO: process error?
return self.ref_to_char_p().value
def getSize(self):
if not self.ref:
pass # TODO: process error?
return len(self.ref_to_char_p().value)
def getPyString(self):
ret = string_at(self.getData(), self.getSize()).decode()
if isinstance(ret, bytes):
ret = ret.decode(encoding='UTF-8')
return ret
def getNGSString(self, py_func):
"""Getter that returns a string-attribute for a given NGS-object (Read, Fragment, Alignment etc.)
:param self: python class representing NGS-object (like Read or Fragment)
:param py_func: PY-function returning NGS_String for a given NGS-object
:returns: python str object
:throws: ErrorMsg
:remarks: NGS_String object is automatically released after this function returns
"""
ngs_str_err = NGS_RawString()
try:
ngs_str_seq = NGS_String()
try:
res = py_func(self.ref, byref(ngs_str_seq.ref), byref(ngs_str_err.ref))
#check_res(res, ngs_str_err)
return ngs_str_seq.getPyString()
finally:
ngs_str_seq.close()
finally:
ngs_str_err.close()
def getNGSValue(self, py_func, value_type):
"""Getter that returns a typed attribute for a given NGS-object (Read, Fragment, Alignment etc.)
:param self: python class representing NGS-object (like Read or Fragment)
:param py_func: PY-function returning a typed object for a given NGS-object
:param value_type: c_type of the object to query from 'self'
:returns: python str object
:throws: ErrorMsg
"""
ret = value_type()
ngs_str_err = NGS_RawString()
try:
res = py_func(self.ref, byref(ret), byref(ngs_str_err.ref))
#check_res(res, ngs_str_err)
finally:
ngs_str_err.close()
return ret.value
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