/usr/lib/python2.7/dist-packages/ngs/Fragment.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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 | # ===========================================================================
#
# 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
from . import NGS
from .Refcount import Refcount
from .String import NGS_String, NGS_RawString, getNGSString, getNGSValue
# Represents an NGS biological fragment
class Fragment(Refcount):
def getFragmentId(self):
return getNGSString(self, NGS.lib_manager.PY_NGS_FragmentGetFragmentId)
def getFragmentBases(self, offset=0, length=-1):
"""
:param: offset is zero-based and non-negative
:param: length must be >= 0
:returns: sequence bases
"""
ngs_str_err = NGS_RawString()
try:
ngs_str_seq = NGS_String()
try:
res = NGS.lib_manager.PY_NGS_FragmentGetFragmentBases(self.ref, offset, length, byref(ngs_str_seq.ref), byref(ngs_str_err.ref))
return ngs_str_seq.getPyString()
finally:
ngs_str_seq.close()
finally:
ngs_str_err.close()
def getFragmentQualities(self, offset=0, length=-1):
"""getFragmentQualities using ASCII offset of 33
:param: offset is zero-based and non-negative
:param: length must be >= 0
:returns: phred quality values
"""
ngs_str_err = NGS_RawString()
try:
ngs_str_seq = NGS_String()
try:
res = NGS.lib_manager.PY_NGS_FragmentGetFragmentQualities(self.ref, offset, length, byref(ngs_str_seq.ref), byref(ngs_str_err.ref))
return ngs_str_seq.getPyString()
finally:
ngs_str_seq.close()
finally:
ngs_str_err.close()
def isPaired(self):
return bool(getNGSValue(self, NGS.lib_manager.PY_NGS_FragmentIsPaired, c_int))
def isAligned(self):
return bool(getNGSValue(self, NGS.lib_manager.PY_NGS_FragmentIsAligned, c_int))
|