/usr/lib/python3/dist-packages/ngs/Fragment.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
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# purpose.
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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))
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