/usr/lib/python3/dist-packages/ngs/Read.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_uint32, c_int32
from . import NGS
from .String import NGS_String, NGS_RawString, getNGSString, getNGSValue
from .FragmentIterator import FragmentIterator
# Read
# represents an NGS machine read
# having some number of biological Fragments
class Read(FragmentIterator):
fullyAligned = 1
partiallyAligned = 2
aligned = fullyAligned | partiallyAligned
unaligned = 4
all = aligned | unaligned
def getReadId(self):
return getNGSString(self, NGS.lib_manager.PY_NGS_ReadGetReadId)
# ----------------------------------------------------------------------
# Fragment
def getNumFragments(self):
return getNGSValue(self, NGS.lib_manager.PY_NGS_ReadGetNumFragments, c_uint32)
def fragmentIsAligned(self, fragIdx):
"""
:param: fragIdx is zero-based and non-negative fragment index
:returns: true if a fragment is aligned
"""
ret = c_int32()
ngs_str_err = NGS_RawString()
try:
res = NGS.lib_manager.PY_NGS_ReadFragmentIsAligned(self.ref, fragIdx, byref(ret), byref(ngs_str_err.ref))
finally:
ngs_str_err.close()
return bool(ret.value)
# ----------------------------------------------------------------------
# read details
# ReadCategory
def getReadCategory(self):
return getNGSValue(self, NGS.lib_manager.PY_NGS_ReadGetReadCategory, c_uint32)
def getReadGroup(self):
return getNGSString(self, NGS.lib_manager.PY_NGS_ReadGetReadGroup)
def getReadName(self):
return getNGSString(self, NGS.lib_manager.PY_NGS_ReadGetReadName)
def getReadBases(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_ReadGetReadBases(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 getReadQualities(self, offset=0, length=-1):
"""
:param: offset is zero-based and non-negative
:param: length must be >= 0
:returns: phred quality values using ASCII offset of 33
"""
ngs_str_err = NGS_RawString()
try:
ngs_str_seq = NGS_String()
try:
res = NGS.lib_manager.PY_NGS_ReadGetReadQualities(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()
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