/usr/lib/python2.7/dist-packages/ngs/Alignment.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_char, c_int, c_int32, c_uint32, c_int64, c_uint64, c_void_p
from . import NGS
from .String import NGS_String, NGS_RawString, getNGSString, getNGSValue
from .Fragment import Fragment
# Represents an alignment between a Fragment and Reference sub-sequence
# provides a path to Read and mate Alignment
class Alignment(Fragment):
# AlignmentFilter constants
passFailed = 1
passDuplicates = 2
minMapQuality = 4
maxMapQuality = 8
noWraparound = 16
startWithinSlice = 32
# AlignmentCategory constants
primaryAlignment = 1
secondaryAlignment = 2
all = primaryAlignment | secondaryAlignment
# ClipEdge constants
clipLeft = 0
clipRight = 1
def getAlignmentId(self):
"""Retrieve an identifying String that can be used for later access.
The id will be unique within ReadCollection.
:returns: alignment id string
:throws: ErrorMsg if the property cannot be retrieved
"""
return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetAlignmentId)
# ------------------------------------------------------------------
# Reference
def getReferenceSpec(self):
return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetReferenceSpec)
def getMappingQuality(self):
return getNGSValue(self, NGS.lib_manager.PY_NGS_AlignmentGetMappingQuality, c_int32)
def getReferenceBases(self):
return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetReferenceBases)
# ------------------------------------------------------------------
# Fragment
def getReadGroup(self):
return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetReadGroup)
def getReadId(self):
return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetReadId)
def getClippedFragmentBases(self):
return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetClippedFragmentBases)
def getClippedFragmentQualities(self):
"""
:returns: clipped fragment phred quality values using ASCII offset of 33
"""
return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetClippedFragmentQualities)
def getAlignedFragmentBases(self):
"""
:returns: fragment bases in their aligned orientation
"""
return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetAlignedFragmentBases)
# ------------------------------------------------------------------
# details of this alignment
def getAlignmentCategory(self):
"""Alignments are categorized as primary or secondary (alternate).
:returns: either Alignment.primaryAlignment or Alignment.secondaryAlignment
:throws: ErrorMsg if the property cannot be retrieved
"""
return getNGSValue(self, NGS.lib_manager.PY_NGS_AlignmentGetAlignmentCategory, c_uint32)
def getAlignmentPosition(self):
"""Retrieve the Alignment's starting position on the Reference
:returns: unsigned 0-based offset from start of Reference
:throws: ErrorMsg if the property cannot be retrieved
"""
return getNGSValue(self, NGS.lib_manager.PY_NGS_AlignmentGetAlignmentPosition, c_int64)
def getAlignmentLength(self):
"""Retrieve the projected length of an Alignment projected upon Reference.
:returns: unsigned length of projection
:throws: ErrorMsg if the property cannot be retrieved
"""
return getNGSValue(self, NGS.lib_manager.PY_NGS_AlignmentGetAlignmentLength, c_uint64)
def getIsReversedOrientation(self):
"""Test if orientation is reversed with respect to the Reference sequence.
:returns: true if reversed
:throws: ErrorMsg if the property cannot be retrieved
"""
return bool(getNGSValue(self, NGS.lib_manager.PY_NGS_AlignmentGetIsReversedOrientation, c_int))
def getSoftClip(self, edge):
ret = c_int32()
ngs_str_err = NGS_RawString()
try:
res = NGS.lib_manager.PY_NGS_AlignmentGetSoftClip(self.ref, edge, byref(ret), byref(ngs_str_err.ref))
finally:
ngs_str_err.close()
return ret.value
def getTemplateLength(self):
return getNGSValue(self, NGS.lib_manager.PY_NGS_AlignmentGetTemplateLength, c_uint64)
def getShortCigar(self, clipped):
"""
:returns: a text string describing alignment details
"""
ngs_str_err = NGS_RawString()
try:
ngs_str_ret = NGS_String()
try:
res = NGS.lib_manager.PY_NGS_AlignmentGetShortCigar(self.ref, clipped, 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 getLongCigar(self, clipped):
"""
:returns: a text string describing alignment details
"""
ngs_str_err = NGS_RawString()
try:
ngs_str_ret = NGS_String()
try:
res = NGS.lib_manager.PY_NGS_AlignmentGetLongCigar(self.ref, clipped, 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 getRNAOrientation(self):
"""
:returns: '+' if positive strand is transcribed
:returns: '-' if negative strand is transcribed
:returns: '?' if unknown
"""
return getNGSValue(self, NGS.lib_manager.PY_NGS_AlignmentGetRNAOrientation, c_char).decode("utf-8")
# ------------------------------------------------------------------
# details of mate alignment
def hasMate(self):
return bool(getNGSValue(self, NGS.lib_manager.PY_NGS_AlignmentHasMate, c_int))
def getMateAlignmentId(self):
return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetMateAlignmentId)
def getMateAlignment(self):
ret = Alignment()
ret.ref = getNGSValue(self, NGS.lib_manager.PY_NGS_AlignmentGetMateAlignment, c_void_p) # TODO: check if it works
return ret
def getMateReferenceSpec(self):
return getNGSString(self, NGS.lib_manager.PY_NGS_AlignmentGetMateReferenceSpec)
def getMateIsReversedOrientation(self):
return bool(getNGSValue(self, NGS.lib_manager.PY_NGS_AlignmentGetMateIsReversedOrientation, c_int))
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