/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetMetaTypes.py is in python-pbcore 1.2.11+dfsg-1.
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 79 80 81 82 83 84 85 | ###############################################################################
# Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of Pacific Biosciences nor the names of its
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
# NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
# OR
# BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
# IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
###############################################################################
# Author: Martin D. Smith
import logging
from pbcore.io.dataset.DataSetErrors import (InvalidDataSetIOError,)
log = logging.getLogger(__name__)
def toDsId(name):
"""Translate a class name into a MetaType/ID"""
return "PacBio.DataSet.{x}".format(x=name)
class DataSetMetaTypes(object):
"""
This mirrors the PacBioSecondaryDataModel.xsd definitions and be used
to reference a specific dataset type.
"""
SUBREAD = toDsId("SubreadSet")
HDF_SUBREAD = toDsId("HdfSubreadSet")
ALIGNMENT = toDsId("AlignmentSet")
BARCODE = toDsId("BarcodeSet")
CCS_ALIGNMENT = toDsId("ConsensusAlignmentSet")
CCS = toDsId("ConsensusReadSet")
REFERENCE = toDsId("ReferenceSet")
GMAPREFERENCE = toDsId("GmapReferenceSet")
CONTIG = toDsId("ContigSet")
ALL = (SUBREAD, HDF_SUBREAD, ALIGNMENT,
BARCODE, CCS, CCS_ALIGNMENT, REFERENCE, CONTIG, GMAPREFERENCE)
@classmethod
def isValid(cls, dsId):
return dsId in cls.ALL
def dsIdToName(dsId):
"""Translate a MetaType/ID into a class name"""
if DataSetMetaTypes.isValid(dsId):
return dsId.split('.')[-1]
else:
raise InvalidDataSetIOError("Invalid DataSet MetaType")
def dsIdToSuffix(dsId):
"""Translate a MetaType/ID into a file suffix"""
dsIds = DataSetMetaTypes.ALL
suffixMap = {dsId: dsIdToName(dsId) for dsId in dsIds}
suffixMap[toDsId("DataSet")] = 'DataSet'
if DataSetMetaTypes.isValid(dsId):
suffix = suffixMap[dsId]
suffix = suffix.lower()
suffix += '.xml'
return suffix
else:
raise InvalidDataSetIOError("Invalid DataSet MetaType")
|