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
86
87
88
89
90
91
|
#################################################################################
# Copyright (c) 2011-2015, 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.
#################################################################################
__all__ = ["tripleFromMetadataXML",
"decodeTriple",
"ChemistryLookupError" ]
import xml.etree.ElementTree as ET, os.path
from pkg_resources import Requirement, resource_filename
from collections import OrderedDict
class ChemistryLookupError(Exception): pass
def _loadBarcodeMappingsFromFile(mapFile):
try:
tree = ET.parse(mapFile)
root = tree.getroot()
mappingElements = root.findall("Mapping")
mappings = OrderedDict()
mapKeys = ["BindingKit", "SequencingKit", "SoftwareVersion", "SequencingChemistry"]
for mapElement in mappingElements:
bindingKit = mapElement.find("BindingKit").text
sequencingKit = mapElement.find("SequencingKit").text
softwareVersion = mapElement.find("SoftwareVersion").text
sequencingChemistry = mapElement.find("SequencingChemistry").text
mappings[(bindingKit, sequencingKit, softwareVersion)] = sequencingChemistry
return mappings
except:
raise ChemistryLookupError, "Error loading chemistry mapping xml"
def _loadBarcodeMappings():
mappingFname = resource_filename(Requirement.parse('pbcore'),'pbcore/chemistry/resources/mapping.xml')
return _loadBarcodeMappingsFromFile(mappingFname)
_BARCODE_MAPPINGS = _loadBarcodeMappings()
def tripleFromMetadataXML(metadataXmlPath):
"""
Scrape the triple from the metadata.xml, or exception if the file
or the relevant contents are not found
"""
nsd = {None: "http://pacificbiosciences.com/PAP/Metadata.xsd",
"pb": "http://pacificbiosciences.com/PAP/Metadata.xsd"}
try:
tree = ET.parse(metadataXmlPath)
root = tree.getroot()
bindingKit = root.find("pb:BindingKit/pb:PartNumber", namespaces=nsd).text
sequencingKit = root.find("pb:SequencingKit/pb:PartNumber", namespaces=nsd).text
# The instrument version is truncated to the first 2 dot delimited components
instrumentControlVersion = root.find("pb:InstCtrlVer", namespaces=nsd).text
verComponents = instrumentControlVersion.split(".")[0:2]
instrumentControlVersion = ".".join(verComponents)
return (bindingKit, sequencingKit, instrumentControlVersion)
except Exception as e:
raise ChemistryLookupError, \
("Could not find, or extract chemistry information from, %s" % (metadataXmlPath,))
def decodeTriple(bindingKit, sequencingKit, softwareVersion):
"""
Return the name of the chemisty configuration given the
configuration triple that was recorded on the instrument.
"""
return _BARCODE_MAPPINGS.get((bindingKit, sequencingKit, softwareVersion), "unknown")
|
