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__all__ = ["tripleFromMetadataXML",
"decodeTriple",
"ChemistryLookupError"]
from collections import OrderedDict
import xml.etree.ElementTree as ET
import os.path
from importlib import resources
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 Exception:
raise ChemistryLookupError("Error loading chemistry mapping xml")
def _loadBarcodeMappings():
try:
mappingFnameContext = resources.as_file(
resources.files('pbcore') /
'chemistry/resources/mapping.xml')
with mappingFnameContext as mappingFname:
mappings = _loadBarcodeMappingsFromFile(mappingFname)
except:
mappingFname = os.path.join(os.path.dirname(__file__),
'resources/mapping.xml')
mappings = _loadBarcodeMappingsFromFile(mappingFname)
updMappingDir = os.getenv("SMRT_CHEMISTRY_BUNDLE_DIR")
if updMappingDir:
import logging
from os.path import join
logging.info(
"Loading updated chemistry mapping XML from {}".format(updMappingDir))
mappings.update(_loadBarcodeMappingsFromFile(
join(updMappingDir, 'chemistry.xml')))
return mappings
_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")
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