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"""Doctest resources"""
import os
from importlib import resources
XML_FILES = ["alignment.dataset.xml", # 0
"barcode.dataset.xml",
"ccsread.dataset.xml",
"contig.dataset.xml",
"reference.dataset.xml", # 4
"subread.dataset.xml",
"transformed_rs_subread_dataset.xml",
"pbalchemysim0.alignmentset.xml",
"pbalchemysim0.referenceset.xml", # 8
"pbalchemysim0.subreadset.xml",
"pbalchemysim1.alignmentset.xml",
"pbalchemysim.alignmentset.xml", # both sim0 and sim1 bam files
"pbalchemysim1.subreadset.xml",
"subreadSetWithStats.xml", # 13
"pbalchemysim0.alignmentset.chunk0contigs.xml",
"pbalchemysim0.alignmentset.chunk1contigs.xml",
"ccsaligned.dataset.xml",
"CollectionMetadata.xml", # 17
]
BAM_FILES = ["pbalchemysim0.pbalign.bam",
"pbalchemysim1.pbalign.bam",
os.path.join('..', 'bam_mapping.bam'),
"empty_lambda.aligned.bam", ]
STATS_FILES = [
"m150430_142051_Mon_p1_b25.sts.xml",
"m150616_053259_ethan_c100710482550000001823136404221563_s1_p0.sts.xml"]
FOFN_FILES = ["fofn.fofn"]
def _getAbsPath(fname):
with resources.as_file(
resources.files('pbcore') /
'data/datasets' / fname) as ret:
return str(ret)
def getXml(no=0):
return _getAbsPath(XML_FILES[no])
def getXmlWithStats():
return _getAbsPath(XML_FILES[13])
def getBam(no=0):
return _getAbsPath(BAM_FILES[no])
def getEmptyAlignedBam():
return _getAbsPath(BAM_FILES[3])
def getStats(no=0):
return _getAbsPath(STATS_FILES[no])
def getFofn(no=0):
return _getAbsPath(FOFN_FILES[no])
def getRef():
return _getAbsPath(XML_FILES[8])
def getSubreadSet():
return _getAbsPath(XML_FILES[5])
def getBarcodedBam():
return _getAbsPath(BAM_FILES[3])
def getMockCollectionMetadata():
return _getAbsPath(XML_FILES[17])
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