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import logging
import os.path as op
import pytest
from pbcore.io import AlignmentSet
from kineticsTools import ReferenceUtils
big_data_dir = "/pbi/dept/secondary/siv/testdata/kineticsTools"
ref_dir = "/pbi/dept/secondary/siv/references"
logging.basicConfig()
log = logging.getLogger()
@pytest.mark.internal_data
class TestReferenceUtils:
def test_bam(self):
bamFile = op.join(big_data_dir, "ecoli_first_50k.mapped.bam")
refFile = op.join(ref_dir, "ecoli_k12_MG1655_first50k",
"ecoli_k12_MG1655_first50k.referenceset.xml")
ds = AlignmentSet(bamFile, referenceFastaFname=refFile)
contigs = ReferenceUtils.loadReferenceContigs(refFile, ds)
assert len(contigs) == 1
assert contigs[0].alignmentID == 0
chemistry = ReferenceUtils.loadAlignmentChemistry(ds)
assert chemistry == "S/P3-C3/5.0"
def test_dataset(self):
pass # TODO
def test_parseReferenceWindow(self):
window = "gi|12057207|gb|AE001439.1|:1-5000"
bamFile = op.join(big_data_dir, "Hpyl_1_5000.bam")
refFile = op.join(ref_dir, "Helicobacter_pylori_J99", "sequence",
"Helicobacter_pylori_J99.fasta")
alnFile = AlignmentSet(bamFile, referenceFastaFname=refFile)
win = ReferenceUtils.parseReferenceWindow(window,
alnFile.referenceInfo)
assert [win.refId, win.start, win.end] == [0, 1, 5000]
def test_createReferenceWindows(self):
bamFile = op.join(big_data_dir, "Hpyl_1_5000.bam")
ds = AlignmentSet(bamFile, referenceFastaFname=None)
refInfoTable = ds.referenceInfoTable
windows = ReferenceUtils.createReferenceWindows(refInfoTable)
assert len(windows) == 1
w = windows[0]
assert w.refId == 0
assert w.refName == 'gi|12057207|gb|AE001439.1|'
assert w.start == 0
assert w.end == 1643831
def test_enumerateChunks(self):
pass # TODO
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