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import deeptools.multiBamSummary as mbs
import numpy as np
import numpy.testing as nt
import os.path
from os import unlink
ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
BAM = ROOT + "test1.bam"
CRAM = ROOT + "test1.cram"
GTF = ROOT + "test.gtf"
BAMA = ROOT + "testA.bam"
BAMB = ROOT + "testB.bam"
def test_multiBamSummary_gtf():
outfile = '/tmp/_test.npz'
for fname in [BAM, CRAM]:
args = 'BED-file --BED {0} -b {1} {1} -o {2}'.format(GTF, fname, outfile).split()
mbs.main(args)
resp = np.load(outfile)
matrix = resp['matrix']
labels = resp['labels']
if fname == BAM:
nt.assert_equal(labels, ['test1.bam', 'test1.bam'])
else:
nt.assert_equal(labels, ['test1.cram', 'test1.cram'])
nt.assert_allclose(matrix, np.array([[144.0, 144.0],
[143.0, 143.0]]))
unlink(outfile)
def test_multiBamSummary_metagene():
outfile = '/tmp/_test.npz'
for fname in [BAM, CRAM]:
args = 'BED-file --BED {0} -b {1} {1} -o {2} --metagene'.format(GTF, fname, outfile).split()
mbs.main(args)
resp = np.load(outfile)
matrix = resp['matrix']
labels = resp['labels']
if fname == BAM:
nt.assert_equal(labels, ['test1.bam', 'test1.bam'])
else:
nt.assert_equal(labels, ['test1.cram', 'test1.cram'])
nt.assert_allclose(matrix, np.array([[25.0, 25.0],
[31.0, 31.0]]))
unlink(outfile)
def test_multiBamSummary_scalingFactors():
outfile = '/tmp/test.scalingFactors.txt'
args = 'bins --binSize 50 -b {} {} --scalingFactors {}'.format(BAMA, BAMB, outfile).split()
mbs.main(args)
resp = open(outfile).read().strip().split('\n')
nt.assert_equal(resp, ["sample\tscalingFactor", "testA.bam\t1.1892", "testB.bam\t0.8409"])
unlink(outfile)
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