def testExtractTouching(self):
passed = [
x.qname for x in ngsutils.bam.extract.bam_extract_reads(
testbam1, 'chr1', 2520, 2540, None)
]
self.assertTrue(_matches(['foo6'], passed))
passed = [
x.qname for x in ngsutils.bam.extract.bam_extract_reads(
testbam1, 'chr1', 2510, 2530, None)
]
self.assertTrue(_matches(['foo6'], passed))
passed = [
x.qname for x in ngsutils.bam.extract.bam_extract_reads(
testbam1, 'chr1', 2530, 2550, None)
]
self.assertTrue(_matches(['foo6'], passed))
passed = [
x.qname for x in ngsutils.bam.extract.bam_extract_reads(
testbam1, 'chr1', 2500, 2600, None)
]
self.assertTrue(_matches(['foo6'], passed))
passed = [
x.qname for x in ngsutils.bam.extract.bam_extract_reads(
testbam1, 'chr1', 2530, 2535, None)
]
self.assertTrue(_matches(['foo6'], passed))
def testExtract(self):
passed = [x.qname for x in ngsutils.bam.extract.bam_extract_reads(testbam1, 'chr1', 200, 250, '+')]
self.assertTrue(_matches(['foo2', 'foo4'], passed))
passed = [x.qname for x in ngsutils.bam.extract.bam_extract_reads(testbam1, 'chr1', 200, 250, '-')]
self.assertTrue(_matches(['foo5'], passed))
passed = [x.qname for x in ngsutils.bam.extract.bam_extract_reads(testbam1, 'chr1', 200, 250, None)]
self.assertTrue(_matches(['foo2', 'foo4', 'foo5'], passed))
def testExtractTouching(self):
passed = [x.qname for x in ngsutils.bam.extract.bam_extract_reads(testbam1, 'chr1', 2520, 2540, None)]
self.assertTrue(_matches(['foo6'], passed))
passed = [x.qname for x in ngsutils.bam.extract.bam_extract_reads(testbam1, 'chr1', 2510, 2530, None)]
self.assertTrue(_matches(['foo6'], passed))
passed = [x.qname for x in ngsutils.bam.extract.bam_extract_reads(testbam1, 'chr1', 2530, 2550, None)]
self.assertTrue(_matches(['foo6'], passed))
passed = [x.qname for x in ngsutils.bam.extract.bam_extract_reads(testbam1, 'chr1', 2500, 2600, None)]
self.assertTrue(_matches(['foo6'], passed))
passed = [x.qname for x in ngsutils.bam.extract.bam_extract_reads(testbam1, 'chr1', 2530, 2535, None)]
self.assertTrue(_matches(['foo6'], passed))
def testExtractBED3(self):
outbam = MockBam(['chr1'])
ngsutils.bam.extract.bam_extract(testbam1,
outbam,
self.fname2,
quiet=True)
passed = [x.qname for x in outbam]
self.assertTrue(_matches(['foo2', 'foo5', 'foo1', 'foo4'], passed))
def testExtract(self):
passed = [
x.qname for x in ngsutils.bam.extract.bam_extract_reads(
testbam1, 'chr1', 200, 250, '+')
]
self.assertTrue(_matches(['foo2', 'foo4'], passed))
passed = [
x.qname for x in ngsutils.bam.extract.bam_extract_reads(
testbam1, 'chr1', 200, 250, '-')
]
self.assertTrue(_matches(['foo5'], passed))
passed = [
x.qname for x in ngsutils.bam.extract.bam_extract_reads(
testbam1, 'chr1', 200, 250, None)
]
self.assertTrue(_matches(['foo2', 'foo4', 'foo5'], passed))
def testBedFile(self):
fname = os.path.join(os.path.dirname(__file__), 'test.bed')
valid = ['chr1|100|150|foo|1|+',
'chr1|100|150|foo|1|-',
'chr1|200|250|foo|1|+',
'chr1|300|350|foo|1|-',
]
regions = ['%s|%s|%s|%s|%s|%s' % (x.chrom, x.start, x.end, x.name, x.score, x.strand) for x in BedFile(fname)]
self.assertTrue(_matches(valid, regions))
def testBedFile(self):
fname = os.path.join(os.path.dirname(__file__), 'test.bed')
valid = ['chr1|100|150|foo|1|+',
'chr1|100|150|foo|1|-',
'chr1|200|250|foo|1|+',
'chr1|300|350|foo|1|-',
]
regions = ['%s|%s|%s|%s|%s|%s' % (x.chrom, x.start, x.end, x.name, x.score_int, x.strand) for x in BedFile(fname)]
self.assertTrue(_matches(valid, regions))
def testBedFileObj(self):
valid = ['chr1|100|150|foo|1|+',
'chr1|100|150|foo|1|-',
]
instr = StringIO.StringIO('''
chr1|100|150|foo|1|+
chr1|100|150|foo|1|-
'''.replace('|', '\t'))
regions = ['%s|%s|%s|%s|%s|%s' % (x.chrom, x.start, x.end, x.name, x.score, x.strand) for x in BedFile(fileobj=instr)]
self.assertTrue(_matches(valid, regions))
def testReduceExtendAsync(self):
valids = '''\
chr1|90|220|foo1,foo2|20|+
chr1|490|720|foo3,foo4,foo5|30|+
'''.replace('|', '\t').split('\n')
out = StringIO.StringIO('')
ngsutils.bed.reduce.bed_reduce(bedtest,
extend=(10, 20),
stranded=False,
out=out)
self.assertTrue(_matches(valids, out.getvalue().split('\n')))
def testBedFileObj(self):
valid = ['chr1|100|150|foo|1|+',
'chr1|100|150|foo|1|-',
]
instr = StringIO.StringIO('''
chr1|100|150|foo|1|+
chr1|100|150|foo|1|-
'''.replace('|', '\t'))
regions = ['%s|%s|%s|%s|%s|%s' % (x.chrom, x.start, x.end, x.name, x.score, x.strand) for x in BedFile(fileobj=instr)]
self.assertTrue(_matches(valid, regions))
def testReduceStranded(self):
valids = '''\
chr1|100|200|foo1,foo2|20|+
chr1|500|550|foo3|10|+
chr1|560|600|foo4|10|-
chr1|600|700|foo5|10|+
'''.replace('|', '\t').split('\n')
out = StringIO.StringIO('')
ngsutils.bed.reduce.bed_reduce(bedtest,
extend=(0, 0),
stranded=True,
count=False,
out=out)
self.assertTrue(_matches(valids, out.getvalue().split('\n')))
def testBedRegion(self):
valid = ['chr1|100|150']
regions = ['%s|%s|%s' % (x.chrom, x.start, x.end) for x in BedFile(region="chr1:101-150")]
self.assertTrue(_matches(valid, regions))
def testExtractBED3(self):
outbam = MockBam(['chr1'])
ngsutils.bam.extract.bam_extract(testbam1, outbam, self.fname2, quiet=True)
passed = [x.qname for x in outbam]
self.assertTrue(_matches(['foo2', 'foo5', 'foo1', 'foo4'], passed))
def testBedRegion(self):
valid = ['chr1|100|150']
regions = ['%s|%s|%s' % (x.chrom, x.start, x.end) for x in BedFile(region="chr1:101-150")]
self.assertTrue(_matches(valid, regions))
