本文整理汇总了Python中pybedtools.IntervalFile类的典型用法代码示例。如果您正苦于以下问题：Python IntervalFile类的具体用法？Python IntervalFile怎么用？Python IntervalFile使用的例子？那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了IntervalFile类的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于我们的系统推荐出更棒的Python代码示例。
示例1: testStart
def testStart(self):
ivf = IntervalFile(self.file)
iv = ivf.next()
orig_string = str(iv)
# 0-based.
orig_start = iv.start
# Setting .start always sets 0-based coord.
iv.start = orig_start
# But for GFF setting .start should also make the .fields[3] the GFF
# 1-based coord
assert iv.start == int(iv.fields[3])-1
second_string = str(iv)
second_start = iv.start
iv.start = second_start
# Check .start and .fields[3] internal consistency again
assert iv.start == int(iv.fields[3])-1
print ' orig:', '(start=%s)'%orig_start, orig_string
print ' second:', '(start=%s)'%second_start, second_string
print 'current:', '(start=%s)'%iv.start, str(iv)
self.assert_(orig_start == second_start == iv.start)
self.assert_(orig_string == second_string == str(iv))
开发者ID:ffrancis，项目名称:pybedtools，代码行数:27，代码来源:test_cbedtools.py
示例2: testName
def testName(self):
ivf = IntervalFile(self.file)
iv = ivf.next()
iv.name = "bart simpson"
self.assertEqual(iv.name, "bart simpson")
if iv.file_type == "gff":
self.assert_("bart" in iv.fields[8])
开发者ID:ffrancis，项目名称:pybedtools，代码行数:7，代码来源:test_cbedtools.py
示例3: testSetItem
def testSetItem(self):
ivf = IntervalFile(self.file)
iv = ivf.next()
iv.chrom = 'chrfake'
print iv.fields
self.assertEqual(iv['chrom'], 'chrfake')
self.assertEqual(iv.chrom, 'chrfake')
开发者ID:ffrancis，项目名称:pybedtools，代码行数:7，代码来源:test_cbedtools.py
示例4: testAppend
def testAppend(self):
ivf = IntervalFile(self.file)
iv = ivf.next()
print iv.fields
iv.append('asdf')
print iv
self.assertEqual(iv[-1], 'asdf')
开发者ID:ffrancis，项目名称:pybedtools，代码行数:7，代码来源:test_cbedtools.py
示例5: testGetItemNegative
def testGetItemNegative(self):
"test negative indexes to feature."
ivf = IntervalFile(self.file)
iv = ivf.next()
self.assert_(iv[-self.fieldcount+self.chrpos].startswith("chr"), iv[-self.fieldcount+self.chrpos])
self.assert_(iv[-self.fieldcount+self.startpos].isdigit(), iv[-self.fieldcount+self.startpos])
self.assert_(iv[-self.fieldcount+self.stoppos].isdigit())
开发者ID:ffrancis，项目名称:pybedtools，代码行数:7，代码来源:test_cbedtools.py
示例6: testGetItem
def testGetItem(self):
"getitem now supports direct access to the line."
ivf = IntervalFile(self.file)
iv = ivf.next()
self.assert_(iv[self.chrpos].startswith("chr"))
self.assert_(iv[self.startpos].isdigit())
self.assert_(iv[self.startpos].isdigit())
开发者ID:ffrancis，项目名称:pybedtools，代码行数:7，代码来源:test_cbedtools.py
示例7: testGetItemSliceNone
def testGetItemSliceNone(self):
" test support for funky slices."
ivf = IntervalFile(self.file)
iv = ivf.next()
self.assertEqual(len(iv[:3]), 3)
self.assertEqual(len(iv[3:3]), 0)
self.assertEqual(len(iv[2:]), self.fieldcount-2, iv[2:])
print len(iv.fields), iv.fields
self.assertRaises(IndexError, lambda x: iv[x], self.fieldcount+1)
开发者ID:ffrancis，项目名称:pybedtools，代码行数:10，代码来源:test_cbedtools.py
示例8: testGetItemSlice
def testGetItemSlice(self):
"getitem now supports direct access to the line."
ivf = IntervalFile(self.file)
iv = ivf.next()
seqid, = iv[self.chrpos:self.chrpos+1]
start, end = iv[self.startpos:self.stoppos+1]
self.assert_(start.isdigit())
self.assertEqual(int(end), iv.end)
self.assertEqual(seqid, iv.chrom)
开发者ID:ffrancis，项目名称:pybedtools，代码行数:10，代码来源:test_cbedtools.py
示例9: testSetAttrs
def testSetAttrs(self):
ivf = IntervalFile(self.file)
iv = ivf.next()
if iv.file_type != 'gff':
self.assertRaises(ValueError, iv.attrs.__setitem__, 'a','b')
return
iv.attrs['ID'] = 'fake'
iv.attrs['field0'] = 'asdf'
self.assertEqual(str(iv.attrs), iv[8])
self.assert_('field0=asdf' in iv[8])
self.assert_('ID=fake' in iv[8])
开发者ID:Fabrices，项目名称:pybedtools，代码行数:11，代码来源:test_cbedtools.py
示例10: IntervalFileTest
class IntervalFileTest(unittest.TestCase):
file = "data/rmsk.hg18.chr21.small.bed"
def setUp(self):
self.file = os.path.join(PATH, self.file)
self.bed = IntervalFile(self.file)
def testFileType(self):
self.assert_(self.bed.file_type == "bed", (self.bed.file_type, self.file))
gff = os.path.join(PATH, "data/c.gff")
i = IntervalFile(gff)
self.assert_(i.file_type == "gff", (i.file_type, gff))
def testOverlaps(self):
i = Interval("chr21", 9719768, 9739768)
hits = self.bed.all_hits(i)
self.assertEqual(len(hits), 8)
for hit in hits:
self.assert_(hit.start <= 9739768 and hit.end >= 9719768)
def testStrands(self):
i = Interval("chr21", 9719768, 9739768, "+")
hits = self.bed.all_hits(i, same_strand=True)
for hit in hits:
self.assert_(hit.strand == '+')
i = Interval("chr21", 9719768, 9739768, "-")
hits = self.bed.all_hits(i, same_strand=True)
for hit in hits:
self.assert_(hit.strand == '-')
def testRichCmp(self):
a = Interval("chr21", 9719768, 9739768)
b = Interval("chr21", 9719767, 9739768)
self.assert_(a < b)
self.assert_(b < a)
c = Interval("chr21", 9719767, 9739768)
self.assert_(c == b)
d = Interval("chr22", 9719767, 9739768)
self.assert_(c != d)
开发者ID:Fabrices，项目名称:pybedtools，代码行数:40，代码来源:test_cbedtools.py
示例11: setUp
def setUp(self):
self.file = os.path.join(PATH, self.file)
self.bed = IntervalFile(self.file)
开发者ID:PanosFirmpas，项目名称:pybedtools，代码行数:3，代码来源:test_cbedtools.py
示例12: IntervalFileTest
class IntervalFileTest(unittest.TestCase):
file = "data/rmsk.hg18.chr21.small.bed"
def setUp(self):
self.file = os.path.join(PATH, self.file)
self.bed = IntervalFile(self.file)
def testFileType(self):
self.assert_(self.bed.file_type == "bed", (self.bed.file_type, self.file))
gff = os.path.join(PATH, "data/c.gff")
i = IntervalFile(gff)
self.assert_(i.file_type == "gff", (i.file_type, gff))
def testOverlaps(self):
i = Interval("chr21", 9719768, 9739768)
hits = self.bed.all_hits(i)
self.assertEqual(len(hits), 8)
for hit in hits:
self.assert_(hit.start <= 9739768 and hit.end >= 9719768)
def testStrands(self):
i = Interval("chr21", 9719768, 9739768, "+")
hits = self.bed.all_hits(i, same_strand=True)
for hit in hits:
self.assert_(hit.strand == '+')
i = Interval("chr21", 9719768, 9739768, "-")
hits = self.bed.all_hits(i, same_strand=True)
for hit in hits:
self.assert_(hit.strand == '-')
def testRichCmp(self):
# be obsessive . . .
#
# ==
a = Interval("chr21", 100, 200)
b = Interval("chr21", 100, 200)
self.assert_(a == b)
self.assertFalse(a != b)
self.assert_(a <= b)
self.assert_(a >= b)
self.assertFalse(a < b)
self.assertFalse(a > b)
a = Interval("chr21", 100, 100)
b = Interval("chr21", 100, 100)
self.assert_(a == b)
self.assertFalse(a != b)
self.assert_(a <= b)
self.assert_(a >= b)
self.assertFalse(a < b)
self.assertFalse(a > b)
# != because of strand
a = Interval("chr21", 100, 200, strand='+')
b = Interval("chr21", 100, 200, strand='-')
self.assertFalse(a == b)
self.assert_(a != b)
self.assertFalse(a <= b)
self.assertFalse(a >= b)
self.assertFalse(a < b)
self.assertFalse(a > b)
# a >= b
a = Interval("chr21", 100, 300)
b = Interval("chr21", 100, 200)
self.assertFalse(a == b)
self.assert_(a != b)
self.assertFalse(a <= b)
self.assert_(a >= b)
self.assertFalse(a < b)
self.assertFalse(a > b)
# a <= b
a = Interval("chr21", 100, 300)
b = Interval("chr21", 300, 300)
self.assertFalse(a == b)
self.assert_(a != b)
self.assert_(a <= b)
self.assertFalse(a >= b)
self.assertFalse(a < b)
self.assertFalse(a > b)
# a <= b
a = Interval("chr21", 100, 300)
b = Interval("chr21", 250, 300)
self.assertFalse(a == b)
self.assert_(a != b)
self.assert_(a <= b)
self.assertFalse(a >= b)
self.assertFalse(a < b)
self.assertFalse(a > b)
# a < b
a = Interval("chr21", 100, 200)
b = Interval("chr21", 201, 300)
self.assertFalse(a == b)
#.........这里部分代码省略.........
开发者ID:PanosFirmpas，项目名称:pybedtools，代码行数:101，代码来源:test_cbedtools.py
示例13: testSetItemString
def testSetItemString(self):
ivf = IntervalFile(self.file)
iv = ivf.next()
iv['chrom'] = 'fake'
self.assertEqual(iv['chrom'], 'fake')
self.assertEqual(iv.chrom, 'fake')
开发者ID:ffrancis，项目名称:pybedtools，代码行数:6，代码来源:test_cbedtools.py
示例14: testGetItemString
def testGetItemString(self):
ivf = IntervalFile(self.file)
iv = ivf.next()
self.assertEqual(iv['chrom'], iv.chrom)
self.assertEqual(iv['start'], iv.start)
self.assertEqual(iv['end'], iv.end)
开发者ID:ffrancis，项目名称:pybedtools，代码行数:6，代码来源:test_cbedtools.py
示例15: size
1 = start_byte,
2 = end_byte,
3 = num_records,
4 = max_interval size (future, for binary search)
"""
# what are the BED files
A_file = sys.argv[1]
B_file = sys.argv[2]
# expected index file name
A_idx_file = A_file + ".idx"
B_idx_file = B_file + ".idx"
# open up the BED files.
A = IntervalFile(A_file) # The Query File
B = IntervalFile(B_file) # The Database File
# create index files if they don't yet exist
if not os.path.exists(A_idx_file):
index_bed.index(A_file)
if not os.path.exists(B_idx_file):
index_bed.index(B_file)
# load the indices for A and B
A_map = [] # list of chrom/offset tuples
for line in open(A_idx_file):
fields = line.strip().split("\t")
A_map.append((fields[0], int(fields[1]), int(fields[2]), int(fields[3]), int(fields[4])))
B_map = [] # list of chrom/offset tuples
for line in open(B_idx_file):
开发者ID:arq5x，项目名称:chrom_sweep，代码行数:31，代码来源:chrom_sweep_with_index.py
注：本文中的pybedtools.IntervalFile类示例由纯净天空整理自Github/MSDocs等源码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。 |
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