Python IntervalFile.all_hits方法代碼示例

本文整理匯總了Python中pybedtools.IntervalFile.all_hits方法的典型用法代碼示例。如果您正苦於以下問題：Python IntervalFile.all_hits方法的具體用法？Python IntervalFile.all_hits怎麽用？Python IntervalFile.all_hits使用的例子？那麽, 這裏精選的方法代碼示例或許可以為您提供幫助。您也可以進一步了解該方法所在類pybedtools.IntervalFile的用法示例。

在下文中一共展示了IntervalFile.all_hits方法的2個代碼示例，這些例子默認根據受歡迎程度排序。您可以為喜歡或者感覺有用的代碼點讚，您的評價將有助於係統推薦出更棒的Python代碼示例。

示例1: IntervalFileTest

# 需要導入模塊: from pybedtools import IntervalFile [as 別名]
# 或者: from pybedtools.IntervalFile import all_hits [as 別名]
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)

開發者ID:Fabrices，項目名稱:pybedtools，代碼行數:42，代碼來源:test_cbedtools.py

示例2: IntervalFileTest

# 需要導入模塊: from pybedtools import IntervalFile [as 別名]
# 或者: from pybedtools.IntervalFile import all_hits [as 別名]
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)
#.........這裏部分代碼省略.........

開發者ID:PanosFirmpas，項目名稱:pybedtools，代碼行數:103，代碼來源:test_cbedtools.py

注：本文中的pybedtools.IntervalFile.all_hits方法示例由純淨天空整理自Github/MSDocs等開源代碼及文檔管理平台，相關代碼片段篩選自各路編程大神貢獻的開源項目，源碼版權歸原作者所有，傳播和使用請參考對應項目的License；未經允許，請勿轉載。