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src/s/e/seal-0.4.0-rc2/tests/seal/seqal/test_utils.py   seal(Download)
import re
 
from seal.lib.aligner.mapping import SimpleMapping
 
def erase_read1(pair):
def pair1():
    p = (SimpleMapping(), SimpleMapping())
    p[0].set_name("p1:read/1") ; p[1].set_name("p1:read/2")
    p[0].tid = "chr1" ; p[1].tid = "chr1"
    p[0].ref_id = 0 ; p[1].ref_id = 0
def pair2():
    # reversed reads such that r2 is at a lower position than r1
    p = (SimpleMapping(), SimpleMapping())
    p[0].set_name("p1:read/1") ; p[1].set_name("p1:read/2")
    p[0].tid = "chr1" ; p[1].tid = "chr1"

src/s/e/seal-0.4.0-rc2/tests/seal/lib/mr/test_filter_link.py   seal(Download)
from seal.lib.mr.hit_processor_chain_link import HitProcessorChainLink
from seal.lib.mr.filter_link import FilterLink
from seal.lib.aligner.mapping import SimpleMapping
from seal.lib.standard_monitor import StandardMonitor
from seal.lib.mr.test_utils import SavingLogger
        #   name = second
        #   tid = tid2
        self.pair = [ SimpleMapping(), SimpleMapping() ]
        self.m1, self.m2 = self.pair
        self.m1.set_name("first") ; self.m2.set_name("second")

src/s/e/seal-0.4.0-rc2/tests/seal/lib/io/test_sam_formatter.py   seal(Download)
 
from seal.lib.io.sam_formatter import SamFormatter
from seal.lib.aligner.mapping import SimpleMapping
 
class TestSamFormatter(unittest.TestCase):
 
    def setUp(self):
        self.mapping = SimpleMapping()

src/s/e/seal-0.4.0-rc2/tests/seal/lib/io/test_protobuf_mapping.py   seal(Download)
 
import seal.lib.io.protobuf_mapping as io
from seal.lib.aligner.mapping import SimpleMapping
 
class TestProtobufSerialization(unittest.TestCase):
    def setUp(self):
        self.mapping = SimpleMapping()
 
    def test_simple(self):
        self.__try_and_compare_maps(self.mapping)
    def setUp(self):
        self.pair = (SimpleMapping(), SimpleMapping())
        self.pair[0].set_read1(True)
        self.pair[1].set_read2(True)