Did I find the right examples for you? yes no

All Samples(8)  |  Call(4)  |  Derive(0)  |  Import(4)

src/s/e/seal-0.4.0-rc2/seal/seqal/mapper.py   seal(Download)
from pydoop.utils import jc_configure, jc_configure_int, jc_configure_bool
 
from seal.lib.aligner.bwa.bwa_aligner import BwaAligner, BWA_INDEX_EXT
import seal.lib.io.protobuf_mapping as protobuf_mapping
import seal.lib.mr.utils as utils
        self.event_monitor = HadoopEventMonitor(self.COUNTER_CLASS, logging.getLogger("mapper"), ctx)
 
        self.aligner = BwaAligner()
        self.aligner.event_monitor = self.event_monitor
        self.aligner.qformat = self.format

src/s/e/seal-0.4.0-rc2/tests/seal/lib/aligner/test_bwa_aligner.py   seal(Download)
 
from seal.lib.io.sam_formatter import SamFormatter
from seal.lib.aligner.bwa.bwa_aligner import BwaAligner
 
class MappingsCollector(object):
  def setUp(self):
    self.aligner = BwaAligner()
    test_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), '..', '..', '..'))
    self.aligner.reference = os.path.join(test_dir, 'seal', 'mini_ref_fixture', 'mini_ref.fasta')
    self.aligner.hit_visitor = MappingsCollector()

src/s/e/seal-0.4.0-rc2/tests/seal/lib/aligner/bwa/test_bwa_aligner.py   seal(Download)
import unittest
 
from seal.lib.aligner.bwa.bwa_aligner import BwaAligner
from seal.lib.io.sam_formatter import SamFormatter
import seal.lib.aligner.bwa.bwa_core as bwa
  def setUp(self):
    utils.build_ref_index()
    self.aligner = BwaAligner()
    self.aligner.reference = utils.reference
    self.aligner.hit_visitor = type(self).SimpleVisitor()

src/s/e/seal-0.4.0-rc2/tests/seal/lib/aligner/bwa/testing_utilities.py   seal(Download)
 
import seal.lib.aligner.bwa.bwa_core as bwa
from seal.lib.aligner.bwa.bwa_aligner import BwaAligner
#import seal.lib.generator as sg
import seal.lib.aligner.bwa.constants as bwa_const
 
    start = time.time()
    aligner = BwaAligner()
    aligner.reference = refseq_fname
    aligner.hit_visitor = result