Python equal_multiline Examples

Example #1

File: test_functional.py Project: minqing1/FALCON

def test_get_daligner_job_descriptions_small():
    # when there is only 1 block, a special case
    example_HPCdaligner = open(example_HPCdaligner_small_fn)
    result = f.get_daligner_job_descriptions(
            example_HPCdaligner, 'preads')
    assert result
    helpers.equal_multiline(result[('.1', '.1')], "daligner -v -h1 -t50 -H1 -e0.99 -l1 -s1000 preads.1 preads.1\nLAcheck -v preads *.las\nLAsort -v preads.1.preads.1.C0 preads.1.preads.1.N0 preads.1.preads.1.C1 preads.1.preads.1.N1 preads.1.preads.1.C2 preads.1.preads.1.N2 preads.1.preads.1.C3 preads.1.preads.1.N3 && LAmerge -v preads.1 preads.1.preads.1.C0.S preads.1.preads.1.N0.S preads.1.preads.1.C1.S preads.1.preads.1.N1.S preads.1.preads.1.C2.S preads.1.preads.1.N2.S preads.1.preads.1.C3.S preads.1.preads.1.N3.S\nLAcheck -vS preads preads.1\n")
    eq_(len(result), 1)

Example #2

File: test_functional.py Project: PacificBiosciences/FALCON

def test_get_daligner_job_descriptions_small():
    # when there is only 1 block, a special case
    example_HPCdaligner = open(example_HPCdaligner_small_fn)
    result = f.get_daligner_job_descriptions(
        example_HPCdaligner, 'preads', single=True)
    assert result
    helpers.equal_multiline(result[('.1', '.1')], 'daligner -v -h1 -t50 -H1 -e0.99 -l1 -s1000 preads.1 preads.1\nLAcheck -v preads *.las\n')
    eq_(len(result), 1)

Example #3

File: test_functional.py Project: minqing1/FALCON

def test_get_daligner_job_descriptions():
    example_HPCdaligner = open(example_HPCdaligner_fn)
    result = f.get_daligner_job_descriptions(
            example_HPCdaligner, 'raw_reads')
    assert result
    helpers.equal_multiline(result[('.1', '.1')], "daligner -v -h1 -t16 -H1 -e0.7 -l1 -s1000 raw_reads.1 raw_reads.1\nLAcheck -v raw_reads *.las\nLAsort -v raw_reads.1.raw_reads.1.C0 raw_reads.1.raw_reads.1.N0 && LAmerge -v L1.1.1 raw_reads.1.raw_reads.1.C0.S raw_reads.1.raw_reads.1.N0.S && rm raw_reads.1.raw_reads.1.C0.S.las raw_reads.1.raw_reads.1.N0.S.las\nLAcheck -vS raw_reads L1.1.1\n")
    helpers.equal_multiline(result[('.2', '.1', '.2')], "daligner -v -h1 -t16 -H1 -e0.7 -l1 -s1000 raw_reads.2 raw_reads.1 raw_reads.2\nLAcheck -v raw_reads *.las\nLAsort -v raw_reads.1.raw_reads.2.C0 raw_reads.1.raw_reads.2.N0 && LAmerge -v L1.1.2 raw_reads.1.raw_reads.2.C0.S raw_reads.1.raw_reads.2.N0.S && rm raw_reads.1.raw_reads.2.C0.S.las raw_reads.1.raw_reads.2.N0.S.las\nLAsort -v raw_reads.2.raw_reads.1.C0 raw_reads.2.raw_reads.1.N0 && LAmerge -v L1.2.1 raw_reads.2.raw_reads.1.C0.S raw_reads.2.raw_reads.1.N0.S && rm raw_reads.2.raw_reads.1.C0.S.las raw_reads.2.raw_reads.1.N0.S.las\nLAsort -v raw_reads.2.raw_reads.2.C0 raw_reads.2.raw_reads.2.N0 && LAmerge -v L1.2.2 raw_reads.2.raw_reads.2.C0.S raw_reads.2.raw_reads.2.N0.S && rm raw_reads.2.raw_reads.2.C0.S.las raw_reads.2.raw_reads.2.N0.S.las\nLAcheck -vS raw_reads L1.1.2\nLAcheck -vS raw_reads L1.2.1\nLAcheck -vS raw_reads L1.2.2\n")
    eq_(len(result), 2)

Example #4

File: test_functional.py Project: malonge/FALCON

def test_get_daligner_job_descriptions_small():
    # when there is only 1 block, a special case
    example_HPCdaligner = open(example_HPCdaligner_small_fn)
    result = f.get_daligner_job_descriptions(
            example_HPCdaligner, 'preads', single=True)
    assert result
    helpers.equal_multiline(result[('.1', '.1')], "daligner -v -h1 -t50 -H1 -e0.99 -l1 -s1000 preads.1 preads.1\nLAcheck -v preads *.las\nLAsort -v preads.1.preads.1.C0 preads.1.preads.1.N0 preads.1.preads.1.C1 preads.1.preads.1.N1 preads.1.preads.1.C2 preads.1.preads.1.N2 preads.1.preads.1.C3 preads.1.preads.1.N3 && LAmerge -v preads.1 preads.1.preads.1.C0.S preads.1.preads.1.N0.S preads.1.preads.1.C1.S preads.1.preads.1.N1.S preads.1.preads.1.C2.S preads.1.preads.1.N2.S preads.1.preads.1.C3.S preads.1.preads.1.N3.S\nLAcheck -vS preads preads.1\n")
    eq_(len(result), 1)

Example #5

File: test_functional.py Project: malonge/FALCON

def test_get_daligner_job_descriptions():
    example_HPCdaligner = open(example_HPCdaligner_fn)
    result = f.get_daligner_job_descriptions(
            example_HPCdaligner, 'raw_reads')
    assert result
    helpers.equal_multiline(result[('.1', '.1')], "daligner -v -h1 -t16 -H1 -e0.7 -l1 -s1000 raw_reads.1 raw_reads.1\nLAcheck -v raw_reads *.las\nLAsort -v raw_reads.1.raw_reads.1.C0 raw_reads.1.raw_reads.1.N0 && LAmerge -v L1.1.1 raw_reads.1.raw_reads.1.C0.S raw_reads.1.raw_reads.1.N0.S && rm raw_reads.1.raw_reads.1.C0.S.las raw_reads.1.raw_reads.1.N0.S.las\nLAcheck -vS raw_reads L1.1.1\n")
    helpers.equal_multiline(result[('.2', '.1', '.2')], "daligner -v -h1 -t16 -H1 -e0.7 -l1 -s1000 raw_reads.2 raw_reads.1 raw_reads.2\nLAcheck -v raw_reads *.las\nLAsort -v raw_reads.1.raw_reads.2.C0 raw_reads.1.raw_reads.2.N0 && LAmerge -v L1.1.2 raw_reads.1.raw_reads.2.C0.S raw_reads.1.raw_reads.2.N0.S && rm raw_reads.1.raw_reads.2.C0.S.las raw_reads.1.raw_reads.2.N0.S.las\nLAsort -v raw_reads.2.raw_reads.1.C0 raw_reads.2.raw_reads.1.N0 && LAmerge -v L1.2.1 raw_reads.2.raw_reads.1.C0.S raw_reads.2.raw_reads.1.N0.S && rm raw_reads.2.raw_reads.1.C0.S.las raw_reads.2.raw_reads.1.N0.S.las\nLAsort -v raw_reads.2.raw_reads.2.C0 raw_reads.2.raw_reads.2.N0 && LAmerge -v L1.2.2 raw_reads.2.raw_reads.2.C0.S raw_reads.2.raw_reads.2.N0.S && rm raw_reads.2.raw_reads.2.C0.S.las raw_reads.2.raw_reads.2.N0.S.las\nLAcheck -vS raw_reads L1.1.2\nLAcheck -vS raw_reads L1.2.1\nLAcheck -vS raw_reads L1.2.2\n")
    eq_(len(result), 2)

Example #6

File: test_functional.py Project: PacificBiosciences/FALCON

def test_get_daligner_job_descriptions():
    example_HPCdaligner = open(example_HPCdaligner_fn)
    result = f.get_daligner_job_descriptions(
        example_HPCdaligner, 'raw_reads')
    assert result
    import sys, pprint
    sys.stderr.write(pprint.pformat(result))
    helpers.equal_multiline(result[('.1', '.1')], 'daligner -v -w1 -h1 -t50 -H2000 -e0.99 -l1 -s1000 -P=. -mdust raw_reads.1 raw_reads.1\nLAcheck -v raw_reads *.las\n')
    helpers.equal_multiline(result[('.2', '.1', '.2')], 'daligner -v -w1 -h1 -t50 -H2000 -e0.99 -l1 -s1000 -P=. -mdust raw_reads.2 raw_reads.1 raw_reads.2\nLAcheck -v raw_reads *.las\n')
    eq_(len(result), 2)

Example #7

File: test_functional.py Project: pythseq/FALCON-1

def test_get_daligner_job_descriptions_small():
    # when there is only 1 block, a special case
    example_HPCdaligner = open(example_HPCdaligner_small_fn)
    result = f.get_daligner_job_descriptions(example_HPCdaligner,
                                             'preads',
                                             single=True)
    assert result
    helpers.equal_multiline(
        result[('.1', '.1')],
        'daligner -v -h1 -t50 -H1 -e0.99 -l1 -s1000 preads.1 preads.1\nLAcheck -v preads *.las\n'
    )
    eq_(len(result), 1)

Example #8

File: test_functional.py Project: pythseq/FALCON-1

def test_get_daligner_job_descriptions():
    example_HPCdaligner = open(example_HPCdaligner_fn)
    result = f.get_daligner_job_descriptions(example_HPCdaligner, 'raw_reads')
    assert result
    import sys, pprint
    sys.stderr.write(pprint.pformat(result))
    helpers.equal_multiline(
        result[('.1', '.1')],
        'daligner -v -w1 -h1 -t50 -H2000 -e0.99 -l1 -s1000 -P=. -mdust raw_reads.1 raw_reads.1\nLAcheck -v raw_reads *.las\n'
    )
    helpers.equal_multiline(
        result[('.2', '.1', '.2')],
        'daligner -v -w1 -h1 -t50 -H2000 -e0.99 -l1 -s1000 -P=. -mdust raw_reads.2 raw_reads.1 raw_reads.2\nLAcheck -v raw_reads *.las\n'
    )
    eq_(len(result), 2)