def test_defaultCtor(self):
header = PacBioBam.BamHeader()
self.assertFalse(header.Version())
self.assertFalse(header.SortOrder())
self.assertEqual(0, len(header.ReadGroups()))
self.assertEqual(0, len(header.Sequences()))
self.assertEqual(0, len(header.Programs()))
self.assertEqual(0, len(header.Comments()))
with self.assertRaises(RuntimeError):
pg = header.Program("foo")
rg = header.ReadGroup("foo")
sq = header.SequenceId("foo")
sl = header.SequenceLength(42)
sn = header.SequenceName(42)
def test_encode(self):
expectedText = ("@HD\tVN:1.1\tSO:queryname\tpb:3.0.1\n"
"@SQ\tSN:chr1\tLN:2038\tSP:chocobo\n"
"@SQ\tSN:chr2\tLN:3042\tSP:chocobo\n"
"@RG\tID:rg1\tPL:PACBIO\tDS:READTYPE=UNKNOWN\tSM:control\tPM:SEQUEL\n"
"@RG\tID:rg2\tPL:PACBIO\tDS:READTYPE=UNKNOWN\tSM:condition1\tPM:SEQUEL\n"
"@RG\tID:rg3\tPL:PACBIO\tDS:READTYPE=UNKNOWN\tSM:condition1\tPM:SEQUEL\n"
"@PG\tID:_foo_\tPN:ide\n"
"@CO\tipsum and so on\n"
"@CO\tcitation needed\n")
rg1 = PacBioBam.ReadGroupInfo("rg1")
rg1.Sample("control")
rg2 = PacBioBam.ReadGroupInfo("rg2")
rg2.Sample("condition1")
rg3 = PacBioBam.ReadGroupInfo("rg3")
rg3.Sample("condition1")
seq1 = PacBioBam.SequenceInfo("chr1")
seq1.Length("2038")
seq1.Species("chocobo")
seq2 = PacBioBam.SequenceInfo("chr2")
seq2.Length("3042")
seq2.Species("chocobo")
prog1 = PacBioBam.ProgramInfo("_foo_")
prog1.Name("ide")
header = PacBioBam.BamHeader()
header.Version("1.1")
header.SortOrder("queryname")
header.PacBioBamVersion("3.0.1")
header.AddReadGroup(rg1)
header.AddReadGroup(rg2)
header.AddReadGroup(rg3)
header.AddSequence(seq1)
header.AddSequence(seq2)
header.AddProgram(prog1)
header.AddComment("ipsum and so on")
header.AddComment("citation needed")
self.assertEqual(expectedText, header.ToSam())
def test_decode(self):
text = ("@HD\tVN:1.1\tSO:queryname\tpb:3.0.1\n"
"@SQ\tSN:chr1\tLN:2038\tSP:chocobo\n"
"@SQ\tSN:chr2\tLN:3042\tSP:chocobo\n"
"@RG\tID:rg1\tSM:control\n"
"@RG\tID:rg2\tSM:condition1\n"
"@RG\tID:rg3\tSM:condition1\n"
"@PG\tID:_foo_\tPN:ide\n"
"@CO\tipsum and so on\n"
"@CO\tcitation needed\n")
header = PacBioBam.BamHeader(text)
self.assertEqual("1.1", header.Version())
self.assertEqual("queryname", header.SortOrder())
self.assertEqual("3.0.1", header.PacBioBamVersion())
self.assertEqual(3, len(header.ReadGroups()))
self.assertTrue(header.HasReadGroup("rg1"))
self.assertTrue(header.HasReadGroup("rg2"))
self.assertTrue(header.HasReadGroup("rg3"))
self.assertEqual("control", header.ReadGroup("rg1").Sample())
self.assertEqual("condition1", header.ReadGroup("rg2").Sample())
self.assertEqual("condition1", header.ReadGroup("rg3").Sample())
self.assertEqual(2, len(header.Sequences()))
self.assertTrue(header.HasSequence("chr1"))
self.assertTrue(header.HasSequence("chr2"))
self.assertEqual("chocobo", header.Sequence("chr1").Species())
self.assertEqual("chocobo", header.Sequence("chr2").Species())
self.assertEqual("2038", header.Sequence("chr1").Length())
self.assertEqual("3042", header.Sequence("chr2").Length())
self.assertEqual(1, len(header.Programs()))
self.assertTrue(header.HasProgram("_foo_"))
self.assertEqual("ide", header.Program("_foo_").Name())
self.assertEqual(2, len(header.Comments()))
self.assertEqual("ipsum and so on", header.Comments()[0])
self.assertEqual("citation needed", header.Comments()[1])
# with the distribution.
#
# * Neither the name of Pacific Biosciences nor the names of its
# contributors may be used to endorse or promote products derived
# from this software without specific prior written permission.
#
# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
# GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
# BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
# OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
# USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
# OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
# SUCH DAMAGE.
#
# Author: Derek Barnett
try:
import PacBioBam as bam
header = bam.BamHeader()
print "\nPython wrapper OK.\n"
except ImportError:
print "\nPython wrapper failed!\n"