def testCommandsWithSpacesNotParsed(self):
header = {'CL': 'bwa aln -q 15 -f $sai_file ' +
'$reference_fasta $fastq_file\tPP:bwa_index',
'ID': 'bwa_aln_fastq',
'PN': 'bwa',
'VN': '0.5.9-r16'}
self.assertEqual(header, reads.parseMalformedBamHeader(header))
def testOriginalTypesUnmodified(self):
# note real field tags, just checking that types are preserved
header = {'int': 2845856850,
'float': 206.6,
'bool': True,
'string': '123'}
self.assertEqual(header, reads.parseMalformedBamHeader(header))
def _readReferences(self):
# Read the reference information from the samfile
referenceSetName = None
for referenceInfo in self._samFile.header['SQ']:
if 'AS' not in referenceInfo:
infoDict = reads.parseMalformedBamHeader(referenceInfo)
# If there's still no reference set name in there we use
# a default name.
name = infoDict.get("AS", "Default")
if referenceSetName is None:
referenceSetName = name
self._addReferenceSet(referenceSetName)
else:
self.assertEqual(referenceSetName, name)
self._addReference(infoDict['SN'])
def _readReferences(self):
# Read the reference information from the samfile
referenceSetName = None
for referenceInfo in self._samFile.header['SQ']:
if 'AS' not in referenceInfo:
infoDict = reads.parseMalformedBamHeader(referenceInfo)
# If there's still no reference set name in there we use
# a default name.
name = infoDict.get("AS", "Default")
if referenceSetName is None:
referenceSetName = name
self._addReferenceSet(referenceSetName)
else:
self.assertEqual(referenceSetName, name)
self._addReference(infoDict['SN'])
def testSpaceSeparatedUnparsedFieldsParsed(self):
header = {'LN': 249250621,
'M5': '1b22b98cdeb4a9304cb5d48026a85128',
'SN': '1',
'UR': 'ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/' +
'technical/reference/phase2_reference_assembly' +
'_sequence/hs37d5.fa.gz AS:NCBI37' +
' SP:Human'}
expected = {'LN': 249250621,
'M5': '1b22b98cdeb4a9304cb5d48026a85128',
'SN': '1',
'UR': 'ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/' +
'technical/reference/phase2_reference_assembly' +
'_sequence/hs37d5.fa.gz',
'AS': 'NCBI37',
'SP': 'Human'}
self.assertEqual(expected, reads.parseMalformedBamHeader(header))
def testGoodHeaderUnmodified(self):
header = {'SO': 'coordinate', 'VN': '1.0'}
self.assertEqual(header, reads.parseMalformedBamHeader(header))