def _importAminoacidSequence5(self):
"""
Import the sequence of chain A of atomic structure 3rrq.cif
"""
args = {
'inputSequenceName': self.NAME,
'inputProteinSequence': ProtImportSequence.IMPORT_FROM_STRUCTURE,
'inputStructureSequence':
ProtImportSequence.IMPORT_STRUCTURE_FROM_ID,
'pdbId': '3RRQ',
'inputStructureChain':
'{"model": 0, "chain": "A", "residues": 108}'
}
protSequence = self.newProtocol(ProtImportSequence, **args)
protSequence.setObjLabel('import aminoacid seq,\n from 3RRQ\n'
'atomic structure')
self.launchProtocol(protSequence)
sequence = protSequence.outputSequence
self.assertEqual("3rrq__0_A", sequence.getId())
self.assertEqual("User_Name", sequence.getSeqName())
self.assertEqual("", sequence.getDescription())
self.assertEqual("NPPTFSPALL", sequence.getSequence()[:10])
self.assertEqual(
"ACDEFGHIKLMNPQRSTVWY",
indexToAlphabet(sequence.getIsAminoacids(),
sequence.getAlphabet()).letters)
return sequence
def _importAminoacidSequence3(self):
"""Import the sequence derived from the mutation
of 1g03 model 7 chain A sequence
"""
args = {
'inputSequenceName':
self.NAME,
'inputProteinSequence':
ProtImportSequence.IMPORT_FROM_FILES,
'fileSequence':
self.dsModBuild.getFile('Sequences/1g03__7_A_mutated.fasta')
}
protSequence = self.newProtocol(ProtImportSequence, **args)
protSequence.setObjLabel('import aminoacid seq,\n1g03__7_A_mutated\n'
'from file')
self.launchProtocol(protSequence)
sequence = protSequence.outputSequence
self.assertEqual("Seq_1g03__7_A_mutated", sequence.getId())
self.assertEqual("User_Name", sequence.getSeqName())
self.assertEqual("Seq_1g03__7_A_mutated", sequence.getDescription())
self.assertEqual("PVMHPHGARR", sequence.getSequence()[:10])
self.assertEqual(
"ACDEFGHIKLMNPQRSTVWY",
indexToAlphabet(sequence.getIsAminoacids(),
sequence.getAlphabet()).letters)
return sequence
def _importAminoacidSequence7(self):
"""Import the sequence derived from UniProtKB ID Q15116
"""
args = {
'inputSequenceName': self.NAME,
'inputProteinSequence': ProtImportSequence.IMPORT_FROM_UNIPROT,
'uniProtSequence': self.UNIPROTID3
}
protSequence = self.newProtocol(ProtImportSequence, **args)
protSequence.setObjLabel('import aminoacid seq,\nQ12LC89\n'
'from UniProtKB')
self.launchProtocol(protSequence)
sequence = protSequence.outputSequence
self.assertEqual("Q2LC89", sequence.getId())
self.assertEqual("User_Name", sequence.getSeqName())
self.assertEqual("PD-1-ligand 2", sequence.getDescription())
self.assertEqual("LQLHQIAALF", sequence.getSequence()[:10])
self.assertEqual(
"ACDEFGHIKLMNPQRSTVWY",
indexToAlphabet(sequence.getIsAminoacids(),
sequence.getAlphabet()).letters)
return sequence
def _importAminoacidSequence9(self):
"""Import the sequence derived from UniProtKB ID Q9NZQ7
"""
args = {
'inputSequenceName': self.NAME,
'inputProteinSequence': ProtImportSequence.IMPORT_FROM_UNIPROT,
'uniProtSequence': self.UNIPROTID5
}
protSequence = self.newProtocol(ProtImportSequence, **args)
protSequence.setObjLabel('import aminoacid seq,\nQ9NZQ7\n'
'from UniProtKB')
self.launchProtocol(protSequence)
sequence = protSequence.outputSequence
self.assertEqual("Q9NZQ7", sequence.getId())
self.assertEqual("User_Name", sequence.getSeqName())
self.assertEqual("Programmed cell death 1 ligand 1",
sequence.getDescription())
self.assertEqual("MRIFAVFIFM", sequence.getSequence()[:10])
self.assertEqual(
"ACDEFGHIKLMNPQRSTVWY",
indexToAlphabet(sequence.getIsAminoacids(),
sequence.getAlphabet()).letters)
return sequence
def _importAminoacidSequence6(self):
"""Import the sequence derived from UniProtKB ID P01832
"""
args = {
'inputSequenceName': self.NAME,
'inputProteinSequence': ProtImportSequence.IMPORT_FROM_UNIPROT,
'uniProtSequence': self.UNIPROTID2
}
protSequence = self.newProtocol(ProtImportSequence, **args)
protSequence.setObjLabel('import aminoacid seq,\nP01832\n'
'from UniProtKB')
self.launchProtocol(protSequence)
sequence = protSequence.outputSequence
self.assertEqual("P01832", sequence.getId())
self.assertEqual("User_Name", sequence.getSeqName())
self.assertEqual("Polymeric immunoglobulin receptor",
sequence.getDescription())
self.assertEqual("MALFLLTCLL", sequence.getSequence()[:10])
self.assertEqual(
"ACDEFGHIKLMNPQRSTVWY",
indexToAlphabet(sequence.getIsAminoacids(),
sequence.getAlphabet()).letters)
return sequence
