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