def testImportStructureAminoacidSequence1(self):
"""
Import the sequence of chain B of atomic structure 3lqd.cif
"""
args = {'inputSequenceName': self.NAME,
'inputSequenceDescription': self.DESCRIPTION,
'inputProteinSequence':
ProtImportSequence.IMPORT_FROM_STRUCTURE,
'inputStructureSequence':
ProtImportSequence.IMPORT_STRUCTURE_FROM_ID,
'pdbId': self.pdbID1,
'inputStructureChain': self.CHAIN1
}
prot15 = self.newProtocol(ProtImportSequence, **args)
prot15.setObjLabel('15_import aminoacid seq,\n from atomic '
'structure')
self.launchProtocol(prot15)
sequence = prot15.outputSequence
self.assertEqual("3lqd_B", sequence.getId())
self.assertEqual("USER_SEQ", sequence.getSeqName())
self.assertEqual("User description", sequence.getDescription())
self.assertEqual("VHLSGEEKSA", sequence.getSequence()[:10])
self.assertEqual("ACDEFGHIKLMNPQRSTVWY",
indexToAlphabet(sequence.getIsAminoacids(),
sequence.getAlphabet()).letters)
def testImportStructureAminoacidSequence2(self):
"""
Import the sequence of chain B of atomic structure 3lqd.cif
"""
args = {'inputSequenceID': self.USERID,
'inputSequenceName': self.NAME,
'inputSequenceDescription': self.DESCRIPTION,
'inputProteinSequence':
ProtImportSequence.IMPORT_FROM_STRUCTURE,
'inputStructureSequence':
ProtImportSequence.IMPORT_STRUCTURE_FROM_FILES,
'pdbFile': self.dsModBuild.getFile('PDBx_mmCIF/3lqd.cif'),
'inputStructureChain': self.CHAIN1
}
prot16 = self.newProtocol(ProtImportSequence, **args)
prot16.setObjLabel('16_import aminoacid seq,\n from atomic '
'structure')
self.launchProtocol(prot16)
sequence = prot16.outputSequence
self.assertEqual("UserID", sequence.getId())
self.assertEqual("USER_SEQ", sequence.getSeqName())
self.assertEqual("User description", sequence.getDescription())
self.assertEqual("VHLSGEEKSA", sequence.getSequence()[:10])
self.assertEqual("ACDEFGHIKLMNPQRSTVWY",
indexToAlphabet(sequence.getIsAminoacids(),
sequence.getAlphabet()).letters)
def testImportGeneBankNucleotideSequence1(self):
"""
Import a single nucleotide sequence from GeneBank
"""
args = {'inputSequenceName': self.NAME,
'inputSequence': SEQ_TYPE_NUCLEOTIDES,
'inputNucleotideSequence':
ProtImportSequence.IMPORT_FROM_GENEBANK,
'geneBankSequence': self.GENEBANKID
}
prot11 = self.newProtocol(ProtImportSequence, **args)
prot11.setObjLabel('11_import nucleotide,\nseq from '
'GeneBank')
self.launchProtocol(prot11)
sequence = prot11.outputSequence
self.assertEqual("AJ520101.1", sequence.getId())
self.assertEqual('USER_SEQ', sequence.getSeqName())
self.assertEqual("AJ520101.1 Rhizobium leguminosarum bv. viciae "
"plasmid partial fixC gene, fixX gene, nifA gene "
"and nifB gene",
sequence.getDescription())
self.assertEqual("GGATCCGAGA", sequence.getSequence()[:10])
self.assertEqual("GAUC",
indexToAlphabet(sequence.getIsAminoacids(),
sequence.getAlphabet()).letters)
def testImportStructureNucleotideSequence4(self):
"""
Import the sequence of chain I of atomic DNA structure 1aoi.cif
"""
args = {'inputSequenceID': self.USERID,
'inputSequenceName': self.NAME,
'inputSequenceDescription': self.DESCRIPTION,
'inputSequence': SEQ_TYPE_NUCLEOTIDES,
'inputNucleotideSequence':
ProtImportSequence.IMPORT_FROM_NUCLEOTIDE_STRUCTURE,
'inputStructureSequence':
ProtImportSequence.IMPORT_STRUCTURE_FROM_FILES,
'pdbFile': self.dsModBuild.getFile('PDBx_mmCIF/1aoi.cif'),
'inputStructureChain': self.CHAIN3
}
prot6 = self.newProtocol(ProtImportSequence, **args)
prot6.setObjLabel('6_import DNA seq,\n from atomic '
'structure')
self.launchProtocol(prot6)
sequence = prot6.outputSequence
self.assertEqual("UserID", sequence.getId())
self.assertEqual("USER_SEQ", sequence.getSeqName())
self.assertEqual("User description",
sequence.getDescription())
self.assertEqual("ATCAATATCC", sequence.getSequence()[:10])
self.assertEqual("GAUC",
indexToAlphabet(sequence.getIsAminoacids(),
sequence.getAlphabet()).letters)
def testImportGeneBankNucleotideSequence2(self):
"""
Import a single nucleotide sequence from GeneBank
"""
args = {'inputSequenceID': self.USERID,
'inputSequenceName': self.NAME,
'inputSequenceDescription': self.DESCRIPTION,
'inputSequence': SEQ_TYPE_NUCLEOTIDES,
'inputNucleotideSequence':
ProtImportSequence.IMPORT_FROM_GENEBANK,
'geneBankSequence': self.GENEBANKID
}
prot12 = self.newProtocol(ProtImportSequence, **args)
prot12.setObjLabel('12_import nucleotide,\nseq from '
'GeneBank')
self.launchProtocol(prot12)
sequence = prot12.outputSequence
self.assertEqual("UserID", sequence.getId())
self.assertEqual('USER_SEQ', sequence.getSeqName())
self.assertEqual("User description",
sequence.getDescription())
self.assertEqual("GGATCCGAGA", sequence.getSequence()[:10])
self.assertEqual("GAUC",
indexToAlphabet(sequence.getIsAminoacids(),
sequence.getAlphabet()).letters)
def testImportFileNucleotideSequence4(self):
"""
Import a single nucleotide sequence from a text file that contains
several sequences
"""
args = {'inputSequenceID': self.USERID,
'inputSequenceName': self.NAME,
'inputSequenceDescription': self.DESCRIPTION,
'inputSequence': SEQ_TYPE_NUCLEOTIDES,
'inputNucleotideSequence':
ProtImportSequence.IMPORT_FROM_NUCLEOTIDE_FILES,
'fileSequence': self.dsModBuild.getFile(
'Sequences/Several_sequences.fasta')
}
prot10 = self.newProtocol(ProtImportSequence, **args)
prot10.setObjLabel('10_import nucleotide,\nseq from file')
self.launchProtocol(prot10)
sequence = prot10.outputSequence
self.assertEqual("UserID", sequence.getId())
self.assertEqual('USER_SEQ', sequence.getSeqName())
self.assertEqual("User description",
sequence.getDescription())
self.assertEqual("TGGCTAAATA", sequence.getSequence()[:10])
self.assertEqual("GAUC",
indexToAlphabet(sequence.getIsAminoacids(),
sequence.getAlphabet()).letters)
def testImportFileNucleotideSequence1(self):
"""
Import a single nucleotide sequence from a text file
"""
args = {'inputSequenceName': self.NAME,
'inputSequence': SEQ_TYPE_NUCLEOTIDES,
'inputNucleotideSequence':
ProtImportSequence.IMPORT_FROM_NUCLEOTIDE_FILES,
'fileSequence': self.dsModBuild.getFile(
'Sequences/AJ520101.fasta')
}
prot7 = self.newProtocol(ProtImportSequence, **args)
prot7.setObjLabel('7_import nucleotide,\nseq from file')
self.launchProtocol(prot7)
sequence = prot7.outputSequence
self.assertEqual("AJ520101.1", sequence.getId())
self.assertEqual('USER_SEQ', sequence.getSeqName())
self.assertEqual("AJ520101.1 Rhizobium leguminosarum bv. viciae "
"plasmid "
"partial fixC gene, fixX gene, nifA gene "
"and nifB gene",
sequence.getDescription())
self.assertEqual("GGATCCGAGA", sequence.getSequence()[:10])
self.assertEqual("GAUC",
indexToAlphabet(sequence.getIsAminoacids(),
sequence.getAlphabet()).letters)
def testImportStructureNucleotideSequence1(self):
"""
Import the sequence of chain A of atomic RNA structure 205d.cif
"""
args = {'inputSequenceName': self.NAME,
'inputSequenceDescription': self.DESCRIPTION,
'inputSequence': SEQ_TYPE_NUCLEOTIDES,
'inputNucleotideSequence':
ProtImportSequence.IMPORT_FROM_NUCLEOTIDE_STRUCTURE,
'inputStructureSequence':
ProtImportSequence.IMPORT_STRUCTURE_FROM_ID,
'pdbId': self.pdbID2,
'inputStructureChain': self.CHAIN2
}
prot3 = self.newProtocol(ProtImportSequence, **args)
prot3.setObjLabel('3_import RNA seq,\n from atomic '
'structure')
self.launchProtocol(prot3)
sequence = prot3.outputSequence
self.assertEqual("205d_A", sequence.getId())
self.assertEqual("USER_SEQ", sequence.getSeqName())
self.assertEqual("User description",
sequence.getDescription())
self.assertEqual("GGACUUUGGU", sequence.getSequence()[:10])
self.assertEqual("GAUC",
indexToAlphabet(sequence.getIsAminoacids(),
sequence.getAlphabet()).letters)
def testImportUniprotAminoacidSequence1(self):
"""
Import a single aminoacid sequence from UniProt
"""
args = {'inputSequenceName': self.NAME,
'inputProteinSequence':
ProtImportSequence.IMPORT_FROM_UNIPROT,
'uniProtSequence': self.UNIPROTID
}
prot19 = self.newProtocol(ProtImportSequence, **args)
prot19.setObjLabel('19_import aminoacids,\nseq from '
'UniProt')
self.launchProtocol(prot19)
sequence = prot19.outputSequence
self.assertEqual("P12345", sequence.getId())
self.assertEqual('USER_SEQ', sequence.getSeqName())
self.assertEqual('Aspartate aminotransferase, mitochondrial',
sequence.getDescription())
self.assertEqual("MALLHSARVL", sequence.getSequence()[:10])
self.assertEqual("ACDEFGHIKLMNPQRSTVWY",
indexToAlphabet(sequence.getIsAminoacids(),
sequence.getAlphabet()).letters)
def testImportUserAminoacidSequence1(self):
"""
Import a single aminoacid sequence provided by the user (protein
alphabet by default)
"""
args = {'inputSequenceName': self.NAME,
'inputSequenceDescription': self.DESCRIPTION,
'inputRawSequence': self.AMINOACIDSSEQ1
}
prot13 = self.newProtocol(ProtImportSequence, **args)
prot13.setObjLabel('13_import aminoacid seq,\n from user\nExtended '
'protein alphabet')
self.launchProtocol(prot13)
sequence = prot13.outputSequence
self.assertEqual("USER_SEQ", sequence.getId())
self.assertEqual("USER_SEQ", sequence.getSeqName())
self.assertEqual("User description", sequence.getDescription())
self.assertEqual("LARKJLAKPA", sequence.getSequence()[:10])
self.assertEqual("ACDEFGHIKLMNPQRSTVWYBXZJUO",
indexToAlphabet(sequence.getIsAminoacids(),
sequence.getAlphabet()).letters
)
def testImportFileNucleotideSequence3(self):
"""
Import a single nucleotide sequence from a text file
"""
args = {'inputSequenceName': self.NAME,
'inputSequence': SEQ_TYPE_NUCLEOTIDES,
'inputNucleotideSequence':
ProtImportSequence.IMPORT_FROM_NUCLEOTIDE_FILES,
'fileSequence': self.dsModBuild.getFile(
'Sequences/Several_sequences.fasta')
}
prot9 = self.newProtocol(ProtImportSequence, **args)
prot9.setObjLabel('9_import nucleotide,\nseq from file')
self.launchProtocol(prot9)
sequence = prot9.outputSequence
self.assertEqual("Seq1", sequence.getId())
self.assertEqual('USER_SEQ', sequence.getSeqName())
self.assertEqual("Seq1 This is the sequence number one",
sequence.getDescription())
self.assertEqual("TGGCTAAATA", sequence.getSequence()[:10])
self.assertEqual("GAUC",
indexToAlphabet(sequence.getIsAminoacids(),
sequence.getAlphabet()).letters)
def testImportUserAminoacidSequence2(self):
"""
Import a single aminoacid sequence provided by the user (protein
alphabet PROTEIN_ALPHABET
"""
args = {'inputSequenceName': self.NAME,
'inputSequenceDescription': self.DESCRIPTION,
'proteinIUPACalphabet': PROTEIN_ALPHABET,
'inputRawSequence': self.AMINOACIDSSEQ1
}
prot14 = self.newProtocol(ProtImportSequence, **args)
prot14.setObjLabel('14_import aminoacid seq,\n from user\nProtein '
'alphabet')
self.launchProtocol(prot14)
sequence = prot14.outputSequence
self.assertEqual("USER_SEQ", sequence.getId())
self.assertEqual("USER_SEQ", sequence.getSeqName())
self.assertEqual("User description", sequence.getDescription())
self.assertEqual("LARKLAKPAV", sequence.getSequence()[:10])
self.assertEqual("ACDEFGHIKLMNPQRSTVWY",
indexToAlphabet(sequence.getIsAminoacids(),
sequence.getAlphabet()).letters
)
def testImportUserNucleotideSequence2(self):
"""
Import a single nucleotide sequence provided by the user (nucleotide
alphabet AMBIGOUS_RNA_ALPHABET)
"""
args = {'inputSequenceName': self.NAME,
'inputSequenceDescription': self.DESCRIPTION,
'inputSequence': SEQ_TYPE_NUCLEOTIDES,
'nucleotideIUPACalphabet': AMBIGOUS_RNA_ALPHABET,
'inputRawSequence': self.NUCLEOTIDESEQ1
}
prot2 = self.newProtocol(ProtImportSequence, **args)
prot2.setObjLabel('2_import RNA,\nseq from user\nAmbigous RNA '
'alphabet')
self.launchProtocol(prot2)
sequence = prot2.outputSequence
self.assertEqual("USER_SEQ", sequence.getId())
self.assertEqual("USER_SEQ", sequence.getSeqName())
self.assertEqual("User description",
sequence.getDescription())
self.assertEqual("AAGCGGGGGB", sequence.getSequence()[:10])
self.assertEqual("GAUCRYWSMKHBVDN",
indexToAlphabet(sequence.getIsAminoacids(),
sequence.getAlphabet()).letters)
def testImportUserNucleotideSequence1(self):
"""
Import a single nucleotide sequence provided by the user (nucleotide
alphabet by default)
"""
args = {'inputSequenceName': self.NAME,
'inputSequenceDescription': self.DESCRIPTION,
'inputSequence': SEQ_TYPE_NUCLEOTIDES,
'nucleotideIUPACalphabet': EXTENDED_DNA_ALPHABET,
'inputRawSequence': self.NUCLEOTIDESEQ1
}
prot1 = self.newProtocol(ProtImportSequence, **args)
prot1.setObjLabel('1_import DNA,\nseq from user\nExtended DNA '
'alphabet')
self.launchProtocol(prot1)
sequence = prot1.outputSequence
self.assertEqual("USER_SEQ", sequence.getId())
self.assertEqual("USER_SEQ", sequence.getSeqName())
self.assertEqual("User description",
sequence.getDescription())
self.assertEqual("AATGCGGTTG", sequence.getSequence()[:10])
self.assertEqual("GATCBDSW",
indexToAlphabet(sequence.getIsAminoacids(),
sequence.getAlphabet()).letters)
def testImportFileAminoacidSequence1(self):
"""
Import a single aminoacid sequence from a text file
"""
args = {'inputSequenceName': self.NAME,
'inputProteinSequence':
ProtImportSequence.IMPORT_FROM_FILES,
'fileSequence': self.dsModBuild.getFile(
'Sequences/COX1_human.fasta')
}
prot17 = self.newProtocol(ProtImportSequence, **args)
prot17.setObjLabel('17_import aminoacid,\nseq from file')
self.launchProtocol(prot17)
sequence = prot17.outputSequence
self.assertEqual("YP_003024028.1", sequence.getId())
self.assertEqual('USER_SEQ', sequence.getSeqName())
self.assertEqual('YP_003024028.1 cytochrome c oxidase '
'subunit I (mitochondrion) [H**o sapiens]',
sequence.getDescription())
self.assertEqual("MFADRWLFST", sequence.getSequence()[:10])
self.assertEqual("ACDEFGHIKLMNPQRSTVWY",
indexToAlphabet(sequence.getIsAminoacids(),
sequence.getAlphabet()).letters)
def testImportUniprotAminoacidSequence2(self):
"""
Import a single aminoacid sequence from UniProt
"""
args = {'inputSequenceID': self.USERID,
'inputSequenceName': self.NAME,
'inputSequenceDescription': self.DESCRIPTION,
'inputProteinSequence':
ProtImportSequence.IMPORT_FROM_UNIPROT,
'uniProtSequence': self.UNIPROTID
}
prot20 = self.newProtocol(ProtImportSequence, **args)
prot20.setObjLabel('20_import aminoacids,\nseq from '
'UniProt')
self.launchProtocol(prot20)
sequence = prot20.outputSequence
self.assertEqual("UserID", sequence.getId())
self.assertEqual('USER_SEQ', sequence.getSeqName())
self.assertEqual('User description',
sequence.getDescription())
self.assertEqual("MALLHSARVL", sequence.getSequence()[:10])
self.assertEqual("ACDEFGHIKLMNPQRSTVWY",
indexToAlphabet(sequence.getIsAminoacids(),
sequence.getAlphabet()).letters)
def testImportFileAminoacidSequence2(self):
"""
Import a single aminoacid sequence from a text file
"""
args = {'inputSequenceID': self.USERID,
'inputSequenceName': self.NAME,
'inputSequenceDescription': self.DESCRIPTION,
'inputProteinSequence':
ProtImportSequence.IMPORT_FROM_FILES,
'fileSequence': self.dsModBuild.getFile(
'Sequences/COX1_human.fasta')
}
prot18 = self.newProtocol(ProtImportSequence, **args)
prot18.setObjLabel('18_import aminoacid,\nseq from file')
self.launchProtocol(prot18)
sequence = prot18.outputSequence
self.assertEqual("UserID", sequence.getId())
self.assertEqual('USER_SEQ', sequence.getSeqName())
self.assertEqual('User description',
sequence.getDescription())
self.assertEqual("MFADRWLFST", sequence.getSequence()[:10])
self.assertEqual("ACDEFGHIKLMNPQRSTVWY",
indexToAlphabet(sequence.getIsAminoacids(),
sequence.getAlphabet()).letters)