def sequenceDatabaseDownloadStep(self, sequenceDB):
"""Download UniProt/GeneBank sequence from its respective database
"""
# sequenceDB = str(sequenceDB)
if self.uniProtSequence.get() is not None:
seqHandler = emconv.SequenceHandler()
elif self._getGeneBankID() is not None:
seqHandler = emconv.SequenceHandler(isAminoacid=False)
seqDic, error = seqHandler.downloadSeqFromDatabase(sequenceDB)
if seqDic is None:
print("Error: ", error)
self.setAborted()
exit(0)
if self.inputSequenceID.get() is not None:
self.id = self.inputSequenceID.get()
elif sequenceDB != '':
self.id = sequenceDB
else:
self.id = self.name
if seqDic['description'] != '':
self.description = seqDic['description']
self.sequence = seqDic['sequence']
self.alphabet = emconv.alphabetToIndex(
self.inputSequence == emconv.SEQ_TYPE_AMINOACIDS,
seqDic['alphabet'])
def fileDownloadStep(self, sequenceFile):
# If sequencePath contains more than one sequence, only
# the first one will be considered
seqHandler = emconv.SequenceHandler()
seqDic = seqHandler.readSequenceFromFile(sequenceFile, type="fasta")
if self.inputSequenceID.get() is not None:
self.id = self.inputSequenceID.get()
elif seqDic['seqID'] != '':
self.id = seqDic['seqID']
else:
self.id = self.name
if seqDic['description'] != '':
self.description = seqDic['description']
self.sequence = seqDic['sequence']
self.alphabet = emconv.alphabetToIndex(
self.inputSequence == emconv.SEQ_TYPE_AMINOACIDS,
seqDic['alphabet'])
def fileDownloadStep(self, sequenceFile):
# If sequencePath contains more than one sequence, only
# the first one will be considered
seqHandler = emconv.SequenceHandler()
record = seqHandler.downloadSeqFromFile(sequenceFile,
type="fasta")
if self.inputSequenceID.get() is not None:
self.id = self.inputSequenceID.get()
elif record.id != '':
self.id = record.id
else:
self.id = self.name
if record.description != '':
self.description = record.description
self.sequence = str(record.seq)
self.alphabet = emconv.alphabetToIndex(self.inputSequence ==
emconv.SEQ_TYPE_AMINOACIDS, record.seq.alphabet)
def getSequenceOfChainStep(self, chainId):
# sequece is obtained from PDB file
# form has a wizard that creates label with the format
# [model: x, chain: x, xxx residues]
import json
chainIdDict = json.loads(self.inputStructureChain.get())
selectedModel = chainIdDict['model']
selectedChain = chainIdDict['chain']
self.structureHandler = AtomicStructHandler()
if self.pdbId.get() is not None:
# PDB from remote database
pdbID = self.pdbId.get()
tmpFilePath = os.path.join("/tmp", pdbID + ".cif").lower()
if exists(tmpFilePath):
# wizard already downloaded the file
self.structureHandler.read(tmpFilePath)
else:
# wizard has not used and the file has not been downloaded yet
self.structureHandler.readFromPDBDatabase(pdbID, dir="/tmp")
else:
# PDB from file
self.structureHandler.read(self.pdbFile.get())
_sequence = self.structureHandler.getSequenceFromChain(
selectedModel, selectedChain)
self.sequence = str(_sequence)
self.alphabet = emconv.alphabetToIndex(self.inputSequence ==
emconv.SEQ_TYPE_AMINOACIDS,
_sequence.alphabet)
# Assignation of sequence ID: if the user has provided a specific
# ID, this will be adopted by default; otherwise, a sequence ID
# related with the starting structure will be selected.
if self.inputSequenceID.get() is not None:
self.id = self.inputSequenceID.get()
else:
self.id = self.structureHandler.getFullID(
selectedModel, selectedChain)
print("Selected chain: %s from model: %s from structure: %s" %
(selectedChain, selectedModel, self.structureHandler.structure.get_id()))