pwem.protocols.protocol_import.sequence module

class pwem.protocols.protocol_import.sequence.ProtImportSequence(**args)[source]

Bases: pwem.protocols.protocol_import.base.ProtImportFiles

Protocol to import an aminoacid/nucleotide sequence file to the project

IMPORT_FROM_FILES = 2
IMPORT_FROM_GENEBANK = 3
IMPORT_FROM_NUCLEOTIDE_FILES = 2
IMPORT_FROM_NUCLEOTIDE_PLAIN_TEXT = 0
IMPORT_FROM_NUCLEOTIDE_STRUCTURE = 1
IMPORT_FROM_PLAIN_TEXT = 0
IMPORT_FROM_STRUCTURE = 1
IMPORT_FROM_UNIPROT = 3
IMPORT_STRUCTURE_FROM_FILES = 1
IMPORT_STRUCTURE_FROM_ID = 0
createOutputStep()[source]

Register the output object.

fileDownloadStep(sequenceFile)[source]
getRawSequenceStep(rawSequence)[source]
getSequenceOfChainStep(chainId)[source]
sequenceDatabaseDownloadStep(sequenceDB)[source]

Download UniProt/GeneBank sequence from its respective database

url = 'http://www.uniprot.org/uniprot/'