pwem.protocols.protocol_import.sequence module

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

Bases: ProtImportFiles

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

IMPORT_FROM_FILES = 2

IMPORT_FROM_NUCLEOTIDE_FILES = 2

IMPORT_FROM_NUCLEOTIDE_GENEBANK = 3

IMPORT_FROM_NUCLEOTIDE_PLAIN_TEXT = 0

IMPORT_FROM_NUCLEOTIDE_STRUCTURE = 1

IMPORT_FROM_PLAIN_TEXT = 0

IMPORT_FROM_PROTEIN_GENEBANK = 4

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/GenBank sequence from its respective database

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