Members:
data Record with SwissProt data.
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Methods
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__init__
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__init__ ( self )
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_chomp
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_chomp (
self,
word,
to_chomp='.,;',
)
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_clean_record
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_clean_record ( self, rec )
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_clean_references
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_clean_references ( self, ref )
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_fix_varsplic_sequences
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_fix_varsplic_sequences ( self, description )
Remove unwanted spaces in sequences.
During line carryover, the sequences in VARSPLIC can get mangled
with unwanted spaces like:
DISSTKLQALPSHGLESIQT -> PCRATGWSPFRRSSPC LPTH
We want to check for this case and correct it as it happens.
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accession
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accession ( self, line )
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comment
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comment ( self, line )
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database_cross_reference
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database_cross_reference ( self, line )
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date
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date ( self, line )
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Exceptions
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SyntaxError, "I don't understand the date line %s" % line
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description
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description ( self, line )
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end_record
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end_record ( self )
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feature_table
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feature_table ( self, line )
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gene_name
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gene_name ( self, line )
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identification
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identification ( self, line )
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Exceptions
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SyntaxError, "Unrecognized data class %s in line\n%s" %( self.data.data_class, line )
SyntaxError, "Unrecognized molecule type %s in line\n%s" %( self.data.molecule_type, line )
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keyword
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keyword ( self, line )
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organelle
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organelle ( self, line )
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organism_classification
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organism_classification ( self, line )
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organism_species
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organism_species ( self, line )
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reference_author
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reference_author ( self, line )
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reference_comment
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reference_comment ( self, line )
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reference_cross_reference
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reference_cross_reference ( self, line )
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Exceptions
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AssertionError( "I don't understand RX line %s" % line )
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reference_location
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reference_location ( self, line )
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reference_number
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reference_number ( self, line )
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reference_position
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reference_position ( self, line )
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reference_title
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reference_title ( self, line )
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sequence_data
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sequence_data ( self, line )
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sequence_header
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sequence_header ( self, line )
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start_record
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start_record ( self )
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taxonomy_id
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taxonomy_id ( self, line )
The OX line is in the format:
OX DESCRIPTION=ID[, ID]...;
If there are too many id's to fit onto a line, then the ID's
continue directly onto the next line, e.g.
OX DESCRIPTION=ID[, ID]...
OX ID[, ID]...;
Currently, the description is always "NCBI_TaxID".
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terminator
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terminator ( self, line )
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