Package Bio :: Package SwissProt :: Module SProt :: Class _RecordConsumer
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Class _RecordConsumer

source code

ParserSupport.AbstractConsumer --+
                                 |
                                _RecordConsumer

Consumer that converts a SwissProt record to a Record object.

Members: data Record with SwissProt data.

Instance Methods [hide private]
 
__init__(self) source code
 
__repr__(self) source code
 
start_record(self) source code
 
end_record(self) source code
 
identification(self, line) source code
 
accession(self, line) source code
 
date(self, line) source code
 
description(self, line) source code
 
gene_name(self, line) source code
 
organism_species(self, line) source code
 
organelle(self, line) source code
 
organism_classification(self, line) source code
 
taxonomy_id(self, line) source code
 
organism_host(self, line) source code
 
reference_number(self, line) source code
 
reference_position(self, line) source code
 
reference_comment(self, line) source code
 
reference_cross_reference(self, line) source code
 
reference_author(self, line) source code
 
reference_title(self, line) source code
 
reference_location(self, line) source code
 
comment(self, line) source code
 
database_cross_reference(self, line) source code
 
keyword(self, line) source code
 
feature_table(self, line) source code
 
_fix_varsplic_sequences(self, description)
Remove unwanted spaces in sequences.
source code
 
protein_existence(self, line) source code
 
sequence_header(self, line) source code
 
sequence_data(self, line) source code
 
terminator(self, line) source code
 
_clean_record(self, rec) source code
 
_clean_references(self, ref) source code

Inherited from ParserSupport.AbstractConsumer: __getattr__

Method Details [hide private]

_fix_varsplic_sequences(self, description)

source code 

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.