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

AbstractConsumer --+
                   |
                  _RecordConsumer


Consumer that converts a SwissProt record to a Record object.

Members: data Record with SwissProt data.
Method Summary
  __init__(self)
  _chomp(self, word, to_chomp)
  _clean_record(self, rec)
  _clean_references(self, ref)
  _fix_varsplic_sequences(self, description)
Remove unwanted spaces in sequences.
  accession(self, line)
  comment(self, line)
  database_cross_reference(self, line)
  date(self, line)
  description(self, line)
  end_record(self)
  feature_table(self, line)
  gene_name(self, line)
  identification(self, line)
  keyword(self, line)
  organelle(self, line)
  organism_classification(self, line)
  organism_species(self, line)
  reference_author(self, line)
  reference_comment(self, line)
  reference_cross_reference(self, line)
  reference_location(self, line)
  reference_number(self, line)
  reference_position(self, line)
  reference_title(self, line)
  sequence_data(self, line)
  sequence_header(self, line)
  start_record(self)
  taxonomy_id(self, line)
  terminator(self, line)
    Inherited from AbstractConsumer
  __getattr__(self, attr)
  _unhandled(self, data)
  _unhandled_section(self)

Method Details

_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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