Package Bio :: Package SeqIO :: Module InsdcIO :: Class GenBankWriter

Class GenBankWriter

      Interfaces.SequenceWriter --+    
                                  |    
Interfaces.SequentialSequenceWriter --+
                                      |
                                     GenBankWriter

Instance Methods

[hide private]

_write_single_line(self, tag, text)
Used in the the 'header' of each GenBank record.

source code

_write_multi_line(self, tag, text)
Used in the the 'header' of each GenBank record.

source code

_write_multi_entries(self, tag, text_list)

source code

_get_date(self, record)

source code

_write_the_first_line(self, record)
Write the LOCUS line.

source code

_get_annotation_str(self, record, key, default='.', just_first=False)
Get an annotation dictionary entry (as a string). source code

_write_comment(self, record)

source code

_write_contig(self, record)

source code

_write_sequence(self, record)

source code

write_record(self, record)
Write a single record to the output file.

source code

_write_feature_qualifier(self, key, value=None, quote=None)

source code

_wrap_location(self, location)
Split a feature location into lines (break at commas).

source code

_write_feature(self, feature)
Write a single SeqFeature object to features table.

source code

Inherited from Interfaces.SequentialSequenceWriter: __init__, write_file, write_footer, write_header, write_records

Inherited from Interfaces.SequenceWriter: clean

Inherited from Interfaces.SequenceWriter (private): _get_seq_string

Class Variables

[hide private]

HEADER_WIDTH = 12

MAX_WIDTH = 80

QUALIFIER_INDENT = 21

Method Details

[hide private]

_get_annotation_str(self, record, key, default=`'.'`, just_first=False)

source code

Get an annotation dictionary entry (as a string).

Some entries are lists, in which case if just_first=True the first entry is returned. If just_first=False (default) this verifies there is only one entry before returning it.

write_record(self, record)

source code

Write a single record to the output file.

Overrides: Interfaces.SequentialSequenceWriter.write_record

Class GenBankWriter

_get_annotation_str(self, record, key, default='.', just_first=False)

write_record(self, record)

_get_annotation_str(self, record, key, default=`'.'`, just_first=False)