Package Bio :: Package SeqIO :: Module InsdcIO :: Class _InsdcWriter
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Class _InsdcWriter

source code

                     object --+        
                              |        
      Interfaces.SequenceWriter --+    
                                  |    
Interfaces.SequentialSequenceWriter --+
                                      |
                                     _InsdcWriter
Known Subclasses:

Base class for GenBank and EMBL writers (PRIVATE).
Instance Methods [hide private]
 
_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, record_length)
Write a single SeqFeature object to features table.
source code
 
_get_annotation_str(self, record, key, default='.', just_first=False)
Get an annotation dictionary entry (as a string).
source code
 
_split_multi_line(self, text, max_len)
Returns a list of strings.
source code
 
_split_contig(self, record, max_len)
Returns a list of strings, splits on commas.
source code

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

Inherited from Interfaces.SequenceWriter: clean

Inherited from Interfaces.SequenceWriter (private): _get_seq_string

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables [hide private]
  MAX_WIDTH = 80
  QUALIFIER_INDENT = 21
  QUALIFIER_INDENT_STR = ' '
  QUALIFIER_INDENT_TMP = ' %s '
  FTQUAL_NO_QUOTE = ('anticodon', 'citation', 'codon_start', 'co...
Properties [hide private]

Inherited from object: __class__

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.

_split_multi_line(self, text, max_len)

source code 

Returns a list of strings.

Any single words which are too long get returned as a whole line (e.g. URLs) without an exception or warning.


Class Variable Details [hide private]

FTQUAL_NO_QUOTE

Value:
('anticodon',
 'citation',
 'codon_start',
 'compare',
 'direction',
 'estimated_length',
 'mod_base',
 'number',
...