Package Bio :: Package GenBank :: Module Scanner :: Class EmblScanner
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Class EmblScanner

source code

  object --+    
           |    
InsdcScanner --+
               |
              EmblScanner
Known Subclasses:

For extracting chunks of information in EMBL files

Instance Methods [hide private]
 
parse_footer(self)
returns a tuple containing a list of any misc strings, and the sequence
source code
 
_feed_first_line(self, consumer, line)
Handle the LOCUS/ID line, passing data to the comsumer
source code
 
_feed_first_line_patents(self, consumer, line) source code
 
_feed_first_line_old(self, consumer, line) source code
 
_feed_first_line_new(self, consumer, line) source code
 
_feed_seq_length(self, consumer, text) source code
 
_feed_header_lines(self, consumer, lines)
Handle the header lines (list of strings), passing data to the comsumer
source code
 
_feed_misc_lines(self, consumer, lines)
Handle any lines between features and sequence (list of strings), passing data to the consumer
source code

Inherited from InsdcScanner: __init__, feed, find_start, parse, parse_cds_features, parse_feature, parse_features, parse_header, parse_records, set_handle

Inherited from InsdcScanner (private): _feed_feature_table

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

Class Variables [hide private]
  RECORD_START = 'ID '
  HEADER_WIDTH = 5
  FEATURE_START_MARKERS = ['FH Key Location/Qualif...
  FEATURE_END_MARKERS = ['XX']
  FEATURE_QUALIFIER_INDENT = 21
  FEATURE_QUALIFIER_SPACER = 'FT '
  SEQUENCE_HEADERS = ['SQ', 'CO']
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

parse_footer(self)

source code 
returns a tuple containing a list of any misc strings, and the sequence

Overrides: InsdcScanner.parse_footer

_feed_first_line(self, consumer, line)

source code 
Handle the LOCUS/ID line, passing data to the comsumer

This should be implemented by the EMBL / GenBank specific subclass

Used by the parse_records() and parse() methods.

Overrides: InsdcScanner._feed_first_line
(inherited documentation)

_feed_header_lines(self, consumer, lines)

source code 
Handle the header lines (list of strings), passing data to the comsumer

This should be implemented by the EMBL / GenBank specific subclass

Used by the parse_records() and parse() methods.

Overrides: InsdcScanner._feed_header_lines
(inherited documentation)

_feed_misc_lines(self, consumer, lines)

source code 
Handle any lines between features and sequence (list of strings), passing data to the consumer

This should be implemented by the EMBL / GenBank specific subclass

Used by the parse_records() and parse() methods.

Overrides: InsdcScanner._feed_misc_lines
(inherited documentation)

Class Variable Details [hide private]

FEATURE_START_MARKERS

Value:
['FH   Key             Location/Qualifiers', 'FH']