Package Bio :: Package GenBank :: Module Scanner :: Class _ImgtScanner
[hide private]
[frames] | no frames]

Class _ImgtScanner

source code

  object --+        
           |        
InsdcScanner --+    
               |    
     EmblScanner --+
                   |
                  _ImgtScanner

For extracting chunks of information in IMGT (EMBL like) files (PRIVATE).

IMGT files are like EMBL files but in order to allow longer feature types
the features should be indented by 25 characters not 21 characters. In
practice the IMGT flat files tend to use either 21 or 25 characters, so we
must cope with both.

This is private to encourage use of Bio.SeqIO rather than Bio.GenBank.

Instance Methods [hide private]
 
parse_features(self, skip=False)
Return list of tuples for the features (if present)
source code

Inherited from EmblScanner: parse_footer

Inherited from InsdcScanner: __init__, feed, find_start, parse, parse_cds_features, parse_feature, 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]
  FEATURE_START_MARKERS = ['FH Key Location/Qualif...

Inherited from EmblScanner: FEATURE_END_MARKERS, FEATURE_QUALIFIER_INDENT, FEATURE_QUALIFIER_SPACER, HEADER_WIDTH, RECORD_START, SEQUENCE_HEADERS

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

parse_features(self, skip=False)

source code 
Return list of tuples for the features (if present)

Each feature is returned as a tuple (key, location, qualifiers)
where key and location are strings (e.g. "CDS" and
"complement(join(490883..490885,1..879))") while qualifiers
is a list of two string tuples (feature qualifier keys and values).

Assumes you have already read to the start of the features table.

Overrides: InsdcScanner.parse_features

Class Variable Details [hide private]

FEATURE_START_MARKERS

Value:
['FH   Key             Location/Qualifiers',
 'FH   Key             Location/Qualifiers (from EMBL)',
 'FH   Key                 Location/Qualifiers',
 'FH']