Package Bio :: Package SeqIO :: Module _index :: Class FastqDict
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Class FastqDict

source code

     object --+            
              |            
           dict --+        
                  |        
_IndexedSeqFileDict --+    
                      |    
  SequentialSeqFileDict --+
                          |
                         FastqDict

Indexed dictionary like access to a FASTQ file (any supported variant).

With FASTQ the records all start with a "@" line, but so can quality lines. Note this will cope with line-wrapped FASTQ files.

Instance Methods [hide private]
 
_build(self)
Actually scan the file identifying records and offsets (PRIVATE).
source code
 
get_raw(self, key)
Similar to the get method, but returns the record as a raw string.
source code

Inherited from SequentialSeqFileDict: __getitem__, __init__

Inherited from _IndexedSeqFileDict: __repr__, __setitem__, __str__, clear, copy, fromkeys, get, items, iteritems, pop, popitem, update, values

Inherited from dict: __cmp__, __contains__, __delitem__, __eq__, __ge__, __getattribute__, __gt__, __iter__, __le__, __len__, __lt__, __ne__, __new__, __sizeof__, has_key, iterkeys, itervalues, keys, setdefault, viewitems, viewkeys, viewvalues

Inherited from object: __delattr__, __format__, __reduce__, __reduce_ex__, __setattr__, __subclasshook__

Class Variables [hide private]

Inherited from dict: __hash__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

_build(self)

source code 

Actually scan the file identifying records and offsets (PRIVATE).

Returns an iterator giving tuples of record names and their offsets.

Overrides: _IndexedSeqFileDict._build
(inherited documentation)

get_raw(self, key)

source code 

Similar to the get method, but returns the record as a raw string.

Overrides: _IndexedSeqFileDict.get_raw