Package BioSQL :: Module BioSeq :: Class DBSeq
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Class DBSeq

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 object --+    
          |    
Bio.Seq.Seq --+
              |
             DBSeq

BioSQL equivalent of the Biopython Seq object.
Instance Methods [hide private]
 
__init__(self, primary_id, adaptor, alphabet, start, length)
Create a new DBSeq object referring to a BioSQL entry.
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__len__(self)
Return the length of the sequence.
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__getitem__(self, index)
Return a subsequence or single letter.
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tostring(self)
Return the full sequence as a python string (DEPRECATED).
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__str__(self)
Return the full sequence as a python string.
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toseq(self)
Return the full sequence as a Seq object.
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__add__(self, other)
Add another sequence or string to this sequence.
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__radd__(self, other)
Add another sequence or string to the left.
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Inherited from Bio.Seq.Seq: __contains__, __eq__, __hash__, __le__, __lt__, __ne__, __repr__, back_transcribe, complement, count, count_overlap, endswith, find, lower, lstrip, reverse_complement, rfind, rsplit, rstrip, split, startswith, strip, tomutable, transcribe, translate, ungap, upper

Inherited from Bio.Seq.Seq (private): _get_seq_str_and_check_alphabet

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

Properties [hide private]
  data
Sequence as string (DEPRECATED)

Inherited from object: __class__

Method Details [hide private]

__init__(self, primary_id, adaptor, alphabet, start, length)
(Constructor)

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Create a new DBSeq object referring to a BioSQL entry.

You wouldn't normally create a DBSeq object yourself, this is done for you when retreiving a DBSeqRecord object from the database.

Overrides: object.__init__

__len__(self)
(Length operator)

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Return the length of the sequence.
Overrides: Bio.Seq.Seq.__len__

__getitem__(self, index)
(Indexing operator)

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Return a subsequence or single letter.
Overrides: Bio.Seq.Seq.__getitem__

tostring(self)

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Return the full sequence as a python string (DEPRECATED).

You are now encouraged to use str(my_seq) instead of my_seq.tostring().

Overrides: Bio.Seq.Seq.tostring

__str__(self)
(Informal representation operator)

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Return the full sequence as a python string.
Overrides: object.__str__

__add__(self, other)
(Addition operator)

source code 

Add another sequence or string to this sequence.

The sequence is first converted to a Seq object before the addition. The returned object is a Seq object, not a DBSeq object

Overrides: Bio.Seq.Seq.__add__

__radd__(self, other)
(Right-side addition operator)

source code 

Add another sequence or string to the left.

The sequence is first converted to a Seq object before the addition. The returned object is a Seq object, not a DBSeq object

Overrides: Bio.Seq.Seq.__radd__

Property Details [hide private]

data

Sequence as string (DEPRECATED)
Get Method:
tostring(self) - Return the full sequence as a python string (DEPRECATED).