Package Bio :: Package Motif :: Package Parsers :: Module MEME :: Class MEMEInstance
[hide private]
[frames] | no frames]

Class MEMEInstance

source code

object --+    
         |    
   Seq.Seq --+
             |
            MEMEInstance

A class describing the instances of a MEME motif, and the data thereof.

Instance Methods [hide private]
 
__init__(self, *args, **kwds)
Create a Seq object.
source code
 
_seqname(self, name) source code
 
_motifname(self, name) source code
 
_start(self, start) source code
 
_pvalue(self, pval) source code
 
_score(self, score) source code
 
_strand(self, strand) source code
 
_length(self, length) source code

Inherited from Seq.Seq: __add__, __getitem__, __len__, __radd__, __repr__, __str__, back_transcribe, complement, count, endswith, find, lstrip, reverse_complement, rfind, rsplit, rstrip, split, startswith, strip, tomutable, tostring, transcribe, translate

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__

Properties [hide private]

Inherited from Seq.Seq: data

Inherited from object: __class__

Method Details [hide private]

__init__(self, *args, **kwds)
(Constructor)

source code 

Create a Seq object.

Arguments:

  • seq - Sequence, required (string)
  • alphabet - Optional argument, an Alphabet object from Bio.Alphabet

You will typically use Bio.SeqIO to read in sequences from files as SeqRecord objects, whose sequence will be exposed as a Seq object via the seq property.

However, will often want to create your own Seq objects directly:

>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import IUPAC
>>> my_seq = Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF",
...              IUPAC.protein)
>>> my_seq
Seq('MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF', IUPACProtein())
>>> print my_seq
MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF
Overrides: object.__init__
(inherited documentation)