Package Bio :: Package Motif :: Package Parsers :: Module MEME :: Class MEMEInstance
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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__, __contains__, __eq__, __getitem__, __hash__, __le__, __len__, __lt__, __ne__, __radd__, __repr__, __str__, back_transcribe, complement, count, endswith, find, lower, lstrip, reverse_complement, rfind, rsplit, rstrip, split, startswith, strip, tomutable, tostring, transcribe, translate, ungap, upper

Inherited from 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]

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
>>> my_seq.alphabet
IUPACProtein()
Overrides: object.__init__
(inherited documentation)