Package ete2 :: Package coretype :: Module seqgroup :: Class SeqGroup
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Class SeqGroup

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object --+
         |
        SeqGroup


SeqGroup class can be used to store a set of sequences (aligned
or not).

CONSTRUCTOR ARGUMENTS:
======================

  * sequences: Path to the file containing the sequences or,
    alternatively, the text string containing the same information.

  * format (optional): the format in which sequences are encoded. Current
    supported formats are: "fasta", "phylip" (phylip sequencial)
    and "iphylip" (phylip interleaved)

RETURNS:
========
 A SeqGroup object to operate with sequencies.

EXAMPLES:
=========
 msf = ">seq1\nAAAAAAAAAAA\n>seq2\nTTTTTTTTTTTTT\n"
 seqs = SeqGroup(msf, format="fasta")
 print seqs.get_seq("seq1")
 

Instance Methods [hide private]
 
__len__(self) source code
 
__contains__(self, item) source code
 
__str__(self)
str(x)
source code
 
__iter__(self) source code
 
__init__(self, sequences=None, format='fasta')
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
source code
 
write(self, format='fasta', outfile=None)
Returns the text representation of the sequences in the supplied given format (default=FASTA).
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iter_entries(self)
Returns an iterator over all sequences in the collection.
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get_seq(self, name)
Returns the sequence associated to a given entry name.
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get_entries(self)
Returns the list of entries currently stored.
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set_seq(self, name, seq, comments=[])
Updates or creates the sequence of "name"
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__str__(self)
(Informal representation operator)

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str(x)

Overrides: object.__str__
(inherited documentation)

__init__(self, sequences=None, format='fasta')
(Constructor)

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x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__
(inherited documentation)

write(self, format='fasta', outfile=None)

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Returns the text representation of the sequences in the supplied given format (default=FASTA). If "oufile" argument is used, the result is written into the given path.

iter_entries(self)

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Returns an iterator over all sequences in the collection. Each item is a tuple with the sequence name, sequence, and sequence comments