Package Bio :: Package SeqIO :: Module ClustalIO
[hide private]
[frames] | no frames]

Module ClustalIO

source code

Bio.SeqIO support for the "clustal" (aka ClustalW) file format.

You were expected to use this module via the Bio.SeqIO functions. This module has now been replaced by Bio.AlignIO.ClustalIO, and is deprecated.

Classes [hide private]
  ClustalWriter
Write Clustal sequence alignments.
Functions [hide private]
 
ClustalIterator(handle, alphabet=SingleLetterAlphabet())
Reads a Clustalw file returning a SeqRecord object iterator.
source code
Variables [hide private]
  __warningregistry__ = {('Bio.SeqIO.ClustalIO is deprecated. Y...
Function Details [hide private]

ClustalIterator(handle, alphabet=SingleLetterAlphabet())

source code 

Reads a Clustalw file returning a SeqRecord object iterator.

The entire file is loaded at once, but the SeqRecord objects are only created "on request".

For more information on the file format, please see: http://www.bioperl.org/wiki/ClustalW_multiple_alignment_format

You might like to look at Bio.Clustalw which has an interface to the command line tool clustalw, and can also clustal alignment files into Bio.Clustalw.ClustalAlignment objects.

We call this the "clustal" format which is consistent with EMBOSS. Sadly BioPerl calls it the "clustalw" format, so we can't match them both.


Variables Details [hide private]

__warningregistry__

Value:
{('Bio.SeqIO.ClustalIO is deprecated.  You can continue to read and wr\
ite \'clustal\' files with Bio.SeqIO, but this is now handled via Bio.\
AlignIO internally.',
  <type 'exceptions.DeprecationWarning'>,
  17): 1}