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Align.Generic.Alignment --+ | ClustalAlignment
Work with the clustal aligment format (OBSOLETE).
This format is the default output from clustal -- these files normally have an extension of .aln.
This obsolete alignment object is a subclass of the more general alignment object used in Bio.AlignIO. The old practical difference is here str(align) would give the alignment as a string in clustal format, whereas in general you must do align.format("clustal"), which supports other formats too.
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DEFAULT_VERSION =
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Initialize a new Alignment object. Arguments: o alphabet - The alphabet to use for the sequence objects that are created. This alphabet must be a gapped type. e.g. >>> from Bio.Alphabet import IUPAC, Gapped >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-")) >>> align.add_sequence("Alpha", "ACTGCTAGCTAG") >>> align.add_sequence("Beta", "ACT-CTAGCTAG") >>> align.add_sequence("Gamma", "ACTGCTAGATAG") >>> print align Gapped(IUPACUnambiguousDNA(), '-') alignment with 3 rows and 12 columns ACTGCTAGCTAG Alpha ACT-CTAGCTAG Beta ACTGCTAGATAG Gamma
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Print out the alignment so it looks pretty. The output produced from this should also be formatted in valid clustal format.
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