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A set of classes to interact with the multiple alignment command line program clustalw.
Clustalw is the command line version of the graphical Clustalx aligment program.
This requires clustalw available from:
ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/.
functions: o read o parse_file o do_alignment
classes: o ClustalAlignment o MultipleAlignCL
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ClustalAlignment Work with the clustal aligment format. |
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MultipleAlignCL Represent a clustalw multiple alignment command line. |
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Parse the given file into a clustal aligment object. Arguments: o file_name - The name of the file to parse. o alphabet - The type of alphabet to use for the alignment sequences. This should correspond to the type of information contained in the file. Defaults to be unambiguous_dna sequence. There is a deprecated optional argument debug_level which has no effect. Since Biopython 1.46, this has called Bio.AlignIO internally. |
Perform an alignment with the given command line. Arguments: o command_line - A command line object that can give out the command line we will input into clustalw. o alphabet - the alphabet to use in the created alignment. If not specified IUPAC.unambiguous_dna and IUPAC.protein will be used for dna and protein alignment respectively. Returns: o A clustal alignment object corresponding to the created alignment. If the alignment type was not a clustal object, None is returned. |
Escape filenames with spaces (PRIVATE). NOTE - This code is duplicated in Bio.Blast.NCBIStandalone, scope for refactoring! |
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