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Code for calling ClustalW and parsing its output (DEPRECATED).
This module has been superseded by the Bio.AlignIO framework for alignment parsing, and the ClustalW command line wrapper in Bio.Align.Applications for calling the tool. These are both described in the current version of the Biopython Tutorial and Cookbook. This means Bio.Clustalw is now deprecated and likely to be removed in future releases of Biopython.
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 (OBSOLETE). |
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MultipleAlignCL Represent a clustalw multiple alignment command line (OBSOLETE). |
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Parse the given file into a clustal aligment object (OBSOLETE). 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. This function is obsolete, and any new code should call Bio.AlignIO instead. For example using Bio.Clustalw, you might have: >>> from Bio import Clustalw >>> from Bio import Alphabet >>> filename = "Clustalw/protein.aln" >>> alpha = Alphabet.Gapped(Alphabet.generic_protein) >>> align = Clustalw.parse_file(filename, alphabet=alpha) >>> print align.get_alignment_length() 411 >>> clustalw_string = str(align) This becomes: >>> from Bio import AlignIO >>> from Bio import Alphabet >>> filename = "Clustalw/protein.aln" >>> alpha = Alphabet.Gapped(Alphabet.generic_protein) >>> align = AlignIO.read(open(filename), "clustal", alphabet=alpha) >>> print align.get_alignment_length() 411 >>> assert clustalw_string == align.format("clustal") |
Perform an alignment with the given command line (OBSOLETE). 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. This function (and the associated command line object) are now obsolete. Please use the Bio.Align.Applications.ClustalwCommandline wrapper with the Python subprocess module (and Bio.AlignIO for parsing) as described in the tutorial. |
Run the Bio.Clustalw module's doctests (PRIVATE). This will try and locate the unit tests directory, and run the doctests from there in order that the relative paths used in the examples work. |
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