|
Clustalw.py
A set of classes to interact with the multiple alignment command
line program Clustalw (which is the command line version of the current
graphical Clustalx aligment program).
This requires Clustalx1.8.1 available from:
ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/.
Older versions may work, but haven't been tested yet.
functions:
o parse_file
o do_alignment
classes:
o ClustalAlignment
o _AlignCreator
o MultipleAlignCL
|
Functions
|
|
do_alignment
parse_file
|
|
|
do_alignment
|
do_alignment ( command_line )
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.
Returns:
o A clustal alignment object corresponding to the created alignment.
If the alignment type was not a clustal object, None is returned.
|
Exceptions
|
|
IOError( "Cannot open sequence file %s" % command_line.sequence_file )
IOError( "Sequence file %s has an invalid format." % command_line.sequence_file )
IOError( "Sequence file %s has only one sequence present." % command_line.sequence_file )
ValueError("Bad command line option in the command: %s" % str( command_line ) )
|
|
|
|
parse_file
|
parse_file ( file_name, alphabet=IUPAC.unambiguous_dna )
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.
|
|
Classes
|
|
|
|
|