Package Bio :: Package Align :: Module FormatConvert :: Class FormatConverter
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Class FormatConverter


Convert between different alignment representation formats.

The basic idea behind the converter is that it takes a given format, converts it into the base Alignment class, and then can return an object in any other supported format with the info from the basal alignment.

Supported formats are: o Clustal format (*.aln) o Fasta format (*.fasta)
Method Summary
  __init__(self, to_convert)
Initialize a converter with a given object.
  to_clustal(self)
Convert the current info into a ClustalAlignment object.
  to_fasta(self)
Convert the current info into a FastaAlignment object.
  _get_base_info(self)
Retrieve all of the basal (ie Generic.Alignment) info.

Method Details

__init__(self, to_convert)
(Constructor)

Initialize a converter with a given object.

Arguments: o to_convert - The class which we are going to be converting.

to_clustal(self)

Convert the current info into a ClustalAlignment object.

to_fasta(self)

Convert the current info into a FastaAlignment object.

_get_base_info(self)

Retrieve all of the basal (ie Generic.Alignment) info.

The idea is that this info is present in all of the classes and this is the information that will be retained in a conversion. Format specific information will be lost.

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