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1 """ 2 For conversion between different formats for representing alignments (DEPRECATED). 3 4 This module is considered obsolete and has been deprecated. Please use 5 Bio.AlignIO instead for reading and writing alignments in different file 6 formats. 7 8 classes: 9 FormatConverter 10 """ 11 12 # biopython 13 from Bio.Fasta.FastaAlign import FastaAlignment 14 from Bio.Clustalw import ClustalAlignment 15 16 import warnings 17 warnings.warn("Bio.Align.FormatConvert is deprecated. Please use Bio.AlignIO " 18 "or the Alignment object's format method instead.", 19 DeprecationWarning) 2022 """Convert between different alignment representation formats. 23 24 The basic idea behind the converter is that it takes a given format, 25 converts it into the base Alignment class, and then can return an object 26 in any other supported format with the info from the basal alignment. 27 28 Supported formats are: 29 o Clustal format (*.aln) 30 o Fasta format (*.fasta) 31 """6633 """Initialize a converter with a given object. 34 35 Arguments: 36 o to_convert - The class which we are going to be converting. 37 """ 38 self.orig_format = to_convert 39 40 self._base_alphabet, self._base_records = self._get_base_info()4143 """Retrieve all of the basal (ie Generic.Alignment) info. 44 45 The idea is that this info is present in all of the classes and 46 this is the information that will be retained in a conversion. 47 Format specific information will be lost. 48 """ 49 return self.orig_format._alphabet, self.orig_format._records5052 """Convert the current info into a FastaAlignment object. 53 """ 54 return_format = FastaAlignment(self._base_alphabet) 55 return_format._records = self._base_records 56 57 return return_format5860 """Convert the current info into a ClustalAlignment object. 61 """ 62 return_format = ClustalAlignment(self._base_alphabet) 63 return_format._records = self._base_records 64 65 return return_format
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