Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / globplot / biopython-1.50 / Bio / Translate.py

diff --git a/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/Translate.py b/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/Translate.py
deleted file mode 100644 (file)
index 05da460..0000000
--- a/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/Translate.py
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@@ -1,133 +0,0 @@
-"""Code to translate DNA or RNA into proteins (OBSOLETE).
-
-Instead of Bio.Translate, for translation you are now encouraged to use the
-Seq object's translate method, or the translate function in the Bio.Seq
-module.  Translate-to-stop functionality is via an optional argument.
-
-Bio.Seq does not offer any back-translation function like the one here. It
-was concluded that a since a simple back-translation giving a Seq or python
-string could only capture some of the possible back translations, there were
-no practical uses for such a method/function.
-
-This module is now considered to be obsolete, and is likely to be deprecated
-in a future release of Biopython, and later removed.
-"""
-from Bio import Alphabet, Seq
-from Bio.Data import CodonTable
-
-class Translator:
-    def __init__(self, table):
-        self.table = table
-        self._encoded = {}
-
-    def __str__(self) :
-        return "Translator object\n" + str(self.table)
-
-    def translate(self, seq, stop_symbol = "*"):
-        #Allow different instances of the same class to be used:
-        assert seq.alphabet.__class__ == \
-               self.table.nucleotide_alphabet.__class__, \
-               "cannot translate from given alphabet (have %s, need %s)" %\
-               (seq.alphabet, self.table.nucleotide_alphabet)
-        s = seq.data
-        letters = []
-        append = letters.append
-        table = self.table
-        get = table.forward_table.get
-        n = len(seq)
-        for i in range(0, n-n%3, 3):
-            append(get(s[i:i+3], stop_symbol))
-
-        # return with the correct alphabet encoding (cache the encoding)
-        try:
-            alphabet = self._encoded[stop_symbol]
-        except KeyError:
-            alphabet = Alphabet.HasStopCodon(table.protein_alphabet,
-                                             stop_symbol)
-            self._encoded[stop_symbol] = alphabet
-
-        return Seq.Seq("".join(letters), alphabet)
-                           
-    def translate_to_stop(self, seq):
-        # This doesn't have a stop encoding
-
-        #Allow different instances of the same class to be used:
-        assert seq.alphabet.__class__ == \
-               self.table.nucleotide_alphabet.__class__, \
-               "cannot translate from given alphabet (have %s, need %s)" %\
-               (seq.alphabet, self.table.nucleotide_alphabet)
-        s = seq.data
-        letters = []
-        append = letters.append
-        table = self.table.forward_table
-        n = len(seq)
-        try:
-            for i in range(0, n-n%3, 3):
-                append(table[s[i:i+3]])
-        except KeyError:
-            # Stop at the first codon failure
-            pass
-        return Seq.Seq("".join(letters), self.table.protein_alphabet)
-
-    def back_translate(self, seq):
-        # includes the stop codon
-        if not isinstance(seq.alphabet, Alphabet.HasStopCodon):
-            return self._back_translate_no_stop(seq)
-        assert seq.alphabet.alphabet == self.table.protein_alphabet, \
-               "cannot back translate from the given alphabet (%s)" % \
-               seq.alphabet.alphabet
-        s = seq.data
-        letter = seq.alphabet.stop_symbol
-        letters = []
-        append = letters.append
-        table = self.table.back_table
-        for c in seq.data:
-            if c == letter:
-                append(table[None])
-            else:
-                append(table[c])
-        return Seq.Seq("".join(letters),
-                       self.table.nucleotide_alphabet)
-
-    def _back_translate_no_stop(self, seq):
-        # does not allow a stop codon
-        assert seq.alphabet == self.table.protein_alphabet, \
-               "cannot back translate from the given alphabet (%s)" % \
-               seq.alphabet
-        s = seq.data
-        letters = []
-        append = letters.append
-        table = self.table.back_table
-        for c in seq.data:
-            append(table[c])
-        return Seq.Seq("".join(letters),
-                       self.table.nucleotide_alphabet)
-
-unambiguous_dna_by_name = {}
-for key, value in CodonTable.unambiguous_dna_by_name.items():
-    unambiguous_dna_by_name[key] = Translator(value)
-unambiguous_dna_by_id = {}
-for key, value in CodonTable.unambiguous_dna_by_id.items():
-    unambiguous_dna_by_id[key] = Translator(value)
-
-unambiguous_rna_by_name = {}
-for key, value in CodonTable.unambiguous_rna_by_name.items():
-    unambiguous_rna_by_name[key] = Translator(value)
-unambiguous_rna_by_id = {}
-for key, value in CodonTable.unambiguous_rna_by_id.items():
-    unambiguous_rna_by_id[key] = Translator(value)
-
-# XXX Ambiguous - can be done the same except for stop codons!
-ambiguous_dna_by_name = {}
-for key, value in CodonTable.ambiguous_dna_by_name.items():
-    ambiguous_dna_by_name[key] = Translator(value)
-ambiguous_dna_by_id = {}
-for key, value in CodonTable.ambiguous_dna_by_id.items():
-    ambiguous_dna_by_id[key] = Translator(value)
-
-ambiguous_rna_by_name = {}
-for key, value in CodonTable.ambiguous_rna_by_name.items():
-    ambiguous_rna_by_name[key] = Translator(value)
-ambiguous_rna_by_id = {}
-for key, value in CodonTable.ambiguous_rna_by_id.items():
-    ambiguous_rna_by_id[key] = Translator(value)