--- /dev/null
+# Copyright 2000 by Andrew Dalke.
+# All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Miscellaneous functions for dealing with sequences (obsolete?)."""
+
+import Seq
+import Alphabet
+
+from PropertyManager import default_manager
+
+def translate(seq, id = None):
+ """Translate a sequence (DEPRECATED)."""
+ import warnings
+ warnings.warn("Bio.utils.translate() has been deprecated, and we" \
+ +" intend to remove it in a future release of Biopython."\
+ +" Please use the translate method or function in Bio.Seq"\
+ +" instead, as described in the Tutorial.",
+ DeprecationWarning)
+ if id is None:
+ s = "translator"
+ else:
+ s = "translator.id.%d" % id
+ translator = default_manager.resolve(seq.alphabet, s)
+ return translator.translate(seq)
+
+def translate_to_stop(seq, id = None):
+ """Translate a sequence up to the first in frame stop codon (DEPRECATED)."""
+ import warnings
+ warnings.warn("Bio.utils.translate_to_stop() has been deprecated, and we" \
+ +" intend to remove it in a future release of Biopython."\
+ +" Please use the translate method or function in Bio.Seq"\
+ +" instead, as described in the Tutorial.",
+ DeprecationWarning)
+ if id is None:
+ s = "translator"
+ else:
+ s = "translator.id.%d" % id
+ translator = default_manager.resolve(seq.alphabet, s)
+ return translator.translate_to_stop(seq)
+
+def back_translate(seq, id = None):
+ """Back-translate a sequence (DEPRECATED)."""
+ import warnings
+ warnings.warn("Bio.utils.back_translate() has been deprecated, and we" \
+ +" intend to remove it in a future release of Biopython."\
+ +" If you use it, please tell us on the mailing list.",
+ DeprecationWarning)
+ if id is None:
+ s = "translator"
+ else:
+ s = "translator.id.%d" % id
+ translator = default_manager.resolve(seq.alphabet, s)
+ return translator.back_translate(seq)
+
+
+def transcribe(seq):
+ """Transcribe a sequence (DEPRECATED)."""
+ import warnings
+ warnings.warn("Bio.utils.transcribe() has been deprecated, and we" \
+ +" intend to remove it in a future release of Biopython."\
+ +" Please use the transcribe method or function in"\
+ +" Bio.Seq instead, as described in the Tutorial.",
+ DeprecationWarning)
+ transcriber = default_manager.resolve(seq.alphabet, "transcriber")
+ return transcriber.transcribe(seq)
+
+def back_transcribe(seq):
+ """Back-transcribe a sequence (DEPRECATED)."""
+ import warnings
+ warnings.warn("Bio.utils.back_transcribe() has been deprecated, and we" \
+ +" intend to remove it in a future release of Biopython."\
+ +" Please use the back_transcribe method or function in"\
+ +" Bio.Seq instead, as described in the Tutorial.",
+ DeprecationWarning)
+ transcriber = default_manager.resolve(seq.alphabet, "transcriber")
+ return transcriber.back_transcribe(seq)
+
+def ungap(seq):
+ """given a sequence with gap encoding, return the ungapped sequence"""
+ #TODO - Fix this? It currently assumes the outmost AlphabetEncoder
+ #is for the gap. Consider HasStopCodon(Gapped(Protein())) as a test case.
+ gap = seq.gap_char
+ letters = []
+ for c in seq.data:
+ if c != gap:
+ letters.append(c)
+ return Seq.Seq("".join(letters), seq.alphabet.alphabet)
+
+def verify_alphabet(seq):
+ letters = {}
+ for c in seq.alphabet.letters:
+ letters[c] = 1
+ try:
+ for c in seq.data:
+ letters[c]
+ except KeyError:
+ return 0
+ return 1
+
+def count_monomers(seq):
+ dict = {}
+# bugfix: string.count(s,c) raises an AttributeError. Iddo Friedberg 16 Mar. 04
+# s = buffer(seq.data) # works for strings and array.arrays
+ for c in seq.alphabet.letters:
+ dict[c] = seq.data.count(c)
+ return dict
+
+def percent_monomers(seq):
+ dict2 = {}
+ seq_len = len(seq)
+ dict = count_monomers(seq)
+ for m in dict:
+ dict2[m] = dict[m] * 100. / seq_len
+ return dict2
+
+def sum(seq, table, zero = 0.0):
+ total = zero
+ for c in getattr(seq, "data", seq):
+ total = total + table[c]
+ return total
+
+# For ranged addition
+def sum_2ple(seq, table, zero = (0.0, 0.0)):
+ x, y = zero
+ data = getattr(seq, "data", seq)
+ for c in data:
+ x2, y2 = table[c]
+ x = x + x2
+ y = y + y2
+ return (x, y)
+
+def total_weight(seq, weight_table = None):
+ if weight_table is None:
+ weight_table = default_manager.resolve(seq.alphabet, "weight_table")
+ return sum(seq, weight_table)
+
+def total_weight_range(seq, weight_table = None):
+ if weight_table is None:
+ weight_table = default_manager.resolve(seq.alphabet, "weight_range_table")
+ return sum_2ple(seq, weight_table)
+
+def reduce_sequence(seq, reduction_table,new_alphabet=None):
+ """ given an amino-acid sequence, return it in reduced alphabet form based
+ on the letter-translation table passed. Some "standard" tables are in
+ Alphabet.Reduced.
+ seq: a Seq.Seq type sequence
+ reduction_table: a dictionary whose keys are the "from" alphabet, and values
+ are the "to" alphabet"""
+ if new_alphabet is None:
+ new_alphabet = Alphabet.single_letter_alphabet
+ new_alphabet.letters = ''
+ for letter in reduction_table:
+ new_alphabet.letters += letter
+ new_alphabet.size = len(new_alphabet.letters)
+ new_seq = Seq.Seq('',new_alphabet)
+ for letter in seq:
+ new_seq += reduction_table[letter]
+ return new_seq
+
+
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