def translate(seq, id = None):
if id is None:
s = "translator"
else:
s = "translator.id.%d" % id
translator = default_manager.resolve(seq.alphabet, s)
return translator.translate(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 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 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 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 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 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 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 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 back_transcribe(seq):
transcriber = default_manager.resolve(seq.alphabet, "transcriber")
return transcriber.back_transcribe(seq)
