ó ,Č/Ic@sČdZddlZddlZddlmZdd„Zdd„Zdd„Zd„Z d„Z d „Z d „Z d „Z d „Zd d„Zdd„Zdd„Zdd„Zdd„ZdS(s?Miscellaneous functions for dealing with sequences (obsolete?).i˙˙˙˙N(tdefault_managercCsiddl}|jddddtƒ|dkr=d}n d|}tj|j|ƒ}|j|ƒS( s"Translate a sequence (DEPRECATED).i˙˙˙˙Ns1Bio.utils.translate() has been deprecated, and wes6 intend to remove it in a future release of Biopython.s7 Please use the translate method or function in Bio.Seqs' instead, as described in the Tutorial.t translatorstranslator.id.%d(twarningstwarntDeprecationWarningtNoneRtresolvetalphabett translate(tseqtidRtsR((s|/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/utils.pyRs    cCsiddl}|jddddtƒ|dkr=d}n d|}tj|j|ƒ}|j|ƒS( sFTranslate a sequence up to the first in frame stop codon (DEPRECATED).i˙˙˙˙Ns9Bio.utils.translate_to_stop() has been deprecated, and wes6 intend to remove it in a future release of Biopython.s7 Please use the translate method or function in Bio.Seqs' instead, as described in the Tutorial.Rstranslator.id.%d(RRRRRRRttranslate_to_stop(R R RR R((s|/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/utils.pyR s    cCseddl}|jdddtƒ|dkr9d}n d|}tj|j|ƒ}|j|ƒS(s'Back-translate a sequence (DEPRECATED).i˙˙˙˙Ns6Bio.utils.back_translate() has been deprecated, and wes6 intend to remove it in a future release of Biopython.s3 If you use it, please tell us on the mailing list.Rstranslator.id.%d(RRRRRRRtback_translate(R R RR R((s|/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/utils.pyR ,s     cCsJddl}|jddddtƒtj|jdƒ}|j|ƒS(s#Transcribe a sequence (DEPRECATED).i˙˙˙˙Ns2Bio.utils.transcribe() has been deprecated, and wes6 intend to remove it in a future release of Biopython.s0 Please use the transcribe method or function ins/ Bio.Seq instead, as described in the Tutorial.t transcriber(RRRRRRt transcribe(R RR((s|/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/utils.pyR;s  cCsJddl}|jddddtƒtj|jdƒ}|j|ƒS(s(Back-transcribe a sequence (DEPRECATED).i˙˙˙˙Ns7Bio.utils.back_transcribe() has been deprecated, and wes6 intend to remove it in a future release of Biopython.s5 Please use the back_transcribe method or function ins/ Bio.Seq instead, as described in the Tutorial.R(RRRRRRtback_transcribe(R RR((s|/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/utils.pyRFs  cCs^|j}g}x-|jD]"}||kr|j|ƒqqWtjdj|ƒ|jjƒS(s@given a sequence with gap encoding, return the ungapped sequencet(tgap_chartdatatappendtSeqtjoinR(R tgaptletterstc((s|/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/utils.pytungapQs   cCs`i}x|jjD]}d||s"