ó
”ƒ½Ic           @   s   d  d l  m Z d  d l  m Z d  d l m Z d  d l  m Z m Z d Z e j e e j ƒ Z	 e j
 j e	 ƒ Z e j ƒ  d k s‹ t ‚ d Z e j e e j ƒ Z	 e j
 j e	 ƒ Z e j ƒ  d k sÐ t ‚ d Z e j e e j ƒ Z e j
 j e ƒ Z	 e	 j ƒ  d k st ‚ e j d	 Z d
 Z e j e e j ƒ Z	 e j e	 ƒ Z e j ƒ  d k sdt ‚ d Z e j e e j ƒ Z	 e j e	 ƒ Z e j ƒ  d k s¦t ‚ d Z e j e e j ƒ Z	 e j e	 ƒ Z e j ƒ  d k sèt ‚ d Z e j e e j ƒ Z	 e j d Z e j e	 ƒ Z e j ƒ  d k s7t ‚ d Z e j e e j ƒ Z	 e j d Z e j e	 ƒ Z e j ƒ  d k s†t ‚ d Z e j e e j ƒ Z	 e j d Z e j e	 ƒ Z e j ƒ  d k sÕt ‚ e j d	 Z d Z d Ge GHe j e e j ƒ Z	 e j e	 ƒ Z e e j e j ƒ s0t ‚ e e ƒ Gd GHe j e	 ƒ Z e e j e j ƒ sit ‚ e j ƒ  GHe e ƒ Gd GHe j ƒ  GHe j d j e	 ƒ Z e e ƒ Gd GHe j ƒ  GHe j d j e	 ƒ Z d Ge j j d ƒ Gd GHe j ƒ  GHe j d j e	 d ƒ Z d Ge j j d ƒ Gd GHe j ƒ  GHe j  e ƒ Z! e! j ƒ  GHe e! ƒ e e ƒ d  k sqt ‚ e e! j e j" ƒ sŒt ‚ e j e! ƒ Z# e# j e j k s³t ‚ e j  e ƒ Z$ e e$ ƒ d  e e ƒ k sät ‚ e j e$ ƒ Z% e j e% j k st ‚ e& e j ƒ Gd! Ge& e% j ƒ GHe j e j' d
 d" ƒ e j ƒ Z e j( d	 Z) d# Ge) j e ƒ Z* e j e* j k sƒt ‚ e j e* j k s›t ‚ d$ GHd% Ge) j e ƒ Z+ e e ƒ e e+ ƒ k sÑt ‚ e j e+ j k sét ‚ d$ GHe) j  e* ƒ Z, e! j j' d
 d" ƒ e, j k s!t ‚ e j d Z e j d& Z d' GHd( Z e j e e j- ƒ Z	 e j. d	 Z e j e	 ƒ Z e j ƒ  GHe j e	 ƒ Z/ e/ j ƒ  GHd) S(*   iÿÿÿÿ(   t   Seq(   t   Alphabet(   t   IUPAC(   t
   Transcribet	   Translatet   ATAt   AUAtF   GAAAATTCATTTTCTTTGGACTTTCTCTGAAATCCGAGTCCTAGGAAAGATGCGTGAGATTCTTCATATTtF   GAAAAUUCAUUUUCUUUGGACUUUCUCUGAAAUCCGAGUCCUAGGAAAGAUGCGUGAGAUUCUUCAUAUUi   t   Tt    t   TCt	   ENSFSLDFLt   GAAi   t   Es   Vertebrate Mitochondrialt   Mt   SGC8t   ENSFSLDFLWNPSPSNDAWDSSYt   TCAAAAAGGTGCATCTAGATGs   Starting withs   ungapped residues translateds#   residues translated, including gapsi   s   SGC1 has a stop codons   Actually, there aret   *s   stops.t   +s   Yep,i   s   ==t   Us   RNA translation ...s   works.s   RNA translation to stop ...t   SGC1s   Forward ambiguoust   RATGATTARAATYTAN(0   t   BioR    R   t   Bio.AlphabetR   R   R   t   st   unambiguous_dnat   dnat   unambiguous_transcribert
   transcribet   rnat   tostringt   AssertionErrort   unambiguous_rnat   back_transcribet   unambiguous_dna_by_idt   transt   translate_to_stopt   proteint   unambiguous_dna_by_namet
   isinstancet   alphabett   IUPACProteint   lent	   translatet   gapped_proteint   HasStopCodont   p2t   datat   countt   back_translatet   back_dnat   IUPACUnambiguousDNAt   double_back_proteint	   back_dna2t   double_back_protein2t   reprt   replacet   unambiguous_rna_by_idt	   rna_transt   protein_from_rnat   gapped_protein_from_rnat   back_rnat   ambiguous_dnat   ambiguous_dna_by_idt   stop_protein(    (    (    s   test_translate.pyt   <module>   sÆ   	""!$