ó lsßIc@s'dZddlmZddlmZddlmZed„Zedkr#dGHddl Z d Z e j j e ƒrx™e j e ƒD]ˆZ e j je ƒdd kr‡He GHd ee ƒGHee j je e ƒƒZx&eeƒD]ZejGeeƒGHqæWejƒq‡q‡Wd GHq#d GHndS(s‡Bio.SeqIO support for the "ig" (IntelliGenetics or MASE) file format. You are expected to use this module via the Bio.SeqIO functions.iÿÿÿÿ(tsingle_letter_alphabet(tSeq(t SeqRecordccs¦x3tr5|jƒ}|sPn|jdƒsPqqWx\|r”|ddkrhtdt|ƒƒ‚ng}x6|jdƒr¦|j|djƒƒ|jƒ}qqW|jƒ}g}xStr|jƒ}|sØPn|ddkrìPn|j|jƒjddƒƒq¼Wdj |ƒ}|j dƒr:|d }nd|krUtd ƒ‚nt t ||ƒd |d |ƒ}d j |ƒ|j d<|Vq9W| s¢t‚dS(sÒIterate over IntelliGenetics records (as SeqRecord objects). handle - input file alphabet - optional alphabet The optional free format file header lines (which start with two semi-colons) are ignored. The free format commentary lines at the start of each record (which start with a semi-colon) are recorded as a single string with embedded new line characters in the SeqRecord's annotations dictionary under the key 'comment'. s;;it;s)Records should start with ';' and not: %sit tt1iÿÿÿÿs5Potential terminator digit one found within sequence.tidtnames tcommentN(tTruetreadlinet startswitht ValueErrortreprtappendtstriptrstriptreplacetjointendswithRRt annotationstAssertionError(thandletalphabettlinet comment_linesttitlet seq_linestseq_strtrecord((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqIO/IgIO.pyt IgIteratorsB      #   t__main__sRunning quick self testNs../../Tests/IntelliGenetics/s.txtt-tDonesCould not find input files(t__doc__t Bio.AlphabetRtBio.SeqRt Bio.SeqRecordRRt__name__tostpathtisdirtlistdirtfilenametsplitexttlentopenRRRRtclose(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqIO/IgIO.pyt s( =