PIc@sdZddlmZddlmZmZddlmZddlmZdefdYZ dZ d Z d Z d Z d Zd ZdZdZdZdefdYZdS(sImplementations of Biopython-like Seq objects on top of BioSQL. This allows retrival of items stored in a BioSQL database using a biopython-like Seq interface. i(tAlphabet(tSeqt UnknownSeq(t SeqRecord(t SeqFeaturetDBSeqcBsbeZdZdZdZdZdZeeddZdZ dZ d Z RS( cCs1||_||_||_||_||_dS(sCreate a new DBSeq object referring to a BioSQL entry. You wouldn't normally create a DBSeq object yourself, this is done for you when retreiving a DBSeqRecord object from the database. N(t primary_idtadaptortalphabett_lengthtstart(tselfRRRR tlength((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/BioSeq.pyt__init__s     cCs|jS(N(R (R ((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/BioSeq.pyt__len__"scCs\t|tr|}|dkrP| |jkr@t|n||j}n||jkrnt|n|jj|j|j||j|dSt|tst dn|jdkrd}n |j}|dkr| |jkrt|n||j}n||jkr.|j}n|j dkrI|j}n |j }|dkr| |jkr}t|n||j}n||jkr|j}n||krt d|j S|jdks|jdkr|j|j|j|j |j|||S|jj|j|j||j|}t |dd|j|j SdS(NiisUnexpected index typet(t isinstancetintR t IndexErrorRtget_subseq_as_stringRR tslicet ValueErrortNonetstopRRtstept __class__(R tindextitjtfull((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/BioSeq.pyt __getitem__%sP            cCs&|jj|j|j|j|jS(sReturns the full sequence as a python string. 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