ó ÜÙÐHc@sëdZddlmZd„Zd„ZeƒZd„Zd„Zd„Ze dkrçd GHd d d Z d d d Z ee ƒee ƒks—t ‚dee ƒks¯t ‚dee ƒksÇt ‚dee ƒksßt ‚dGHndS(s3Functions to calculate assorted sequence checksums.iÿÿÿÿ(tcrc32cCs3yt|jƒƒSWntk r.t|ƒSXdS(s@Returns the crc32 checksum for a sequence (string or Seq object)N(t_crc32ttostringtAttributeError(tseq((sˆ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqUtils/CheckSum.pyRs cCs™g}xŒtdƒD]~}|}d}x\tdƒD]N}|d@}|dL}|d@rc|dO}n|dL}|r2|dN}q2q2W|j|ƒqW|S( Niiiilil0l(trangetappend(t_table_htitltpart_htjtrflag((sˆ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqUtils/CheckSum.pyt _init_table_hs    cCsyd}d}x\|D]T}|d@d>}|d?}|d?|B}|t|ƒAd@}|t|A}|}qWd||fS(s@Returns the crc64 checksum for a sequence (string or Seq object)iiÿiis CRC-%08X%08X(tordR(tstcrcltcrchtctshrttemp1httemp1ltidx((sˆ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqUtils/CheckSum.pytcrc64(s   cCsƒd}}t|ƒtdƒkr1|jƒ}nxG|D]?}|d7}||t|jƒƒ7}|dkr8d}q8q8W|dS(sŽReturns the GCG checksum (int) for a sequence (string or Seq object) Given a nucleotide or amino-acid secuence (or any string), returns the GCG checksum (int). Checksum used by GCG program. seq type = str. Based on BioPerl GCG_checksum. Adapted by Sebastian Bassi with the help of John Lenton, Pablo Ziliani, and Gabriel Genellina. All sequences are converted to uppercase itaaii9i'(ttypeRRtupper(Rtindextchecksumtchar((sˆ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqUtils/CheckSum.pytgcg7s    cCsïyddl}|jƒ}Wnddl}|jƒ}nXddl}t|ƒtdƒkrw|jƒjƒ}n |jƒ}|j|ƒy |j |j ƒƒj dƒSWn8ddl }|j |j ƒƒjddƒj dƒSXdS(sXReturns the SEGUID (string) for a sequence (string or Seq object) Given a nucleotide or amino-acid secuence (or any string), returns the SEGUID string (A SEquence Globally Unique IDentifier). seq type = str. For more information about SEGUID, see: http://bioinformatics.anl.gov/seguid/ DOI: 10.1002/pmic.200600032 iÿÿÿÿNRt=s t(thashlibtsha1tshatnewtbase64RRRtupdatet b64encodetdigesttrstriptost encodestringtreplace(RR!tmR#R%R*((sˆ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqUtils/CheckSum.pytseguidIs        t__main__sQuick self testt,QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGKt,APKLMIYEGSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYtYCSSYAGSSTLVFGGGTKLTVLtYCCSYAGSSTWVFGGGTKLTVLsCRC-44CAAD88706CC153tBpBeDdcNUYNsdk46JoJdw7Pd3BItX5XEaayob1nZLOc7eVT9qyczarYtDoneN( t__doc__tbinasciiRRR RRRR.t__name__tstr_light_chain_onetstr_light_chain_twotAssertionError(((sˆ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqUtils/CheckSum.pyts      "