ó gbc@s^ddlmZddlmZmZddlmZd„Zd„Zd„Zd„ZdS( i˙˙˙˙(t wordSelector(tallDNAWordIteratort encodeWord(t predicatecCsAt|jdƒs!g|j_n|jjjtj|ƒƒdS(Nt acceptedOligo(thasattrtvaluesRtappendRtpredicateMatchPattern(toptionstopttvaluetparser((s4lib/python2.7/site-packages/obitools/word/options.pyt_acceptedOptionCallbackscCsAt|jdƒs!g|j_n|jjjtj|ƒƒdS(Nt rejectedOligo(RRRRRR(R R R R ((s4lib/python2.7/site-packages/obitools/word/options.pyt_rejectedOptionCallback scCsĆ|jddddddddd d d d ƒ|jd dddddddd dd dƒ|jddddddddd dd dƒ|jddddddddd dddd dƒ|jddddddddd ddd d d!ƒ|jd"d#dd$dd%dd&dgd d d d'ƒ|jd(d)dd$dd*dd&dgd d d d+ƒ|jd,d-dddd.ddd ddd d d/ƒ|jd0d1dddd2ddd ddd d d3ƒdS(4Ns-Ls --oligo-listtactiontstoretdestt oligoListtmetavars ttypetstrthelps-filename containing a list of oligonucleotides-ss --oligo-sizet oligoSizes<###>tints#Size of oligonucleotide to generates-fs --family-sizet familySizes*Size of oligonucleotide family to generates-ds --distancet oligoDisttdefaultis-minimal distance between two oligonucleotidess-gs--gc-maxtgcMaxis7maximum count of G or C nucleotide acceptable in a words-as --acceptedRtacceptedPatternss#pattern of accepted oligonucleotides-rs --rejectedtrejectedPatterns#pattern of rejected oligonucleotides-ps --homopolymert homopolymeres*reject oligo with homopolymer longer than.s-Ps--homopolymer-minthomopolymere_mins6accept only oligo with homopolymer longer or equal to.(t add_option(t optionManager((s4lib/python2.7/site-packages/obitools/word/options.pytaddOligoOptionssf         cCs$|jdk s*|jdk s*tdƒ‚|jdk sEtdƒ‚|jdk s`tdƒ‚|jdk rŻtt|jƒjƒj ƒƒ|_d„t|jƒDƒ}nt |jƒ}g|_ xU|j D]J}t|ƒ|jksütd|ƒ‚|j j tj||jƒƒqŃWg|_xU|jD]J}t|ƒ|jks]td|ƒ‚|jj tj||jƒƒq2W|jrŽ|jj tj|j|jƒƒn|jrŕ|j j tj|jd|jƒƒn|jr|jj tj|j|jƒƒnt||j |jƒS(Ns+option -s or --oligo-size must be specifieds,option -f or --family-size must be specifieds)option -d or --distance must be specifiedcss'|]}t|jƒjƒƒVqdS(N(Rtstriptlower(t.0tx((s4lib/python2.7/site-packages/obitools/word/options.pys [ss"Accept pattern with bad lenth : %ss"Reject pattern with bad lenth : %si(RtNoneRtAssertionErrorRRtlentopentnextR%RRRRRRRRR tpredicateHomoPolymerLargerR!RtpredicateGCUpperBondR(R twordstp((s4lib/python2.7/site-packages/obitools/word/options.pytdnaWordIteratorSs,*$ %# %# % ) %N( t obitools.wordRRRRR RR$R2(((s4lib/python2.7/site-packages/obitools/word/options.pyts    ?