ó ÷VźNc@sšddlZddlmZddlmZejdƒrMejdƒZndZdeZd„Zd„Z d „Z d „Z d „Z ed „Z dS( i’’’’N(tGenome(tenvirontCISTEMATIC_ROOTs /proj/genomes%s/C_briggsae/cbriggsae.genedbcCs›g}d}tdd|ƒ}t|dƒ}|jƒ}xQ|dkrŒg}d}|jƒd}|jƒ} xU| dkrĒ| ddkrĒ| jƒ} |t| ƒ7}|j| ƒ|jƒ} qsWtj|dƒ} |dkr'd |GH|jd|f| d t |ƒƒ|j ||d ƒn\d ||f} td t | fdƒ} | j | ƒ| j ƒd| GH|j || dƒ| }q<W|j ƒdS(Nit cbriggsaetdbFiletrtit>i » sAdded contig %s to databaset chromosometdbs%s%s.bins%s%stws Added contig file %s to databasetfile(Rtopentreadlinetstriptlentappendtstringtjoint addSequencetstrtaddChromosomeEntrytcisRoottwritetclose(R t chromPatht chromOutPathtseqArraytseqLentcbGenometinFiletheadertchromIDt currentLinetlineSeqtseqt outFileNametoutFile((sW/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/cbriggsae.pytloadChromosome+s8      "    c Csįtdd|ƒ}t|dƒ}g}g}xu|D]m}|d jdƒ}|ddkrcq4n|dd kryq4n|d jd ƒ}|d} d| f} tj|d d ƒ} d} ytd} WnnXt|d ƒd} t|dƒd}|d}|djƒ}|dkr-d}nd}| || ||d | f|kry|j| || ||d | fƒn| | f|kr4|j| | fƒq4q4Wdt |ƒGH|j |ƒdt |ƒGH|j |ƒdS(NRRRi’’’’s ithybriditCDSit"iRiiit+tFtRsAdding %d gene entriessAdding %d annotations( RR tsplitRRtgiddotstintRRRtaddGeneEntryBatchtaddAnnotationBatch(R tgffFileRtgeneFilet geneEntriestgeneAnnotationstlinetfieldtannottgidtgeneIDt annotationt gidVersiontstarttstoptsensetchrom((sW/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/cbriggsae.pytloadGeneEntriesNsD      !% c CsŃtdd|ƒ}t|dƒ}g}i}idd6dd6dd 6}xf|D]^}|jd ƒ}|d d krzqOn|d jƒ|kr–qOn||d jƒ} |djdƒ} | d } d| f} d } t|dƒd }t|dƒd }|d}|djƒ}|dkr0d}nd}| |krOg|| R?R@((sW/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/cbriggsae.pytloadFeatureEntrieszs@          "$cCs)tdddd|ƒ}|j|ƒdS(NRtversiontCB25R(Rt createGeneDB(R R((sW/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/cbriggsae.pyt createDBFile¤scCs&tdddd|ƒ}|jƒdS(NRRORPR(Rt createIndices(R R((sW/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/cbriggsae.pytcreateDBindices©scCs‚dt}dt}d}d|GHt|ƒdGHt||ƒdGHt||ƒdGHt|||ƒdGHt|ƒd |GHdS( Ns!%s/download/briggsae_25.WS132.gffs%s/download/briggsae_25.fas /C_briggsae/sCreating database %ssAdding gene entriessAdding feature entriessLoading genomic sequencesCreating IndicessFinished creating database %s(RRRRARNR&RT(R tgffPatht chromoPatht chromoOutPath((sW/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/cbriggsae.pytbuildCbriggsaeDB®s       (Rtcistematic.genomesRtosRtgetRtgeneDBR&RARNRRRTRX(((sW/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/cbriggsae.pyts   # , *