ó óVêNc@sUyddlmZWnddlmZnXddlZddlZddlZddlmZejdƒrƒejdƒZ ndZ de Z ejdƒr´ejdƒZ ndZ e e_ id d 6d d 6d d6dd6dd6dd6dd6dd6dd6dd6dd6dd 6d!d"6d#d$6d%d&6Z d'd*d(„ƒYZe d)„ZdS(+iÿÿÿÿ(tdbapi2N(tenvirontCISTEMATIC_ROOTs /proj/genomes%s/db/gene_info.dbtCISTEMATIC_TEMPs/tmpt athalianat3702t scerevisiaet4932tceleganst6239t dmelanogastert7227t spurpuratust7668tdreriot7955t xtropicalist8364tggallust9031thsapienst9606t cfamiliarist9615t ecaballust9796tbtaurust9913t mmusculust10090t rnorvegicust10116t mdomesticat13616t geneinfoDBcBsƒeZdZdZgZdZged„Zd„Zd„Z d„Z d„Z d„Z dd „Z d „Zd „Zd „ZRS( sE The geneinfoDB class allows for the querying of NCBI gene data. tcCs ||_|r|jƒndS(s` initialize the geneinfoDB object with a target genome and cache database, if desired. N(t targetGenomestcacheDB(tselfttGenomestcache((sS/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/core/geneinfo.pyt__init__Ns cCs |jdkr|jƒndS(s3 cleanup copy in local cache, if present. R#N(tcachedDBt uncacheDB(R&((sS/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/core/geneinfo.pyt__del__VscCs*dtjƒ|_tjt|jƒdS(s, copy geneinfoDB to a local cache. s%s.dbN(ttempfiletmktempR*tshutiltcopyfiletdbPath(R&((sS/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/core/geneinfo.pyR%]scCsS|jdkrOytj|jƒWntk rBd|jGHnXd|_ndS(s. delete geneinfoDB from local cache. R#scould not delete %sN(R*tostremovetOSError(R&((sS/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/core/geneinfo.pyR+ds  cCs4t}|jdkr!|j}ntj|ddƒS(s+ return a handle to the database. R#ttimeouti<(R1R*tsqlitetconnect(R&tpath((sS/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/core/geneinfo.pyt connectDBqs c Cs¿|jƒ}|jƒ}g}|\}}|jdtƒƒ|jƒ}|jƒ|jƒyJ|\}} } } } t|ƒt| ƒt| ƒt| ƒt| ƒfSWntk rºnX|S(sk returns a list of one or more (symbol, locustag, dbxrefs, chromosome, map_location) for a geneID. smselect symbol, locustag, dbxrefs, chromosome, map_location from gene_info where genome = :gen and gID = :gid (R9tcursortexecutetlocalstfetchonetclosetstrt ValueError( R&tgeneIDtdbR:temptyRestgentgidtentrytsymboltlocustagtdbxrefst chromosomet map_location((sS/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/core/geneinfo.pyt getGeneInfo{s      5 REc CsY|jƒ}|jƒ}i}|jdtƒƒ|jƒ}|jƒ|jƒx|D]ù\}}} } } } |dkrèt| ƒ|kr¡g|t| ƒR?tappend( R&tgenometinfoKeyRBR:tresDicttresultsRERGRHRIRJRK((sS/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/core/geneinfo.pytgetallGeneInfos       GHc Cs‰|jƒ}|jƒ}g}|\}}|jdtƒƒ|jƒ}|jƒ|jƒx%|D]}|jt|dƒƒqdW|S(sG returns a list of one or more gene description for a geneID. sKselect description from gene_description where genome = :gen and gID = :gidi(R9R:R;R<RNR>ROR?( R&RARBR:RSRDREtentriesRF((sS/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/core/geneinfo.pytgetDescription©s       c Cs‰|jƒ}|jƒ}g}|\}}|jdtƒƒ|jƒ}|jƒ|jƒx%|D]}|jt|dƒƒqdW|S(s3 returns a list of synonyms for a geneID. sDselect synonym from gene_synonyms where genome = :gen and gID = :gidi(R9R:R;R<RNR>ROR?( R&RARBR:RSRDRERURF((sS/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/core/geneinfo.pytgeneIDSynonymsºs       cCs |jƒ}|jƒ}g}|jdtƒƒ|jƒ}|rk|jƒ|jƒ|t|dƒfS|jdtƒƒ|jƒ}|r¸|jƒ|jƒ|t|dƒfS|jdtƒƒ|jƒ}|jƒ|jƒ|r|t|dƒfS|S(s9 returns a geneID given a genome and a synonym. sDselect gID from gene_info where genome= :genome and symbol= :synonymisKselect gID from gene_synonyms where genome = :genome and synonym = :synonymsHselect gID from gene_info where genome = :genome and locustag = :synonym(R9R:R;R<R=R>R?(R&RPtsynonymRBR:RSRF((sS/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/core/geneinfo.pyt getGeneIDËs,           (t__name__t __module__t__doc__tstartingGenomeR$R*tFalseR)R,R%R+R9RLRTRVRWRY(((sS/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/core/geneinfo.pyR"Fs      c Csªt|dƒ}tƒ}|jƒ}|jƒ}|jdƒ|jdƒ|jdƒtjƒ}xÇ|D]¿}|jddƒ}|jdƒ}|d|krjyet|d} d | |d |d |d |d |d|df} |j| ƒ|dj ƒ} t | ƒd krId| |d |dj ƒf} |j| ƒnd| |d |d j ƒf} |j| ƒ|djdƒ}xx|D]p}yS|dkré||d j ƒkréd| |d |j ƒf} |j| ƒnWq‘t j k rq‘Xq‘WWq)t j k r%d|GHq)XqjqjW|jdƒ|jdƒ|jdƒ|jdƒ|jdƒ|jdƒ|jdƒ|j ƒ|jƒ|jƒdS(s= populate geneinfo database from NCBI gene information. trs¨create table gene_info(ID INTEGER PRIMARY KEY, genome varchar, gID varchar, symbol varchar, locustag varchar, dbxrefs varchar, chromosome varchar, map_location varchar)sgcreate table gene_description(ID INTEGER PRIMARY KEY, genome varchar, gID varchar, description varchar)s`create table gene_synonyms(ID INTEGER PRIMARY KEY, genome varchar, gID varchar, synonym varchar)t'tprimes is“INSERT into gene_info(ID, genome, gID, symbol, locustag, dbxrefs, chromosome, map_location) values (NULL, '%s', '%s', '%s', '%s', '%s', '%s', '%s')iiiiiiisZINSERT into gene_description(ID, genome, gID, description) values (NULL, '%s', '%s', '%s')sSINSERT into gene_synonyms(ID, genome, gID, synonym) values (NULL, '%s', '%s', '%s')it|t-scould not register %ss)create index genIdx1 on gene_info(genome)s0create index genIdx2 on gene_description(genome)s-create index genIdx3 on gene_synonyms(genome)s&create index gIDIdx1 on gene_info(gID)s-create index gIDIdx2 on gene_description(gID)s*create index gIDIdx3 on gene_synonyms(gID)s-create index synIdx on gene_synonyms(synonym)N(topenR"R9R:R;t speciesMaptkeystreplacetsplittstriptlenR6tOperationalErrortcommitR>(tdatafileR8tinFiletidbRBR:t genomeKeystlinetfieldRPtsqlstmttdescrtsqlstmt2tsqlstmt3tsynonymsRF((sS/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/core/geneinfo.pytbuildgeneinfoDBésT        7 !!  "          ((t pysqlite2RR6tsqlite3R-R/R2RtgettcisRootR1tcisTempttempdirReR"Rx(((sS/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/core/geneinfo.pyts<$    £