xTc @s ddlmZddlmZddlZddlZddlZddlZddlZ ddl Z de fdYZ de fdYZ de fd YZd e fd YZd efd YZdefdYZdefdYZdefdYZdefdYZdefdYZdefdYZdZdZdZdZdZdZd Zd!efd"YZd#efd$YZ d%efd&YZ!d'efd(YZ"d)efd*YZ#d+efd,YZ$d-efd.YZ%d/efd0YZ&d1efd2YZ'd3e'fd4YZ(d5e'fd6YZ)id7d86gd96e!d:ej*d;ej+ed<d=d>e d?d@e dAdBgdC6egdD6idEe6dF6Z,id7d86gd96ed<dGd>e d?d@e dAdHgdC6edgdD6idId6dIe6dF6Z-idJd86ed<dKd>e.d?dLe dAdMgd96ed<dNd>ed?dOe dAdPe dAdQgdC6eddRgdD6idId6dIe6dSdR6dF6Z/id7d86gd96e dAdTgdC6egdD6ie0dU6dVe6dF6Z1id7d86gd96e"e dAdWgdC6egdD6ie2dU6dIe6dF6Z3ed<dXd>e.d?dYe dAdZgZ4ed<d[d>e.d?dYe dAd\gZ5ed<d]d>ed?d^e dAd_gZ6ed<d`d>ed?d^e dAdaed<dbd>ed?d^e dAdcgZ7ed<ddd>ed?d^e dAdegZ8gggidfZ9dgZ:idhd86e4d96e7dC6egdD6idF6Z;idid86e5d96e8dC6egdD6idF6Z<e9d8djdke dAdlgdmeeedngdodpdqdrdsdtdudvdwdxdydzg dFidIe6d{e6e2dz6d|dn6Z=e>e<j?dFid}e6fgZ@e9d8d~dke dAdgdmedngdodzdddddddddddddddddrddddgdFie2dz6d|dn6dd6ZAe>e<j?dFide6fgZBidd86e#didd6gd96gdC6eeedddddddqdddddddddddddddddddddgdD6idIe6d{e6dF6ZCidd86e#dide6gd96e dAde dAdgdC6egdD6idF6ZDidd86e#dide6de6gd96e dAdgdC6eddddddddddddg dD6ide6dF6ZEdS(i(thomology(tbioinformaticsNtServiceExceptioncBseZRS((t__name__t __module__(((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR stNotFoundExceptioncBseZRS((RR(((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRstUnexpectedResponsecBseZRS((RR(((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRst JobExceptioncBseZRS((RR(((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRstJobBeingProcessedcBseZdZRS(cCsdS(NsJob is being processed((tself((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyt__str__s(RRR (((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRst JobPendingcBseZdZRS(cCsdS(NsJob is waiting in the queue((R ((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR $s(RRR (((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR "st JobRunningcBseZdZRS(cCsdS(NsJob is running((R ((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR +s(RRR (((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR )stJobProcessingCompletedcBseZdZRS(cCsdS(NsJob processing completed((R ((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR 2s(RRR (((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR 0st JobFailurecBseZdZRS(cCsdS(Ns Job failed((R ((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR 9s(RRR (((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR7st JobSuccesscBseZdZRS(cCsdS(NsJob finished successfully((R ((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR @s(RRR (((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR>st JobNotFoundcBseZdZRS(cCsdS(Ns Job not found((R ((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR Gs(RRR (((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyREst identifiertjobidtformattprogramtdatabasetsequencet sequencest ValidatorcBs eZdZdZdZRS(sC Raises exception if check fails, else returns data passed cCs||_||_||_dS(N(tcheckt exceptiontmessage(R RRR((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyt__init__\s  cCs)|j|s!|j|jn|SdS(N(RRR(R tdata((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pytprocesscs(RRt__doc__RR(((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRWs tFilterProcessorcBs eZdZdZdZRS(s: Convert data by a simple functional modification cCs ||_dS(N(t conversion(R R!((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRqscCs |j|S(N(R!(R R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRvs(RRRRR(((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR ls tExtractProcessorcBs eZdZdZdZRS(sA Extract data from some text using a regular expression cCs ||_dS(N(tregex(R R#((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRscCs5|jj|}|s(td|n|jdS(NsUnexpected response: %si(R#tsearchRtgroup(R Rtresult((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRs(RRRRR(((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR"{s tGunzipProcessorcBseZdZdZRS(s Unzips data cCsLy%tjdtj|j}Wn tk rG}td|nX|S(NtfileobjsBad compression: error '%s'(tgziptGzipFiletStringIOtreadtIOErrorR(R Rtuncompressed_datate((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRs  (RRRR(((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR'stDictKeyTranslatorcBs eZdZdZdZRS(s& Renames keys in dictionaries cCs ||_dS(N(t translation(R R1((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRscCs>tg|jD]'\}}|jj|||f^qS(N(tdicttitemsR1tget(R Rtnametvalue((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRs(RRRRR(((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR0s tForwardedServiceMethodcBs5eZdZgggidZdZdZRS(sK A function object that simply forwards the call to something else cCs1||_||_||_||_||_dS(N(tfunctiont preprocessorstpostprocessorst argumentstdefaults(R R8R9R:R;R<((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRs    cCs||j|RG(((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR7s t ProxyServicecBs>eZdZdZgggidZdZdZRS(s= Class to interact with potentially remote resources cCs||_||_dS(N(tproxyR5(R RIR5((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRs c Cslt||rtd|ntdt|j|d|d|d|d|dt}t|||dS(NsCannot overwrite existing '%s'R8R9R:R;R<texception_type(thasattrtAttributeErrorR7tgetattrRIRJtsetattr(R R5tproxy_method_nametrequest_constructorstresponse_evaluatorsR;R<tmethod((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pytregisters  cCsNt||std|nt|j|r=tdnt||dS(NsNo such method: %ssCannot unregister class method(RKRLt __class__tdelattr(R R5((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyt unregister s  cCsd|jt|jfS(Ns%s (provided by %s)(R5tstrRI(R ((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR s(RRRRRSRVR (((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRHs   tMemoizedFunctioncBs/eZdZdZdZedZRS(s5 Holds information about a memoized function cCs||_||_||_dS(N(R8t key_generatortmemoizer(R R8RYRZ((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR"s  cOsj|j||}|jj|r7|jjd|S|j||}|jjd|d||SdS(NtkeyR(RYRZtcontainstretrieveR8tinsert(R targsRCR[R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRG)s cOs(|t|j}|r$|dS|S(Ni(ttupletvalues(R_RCtall((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyt simple_key6s(RRRRRGt staticmethodRc(((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRXs  tMemoizercBs eZdZdZdZRS(s/ General caching-related functionality cCs5td|d|d|}t|j|j|dS(NR8RYRZ(RXRNtim_selfR(R RRRYtmemoized_function((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyt attach_methodCs  cCs>t|tstdnt|jj|jj|jdS(Ns#Cannot detach non-memoized function(t isinstanceRXt ValueErrorRNR8RfR(R Rg((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyt detach_methodNs    (RRRRhRk(((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRe>s tMemoryMemoizercBs;eZdZdZdZdZdZdZRS(s# Caches data in the memory cCs i|_dS(N(tcache(R ((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR`scCs||j|z,t|jd|d}|j|Wd|jXdS(NR[tw(tfileR{twritetclose(R R[Rtofile((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR^scCst|jd|jS(NR[(R}R{R,(R R[((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR]scCs"|jd|tj|jkS(NR[(RyRptlistdirRu(R R[((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR\scCsdS(N((R ((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRns( RRRRRyR{R^R]R\Rn(((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRoys     tfetchRORPR#s
(.*)
RcCs|S(N((ts((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pytsRRs Not foundR!cCs tj|S(N(Rtseq_sequence_parse(R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRsRQR;tseqR<cCs |dkS(NsNo entries found. ((R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRscCstjjd|ddS(Ntlinest source_infosEBI Dbfetch HTTP(tiotbxtpdbtinput(R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRs Rt fetchDatacCs t|kS(N(t IDENTIFIER(R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRssIncomplete querycCs?id|dj|tjfd6|td6|dd6S(Ns%s:%sRtqueryRtstyle(tlowerRtFORMAT(R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRs% cCs d|kS(NtfetchDataReturn((R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRss!Badly formed response from servercCs#tjjj|djddS(NRtasciitignore(txmltsaxtsaxutilstunescapetencode(R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRs cCstjjd|ddS(NRRsEBI Dbfetch SOAP(RRR(R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRs RtrawcCs tj|S(N(RR(R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRst compressiontfastacCstjjd|ddS(NRRsRCSB PDB(RRR(R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRs cCs t|kS(N(tJOBID(R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR'ssIncomplete callcCsi|td6S(NR(R(R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR,scCst|kot|kS(N(RR(R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR1scCsi|td6|td6S(NRttype(RR(R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR6s cCs d|kS(NR((R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR>ssInvalid response from servicecCs|dS(NR((R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRCscCs d|kS(Ntstatus((R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRHscCs|dS(NR((R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRLscCs |dkS(NtDONEtERRORt NOT_FOUNDtPENDINGtRUNNING(RRRRR((R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRNscCs:itd6td6td6td6td6|S(NRRRRR(RRRR R (R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRSs      cCs d|kS(NR&((R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyR^scCs|dS(NR&((R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRbscsPi|d6tdfddtddg|d6td6|d 6|d 6S( NRORcs#tgD]}||k^q S(N(Rb(RR[(tcompulsory_arguments(sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRrsRRsIncomplete callRPRQR;R<(RRjt+EBI_GENERIC_SOAP_SUBMIT_RESPONSE_EVALUATORS(ROtparameter_conversionsRtadditional_argumentsR<((RsF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pytEBICustomisedSOAPSubmitParamsfs  cCs8idd6td6t|gd6tgd6i|t6d6S(NtpollRORPRQR;R<(t.EBI_GENERIC_SOAP_RETRIEVE_REQUEST_CONSTRUCTORSt-EBI_GENERIC_SOAP_RETRIEVE_RESPONSE_EVALUATORSRR(tparserR((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pytEBICustomisedSOAPRetrieveParams~s t checkStatusRt runWUBlastRcCs\itg|D]"}|tkr |||f^q d6idd6t|td6gd6S(NtparamsRRtcontent(R2tSEQUENCERW(RR5((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRs 3RtemailRtsorttfiltertmatrixtnumaltscorestexpt echofiltertstatststrandt sensitivitytasynctblastpsgb360@cam.ac.ukttoolxmlt runClustalW2cCsxitg|D]"}|tkr |||f^q d6idd6djg|tD]}t|^qTd6gd6S(NRRRs R(R2t SEQUENCESRzRW(RR5R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRs 3talignttreet iterationtnumitertoutordert alignmentt quicktreetktuptwindowttopdiagstpairgaptscoretgapopentendgapstgapexttgapdistt outputtreetkimurattossgapst clusteringtaln1toutputttoolalntputR1Rt auto_formattcomposition_based_statisticstdb_genetic_codet endpointst entrez_querytexpecttgapcostst genetic_codet hitlist_sizetI_threshtlayoutt lcase_maskt matrix_namet nucl_penaltyt nucl_rewardtother_advancedt perc_identt phi_patternt query_filetquery_believe_deflinet query_fromtquery_tot searchsp_efftservicet thresholdtungapped_alignmentt word_sizeRtridcCs|jjS(N(tstriptupper(R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRscCs&itd6td6td6|S(NtREADYtWAITINGtUNKNOWN(RR R(R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRs   R4t format_typecCstjj|S(N(RtNCBIBlastXMLParsetparse(R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyRst alignmentstalignment_viewt descriptionstentrez_links_new_windowt expect_lowt expect_hightformat_entrez_queryt format_objecttncbi_git results_filet show_overviewtXML(Ftphaser.pipelineRRRt iotbx.pdbR+R)tretxml.sax.saxutilsRRpRBRRRRtobjectRR R R RRRRRRtPROGRAMtDATABASERRRR R"R'R0R7RHRXReRlRotcompiletDOTALLtOCA_HTTP_FETCH_PARAMStDBFETCH_HTTP_FETCH_PARAMSRjtDBFETCH_SOAP_FETCH_PARAMStFalset#RCSB_HTTP_FETCH_UNCOMPRESSED_PARAMStTruet!RCSB_HTTP_FETCH_COMPRESSED_PARAMSt,EBI_GENERIC_SOAP_STATUS_REQUEST_CONSTRUCTORSRRt+EBI_GENERIC_SOAP_STATUS_RESPONSE_EVALUATORSRRRtEBI_GENERIC_SOAP_STATUS_PARAMSt EBI_GENERIC_SOAP_RETRIEVE_PARAMStEBI_WUBLAST_SOAP_SUBMIT_PARAMSR2R3t EBI_WUBLAST_SOAP_RETRIEVE_PARAMSt EBI_CLUSTALW2_SOAP_SUBMIT_PARAMSt"EBI_CLUSTALW2_SOAP_RETRIEVE_PARAMStNCBI_BLAST_HTTP_SUBMIT_PARAMStNCBI_BLAST_HTTP_STATUS_PARAMStNCBI_BLAST_HTTP_RETRIEVE_PARAMS(((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/services.pyts      65!0