ó {™xTc@ sËddlmZddlmZddlmZddlZddlZddlZddlZddl Z dddd„Z defd „ƒYZ ddddd „Z d „Zddd d d„ZdS(iÿÿÿÿ(tdivision(tSorry(t+slots_getstate_setstate_default_initializerNtblastpg{®Gáz„?cC sô|d kst‚|ddkr/|d }n|jƒsNtddƒ‚n|dks`t‚yddlm}Wntk r“td ƒ‚nX|j|d |d |ƒ}|jƒ}|dk rðt |d ƒ}|j |ƒ|j ƒn|S(se Run BLAST against the PDB sequence database on the NCBI's web server. Basically just a frontend to a BioPython module. :param sequence: plaintext amino-acid or nucleotide sequence :param file_name: optional output file name :param blast_type: program to run ("blastp" or "blastn") :param expect: BLAST e-value cutoff :returns: XML string Rtblastniÿÿÿÿt*s6The sequence contains non-alphabetical characters; in sEaddition to A-Z, only an asterisk denoting a stop codon is permitted.i(tNCBIWWWs:You need to have BioPython installed to use this function.tpdbtexpecttw(RRN( tAssertionErrortisalphaRt Bio.BlastRt ImportErrortqblasttreadtNonetopentwritetclose(tsequencet file_namet blast_typeRRtblastt blast_outtf((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/structure.pytget_ncbi_pdb_blast s$         t blast_hitcB s2eZddddddddgZd d„ZRS( thit_numtpdb_idtchain_idtevaluetlengthtidentityt positivestall_idsc C sZ|dkrtj}n|d|j|j|j|j|j|jt |j ƒfIJdS(Ns'%3s %1s %12g %6d %6.2f %6.2f %4d( RtsyststdoutRRRR R!R"tlenR#(tselftout((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/structure.pytshow0s   N(t__name__t __module__t __slots__RR)(((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/structure.pyR,scC sm||gjdƒdks!t‚ddlm}ddl}|dk r[tj|ƒ}n$tj j |ƒsst‚t |ƒ}|j |ƒ}|j ƒ}t|jƒdkr¾tdƒ‚ng} x¢t|jƒD]‘\} } t| jƒ} | jdƒ\} }| jd}|jdks&t‚d|j|j}|dk rX||krXqÔn| jjd ƒ}g}xrt|ƒD]d\}}|d kr}|t|ƒdkr}||d}|jjj|ƒrá|j|ƒqáq}q}Wt|ƒdkr|j| ƒntd | dd | d |d|jd|jd|dd|j|jd|ƒ}| j|ƒqÔW| S(sÜ Parse NCBI BLAST XML output and convert to a list of simple summary objects. Note that this is very specific to searching the PDB, and returns incomplete information (suitable for summarizing in a flat table). iiÿÿÿÿ(tNCBIXMLNisNo matching sequences!t_idt|RRRRRR R!R"R#( tcountRR R R-tiotbx.pdb.fetcht cStringIOtStringIOtostpathtisfileRtparsetnextR&t alignmentsRt enumeratetstrt accessiontsplitthspst align_lengtht identitiesthit_defRtfetchtlooks_like_pdb_idtappendRRR"(Rt blast_filet min_identityRR-tiotbxtblast_intparsedRtresultsti_hitthitt pdb_chain_idRRthspR!thit_def_fieldsR#ti_fieldtfieldtnext_idtsummary((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/structure.pytsummarize_blast_output6sP!     "    cC shtd|ƒ}td|d|ƒ}g}x7|D]/}|jg|jD]}|jƒ^qGƒq1W|S(NRRRF(RRTtextendR#tlower(RRFRRJtidstresultR((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/structure.pytget_all_matching_pdb_idsjs   -tproteins1e-3c C sQ|dk st‚d}tji|d6td6|d6|d6dd6dd 6ƒ}tjj||ƒjƒ}xÞt rLt j d ƒd |}tjj|ƒjƒ} | d kr¶qoqo| d krèd|}tjj|ƒjƒ} | S| dkrt dƒ‚qo| dkrt dƒ‚qo| dkr9t dƒ‚qot d| ƒ‚qoWdS(s" Run WU-BLAST against the PDB sequence database on the EBI's web server. Somewhat more complicated than the NCBI BLAST service, because of two-step process (submission and retrieval). An email address is required to submit a job. :param sequence: plaintext amino-acid or nucleotide sequence :param email: user email address :param file_name: optional output file name :param blast_type: program to run ("blastp" or "blastn") :param sequence_type: currently ignored :param exp: BLAST e-value cutoff :returns: XML string s5http://www.ebi.ac.uk/Tools/services/rest/wublast/run/RtprogramtemailtexpRtdatabaseRZtstypeis:http://www.ebi.ac.uk/Tools/services/rest/wublast/status/%stRUNNINGtFINISHEDs>http://www.ebi.ac.uk/Tools/services/rest/wublast/result/%s/xmltERRORs!The EBI server reported an error.tFAILUREsSearch failed!t NOT_FOUNDs"The EBI server can't find the job!sUnknown status %sN(RR turllibt urlencodeR[tlibtbxtutilsturlopenRtTruettimetsleept RuntimeErrorR( RR\RRt sequence_typeR]turltparamstjob_idtstatusRX((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/structure.pytget_ebi_pdb_wublastss8          (t __future__Rt libtbx.utilsRRgRR2ReRkR4RRRRTRYRs(((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/structure.pyts       3