Ic @sdZddlmZddlZddlmZdefdYZdefdYZd d Z d d Z e d krddl Z ddl Z ee jd Ze eZx2eD]*ZdGejGHdeejedgejD]Zeej^qfGHx9ejD].Zejd GejGdGeejGdGHqWdZxejD]Zx|ejD]qZejekrdGHdGejGHdGejGHdGejGHejd dGHej d dGHej!d dGHnqqWqaWqWndS(sThis module provides code to work with the BLAST XML output following the DTD available on the NCBI FTP ftp://ftp.ncbi.nlm.nih.gov/blast/documents/xml/NCBI_BlastOutput.dtd Classes: BlastParser Parses XML output from BLAST (direct use discouraged). This (now) returns a list of Blast records. Historically it returned a single Blast record. You are expected to use this via the parse function. _XMLParser Generic SAX parser (private). Functions: parse Incremental parser, this is an iterator that returns Blast records. It uses the BlastParser internally. i(tRecordN(tContentHandlert _XMLparsercBs>eZdZddZdZdZdZdZRS(s}Generic SAX Parser Just a very basic SAX parser. 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Save this to put on each blast record object iiiit[it]N(RtsplitR.R;tlenR:(Rtparts((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_BlastOutput_versions (cCs|j|j_dS(sra reference to the article describing the algorithm Save this to put on each blast record object N(RR.R9(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_BlastOutput_referencescCs|j|j_dS(sWthe database(s) searched Save this to put on each blast record object N(RR.R<(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_BlastOutput_dbscCs|j|j_dS(sthe identifier of the query Important in old pre 2.2.14 BLAST, for recent versions is enough N(RR.R7(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_BlastOutput_query_IDscCs|j|j_dS(sthe definition line of the query Important in old pre 2.2.14 BLAST, for recent versions is enough N(RR.R6(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_BlastOutput_query_defscCst|j|j_dS(sthe length of the query Important in old pre 2.2.14 BLAST, for recent versions is enough N(tintRR.R8(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_BlastOutput_query_lenscCs|j|j_dS(s$the identifier of the query N(RR4R7(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Iteration_query_IDscCs|j|j_dS(s)the definition line of the query N(RR4R6(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Iteration_query_defscCst|j|j_dS(s the length of the query N(RTRR4R8(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Iteration_query_lenscCst|j|j_dS(s?hits to the database sequences, one for every sequence N(RTRR4tnum_hits(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_BlastOutput_hits)scCs|j|j_dS(smatrix used (-M) N(RR0RA(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Parameters_matrix4scCs|j|j_dS(s"expect values cutoff (-e) N(RR0RD(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Parameters_expect9s cCst|j|j_dS(s?match score for nucleotide-nucleotide comparaison (-r) N(RTRR0RE(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Parameters_sc_matchJscCst|j|j_dS(sDmismatch penalty for nucleotide-nucleotide comparaison (-r) N(RTRR0RF(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Parameters_sc_mismatchOscCst|j|j_dS(s gap existence cost (-G) N(RTRR0RC(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Parameters_gap_openTscCs%|jjt|jf|j_dS(s gap extension cose (-E) N(R0RCRTR(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Parameters_gap_extendYs cCs|j|j_dS(sfiltering options (-F) N(RR0R2(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Parameters_filter_scCst|jjjtj|jjjtjg|j_|jjd|_|jjd|_ d|j _ dS(Nii( R4t alignmentsRRt Alignmentt descriptionst Descriptiontmultiple_alignmentt_hitt_descrtnum_alignments(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt _start_Hitos  cCs"d|j_d|_d|_dS(N(R1R4RfRgRh(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Hitws  cCs&|j|j_|jd|j_dS(s,identifier of the database sequence t N(RRgthit_idttitle(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt _end_Hit_id}scCs:|j|j_|jj|j7_|jj|j_dS(s1definition line of the database sequence N(RRgthit_defRnRh(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt _end_Hit_defscCs"|j|j_|j|j_dS(s+accession of the database sequence N(RRgt accessionRh(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Hit_accessionscCst|j|j_dS(N(RTRRgtlength(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt _end_Hit_lenscCsn|jjjtj|jjd|_|jjd7_|jj jtj |jj d|_ dS(Nii( 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query_start(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Hsp_query_fromscCst|j|j_dS(sAoffset of query at the end of the alignment (one-offset) N(RTRRxt query_end(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Hsp_query_toscCst|j|j_dS(sJoffset of the database at the start of the alignment (one-offset) N(RTRRxt sbjct_start(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Hsp_hit_fromscCst|j|j_dS(sHoffset of the database at the end of the alignment (one-offset) N(RTRRxt sbjct_end(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Hsp_hit_toscCst|jf|j_dS(s)frame of the query if applicable N(RTRRxtframe(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Hsp_query_framescCs"|jjt|jf7_dS(s5frame of the database sequence if applicable N(RxRRTR(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Hsp_hit_framescCst|j|j_dS(s.number of identities in the alignment N(RTRRxt identities(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Hsp_identityscCst|j|j_dS(sInumber of positive (conservative) substitutions in the alignment N(RTRRxt positives(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Hsp_positivescCst|j|j_dS(s(number of gaps in the alignment N(RTRRxtgaps(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt _end_Hsp_gapsscCst|j|j_dS(s length of the alignment N(RTRRxt align_length(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Hsp_align_lenscCs|j|j_dS(s'alignment string for the query N(RRxR6(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt _end_Hsp_qseqscCs|j|j_dS(s*alignment string for the database N(RRxtsbjct(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt _end_Hsp_hseqscCs|j|j_dS(s@Formatting middle line as normally seen in BLAST report N(RRxtmatch(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Hsp_midlinescCst|j|j_dS(s,number of sequences in the database N(RTRR4tnum_sequences_in_database(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Statistics_db_numscCst|j|j_dS(s*number of letters in the database N(RTRR4R?(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Statistics_db_len scCst|j|j_dS(s!the effective HSP length N(RTRR4teffective_hsp_length(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Statistics_hsp_lenscCst|j|j_dS(s#the effective search space N(R|RR4teffective_search_space(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Statistics_eff_spacescCst|j|j_dS(s$Karlin-Altschul parameter K N(R|RR4t ka_params(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Statistics_kappascCs%t|j|jjf|j_dS(s)Karlin-Altschul parameter Lambda N(R|RR4R(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Statistics_lambdas cCs&|jjt|jf|j_dS(s$Karlin-Altschul parameter H N(R4RR|R(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyt_end_Statistics_entropy#s(7RRRR 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This function is for use when there is one and only one BLAST result in your XML file. Use the Bio.Blast.NCBIXML.parse() function if you expect more than one BLAST record (i.e. if you have more than one query sequence). sNo records found in handles$More than one record found in handleN(tparsetnextt StopIterationR1t ValueError(thandleR titeratortfirsttsecond((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pytread(s       c csddlm}d}d}d}|j|}d}|sLtdnx|rQ|j|swtd|n|j}t|} | j|_| j |_ | j |_ |j |tx/| jr| jd } | jd | _| VqWx)tr ||j|d}}|s2|j dtPn|j|}||jd |dkr|j |tx| jr| jd } | jd | _| VqqWq||jd |d \}}||}|j |tx/| jr| jd } | jd | _| VqW|d}}PqW|dks3tt| jd ksOtqOW|dksdt|dksvtt| jd kstd S( sReturns an iterator a Blast record for each query. handle - file handle to and XML file to parse debug - integer, amount of debug information to print This is a generator function that returns multiple Blast records objects - one for each query sequence given to blast. The file is read incrementally, returning complete records as they are read in. Should cope with new BLAST 2.2.14+ which gives a single XML file for mutliple query records. Should also cope with XML output from older versions BLAST which gave multiple XML files concatenated together (giving a single file which strictly speaking wasn't valid XML).i(texpatii ssi2tbptHSPsg{Gz?s*****tsequenceRtse valueiKs...("Rt Bio.BlastRtxml.saxR txml.sax.handlerRRRRRRtsystostopentargvRtr_listtrR6RMRbtreduceRRvtalRnRttE_VALUE_THRESHt alignmentthspRDRR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.pyts> U  `       +,