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%si(RRtbitsRYRRRtexpect(RR/Rqty((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pyRY#scCs0td|d|\}}t|t|f|j_t||j_|jddkrtd|d|\}}t|t|f|j_|jjt|kstn|jddkr,td|d	|\}}t|t|f|j_|jjt|ks,tndS(
NsIdentities = (\d+)\/(\d+)s*I could not find the identities in line
%st	PositivesisPositives = (\d+)\/(\d+)s)I could not find the positives in line
%stGapssGaps = (\d+)\/(\d+)s$I could not find the gaps in line
%s(	RRRRZtalign_lengthR5t	positivesR*tgaps(RR/RqR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pyRZ3s"!cCs td|d||j_dS(NsStrand = (\w+) / (\w+)s&I could not find the strand in line
%s(RRR[(RR/((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pyR[IscCsT|jddkr4td|d||j_ntd|d||j_dS(Nt/is!Frame = ([-+][123]) / ([-+][123])s%I could not find the frame in line
%ssFrame = ([-+][123])(R5RRR\(RR/((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pyR\NssQuery(:?) \s*(\d+)\s*(.+) (\d+)cCs|jj|}|dkr1td|n|j\}}}}|jj||j_|jjdkrt||j_nt||j_	|j
d|_t||_
dS(Ns%I could not find the query in line
%si(t	_query_reR3R4R-tgroupsRR_tquery_startRt	query_endRt_query_start_indexRt
_query_len(RR/tmtcolonRRR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pyR_ascCs||jj}t||jkrF|d|jt|}n(t||jkrntd|n|jj||j_dS(NRs)Match is longer than the query in line
%s(RRRRR-Rtmatch(RR/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/NCBIStandalone.pyR`us
sSbjct(:?) \s*(\d+)\s*(.+) (\d+)cCs|jj|}|dkr1td|n|j\}}}}|jsed|j}n|jj||j_|jj	dkrt
||j_	nt
||j_t||jkrtd|n|`
|`dS(Ns%I could not find the sbjct in line
%sRs7QUERY and SBJCT sequence lengths don't match in line
%s(t	_sbjct_reR3R4R-RR)RRRatsbjct_startRt	sbjct_endRR(RR/RRRRR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pyRas 
cCsdS(N((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/NCBIStandalone.pyRXs(RRRURYRZR[R\R2RARR_R`RRaRX(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pyRs								t_DatabaseReportConsumercBsYeZdZdZdZdZdZdZdZdZ	dZ
RS(	cCstj|_dS(N(RtDatabaseReportt_dr(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/NCBIStandalone.pyRgscCsttjd|}|r7|jjj|jdn9|jjrpd|jjd|jf|jjdt|ddddidd6\|j_n\|d dkrt|ddd
didd6dd6d
d6\|j_ntd|t|jj|j_dS(NisT:iRRiisNeighboring words threshold:iitNeighboringtwordss
threshold:sUnrecognised threshold line:
%s(i(i(RRRR-R(RR/((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pyR<s+9c	Cs|d dkr>t|ddddidd6\|j_n\|d dkrt|ddd
didd6dd6d
d6\|j_ntd|t|jj|j_dS(NisA:iRRiisWindow for multiple hits:iitWindowtmultipleshits:is!Unrecognised window size line:
%s(i(i(RRRR-R(RR/((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pyRHs+9cCs>td|d|\}}t|t|f|j_dS(Ns X1: (\d+) \(\s*([0-9,.]+) bits\)s'I could not find the dropoff in line
%s(RRRRR(RR/RYR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pyRSscCs>td|d|\}}t|t|f|j_dS(Ns X2: (\d+) \(\s*([0-9,.]+) bits\)s+I could not find the gap dropoff in line
%s(RRRRR(RR/RYR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pyRYscCs>td|d|\}}t|t|f|j_dS(Ns X3: (\d+) \(\s*([0-9,.]+) bits\)s1I could not find the gap dropoff final in line
%s(RRRRR(RR/RYR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pyR_scCs>td|d|\}}t|t|f|j_dS(Ns S1: (\d+) \(\s*([0-9,.]+) bits\)s+I could not find the gap trigger in line
%s(RRRRR(RR/RYR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pyRescCs>td|d|\}}t|t|f|j_dS(Ns S2: (\d+) \(\s*([0-9,.]+) bits\)s,I could not find the blast cutoff in line
%s(RRRRR(RR/RYR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pyRkscCsdS(N((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/NCBIStandalone.pyRqs(RRR}R~RRRRRRRRRRRRRRRRRRtRRRRRRRR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pyRs8																											RcBsYeZdZdZdZdZdZdZdZdZ	dZ
RS(	cCs
d|_dS(N(R4R(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/NCBIStandalone.pyRscCstddS(Ns+This consumer doesn't handle PSI-BLAST data(R-(RR/((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pyR?scCs tj|_tj|dS(N(RtBlastRRR(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/NCBIStandalone.pyRscCs*tj||jjj|jjdS(N(RR.Rt__dict__tupdateR(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/NCBIStandalone.pyR.s
cCs|j|j_dS(N(RRtdescriptions(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/NCBIStandalone.pyRCscCsTtj||jjr2|jjj|jn|jjrP|j|j_	ndS(N(
RRPRthspsRt
alignmentsRRRtmultiple_alignment(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/NCBIStandalone.pyRPs

cCsKtj|y|jjj|jWntk
rFtdnXdS(Ns Found an HSP before an alignment(RRXRR
RRRR-(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/NCBIStandalone.pyRXs


cCs*tj||jjj|jjdS(N(RRiRR
RR(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/NCBIStandalone.pyRis
cCs*tj||jjj|jjdS(N(RRRR
RR(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/NCBIStandalone.pyRs
(RRRR?RR.RCRPRXRiR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pyRus								RcBsYeZdZdZdZdZdZdZdZdZ	dZ
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RR(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/NCBIStandalone.pyR.s
cCs6tj|_|jjj|jtj|dS(N(RtRoundt_roundRtroundsRRR>(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/NCBIStandalone.pyR>scCstj||j|j_|jr>|jjj|jn|jjj|j	|jjj|j
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ndS(Ni(RRCRRtnumberRtnew_seqstextendtreused_seqsRRRRRG(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/NCBIStandalone.pyRCs
		cCsQtj||jjr2|jjj|jn|jrM|j|j_ndS(N(	RRPRR
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	cCsKtj|y|jjj|jWntk
rFtdnXdS(Ns Found an HSP before an alignment(RRXRR
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cCs*tj||jjj|jjdS(N(RRiRR
RR(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/NCBIStandalone.pyRis
cCs*tj||jjj|jjdS(N(RRRR
RR(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/NCBIStandalone.pyRs
(RRRRR.R>RCRPRXRiR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pyRs					
			tIteratorcBs,eZdZddZdZdZRS(sIterates over a file of multiple BLAST results.

    Methods:
    next   Return the next record from the stream, or None.

    cCsTy|jWn'tk
r4tdt|nXtj||_||_dS(s__init__(self, handle, parser=None)

        Create a new iterator.  handle is a file-like object.  parser
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        s4I expected a file handle or file-like object, got %sN(R%RR-ttypeRRt_uhandlet_parser(RRtparser((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pyRs
cCsg}xt|jj}|s"Pn|rl|jdsX|jddsX|jdrl|jj|Pn|j|q	W|sdSdj|}|jdk	r|jjt	j
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        Return the next Blast record from the file.  If no more records,
        return None.

        R
is6d?d@6}g}|j|d$|g|j|d&|g|j|d(t|g|j|d:t|gx5|jD]'}|j||t||gqkWt||S(As[
Execute and retrieve data from standalone BLASTPALL as handles.
    
    Execute and retrieve data from blastall.  blastcmd is the command
    used to launch the 'blastall' executable.  program is the blast program
    to use, e.g. 'blastp', 'blastn', etc.  database is the path to the database
    to search against.  infile is the path to the file containing
    the sequence to search with.

    The return values are two handles, for standard output and standard error.

    You may pass more parameters to **keywds to change the behavior of
    the search.  Otherwise, optional values will be chosen by blastall.
    The Blast output is by default in XML format. Use the align_view keyword
    for output in a different format.
    
        Scoring
    matrix              Matrix to use.
    gap_open            Gap open penalty.
    gap_extend          Gap extension penalty.
    nuc_match           Nucleotide match reward.  (BLASTN)
    nuc_mismatch        Nucleotide mismatch penalty.  (BLASTN)
    query_genetic_code  Genetic code for Query.
    db_genetic_code     Genetic code for database.  (TBLAST[NX])

        Algorithm
    gapped              Whether to do a gapped alignment. T/F (not for TBLASTX)
    expectation         Expectation value cutoff.
    wordsize            Word size.
    strands             Query strands to search against database.([T]BLAST[NX])
    keep_hits           Number of best hits from a region to keep.
    xdrop               Dropoff value (bits) for gapped alignments.
    hit_extend          Threshold for extending hits.
    region_length       Length of region used to judge hits.
    db_length           Effective database length.
    search_length       Effective length of search space.

        Processing
    filter              Filter query sequence for low complexity (with SEG)?  T/F
    believe_query       Believe the query defline.  T/F
    restrict_gi         Restrict search to these GI's.
    nprocessors         Number of processors to use.
    oldengine           Force use of old engine T/F

        Formatting
    html                Produce HTML output?  T/F
    descriptions        Number of one-line descriptions.
    alignments          Number of alignments.
    align_view          Alignment view.  Integer 0-11,
                        passed as a string or integer.
    show_gi             Show GI's in deflines?  T/F
    seqalign_file       seqalign file to output.
    outfile             Output file for report.  Filename to write to, if
                        ommitted standard output is used (which you can access
                        from the returned handles).
    s-MR~s-Gtgap_opens-Et
gap_extends-rt	nuc_matchs-qtnuc_mismatchs-Qtquery_genetic_codes-Dtdb_genetic_codes-gRns-etexpectations-Wtwordsizes-Ststrandss-Kt	keep_hitss-Xtxdrops-ft
hit_extends-Lt
region_lengths-zt	db_lengths-Yt
search_lengths-ptprograms-dRhs-itinfiles-Ftfilters-Jt
believe_querys-ltrestrict_gis-atnprocessorss-Vt	oldengines-Tthtmls-vRs-bRs-mt
align_views-Itshow_gis-Ot
seqalign_files-otoutfile(t_security_check_parametersRt_escape_filenameRptkeyst
_invoke_blast(	tblastcmdR3RhR4R;tkeywdst	att2paramtparamstattr((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pytblastallsT9

%cKst|i(dd6dd6dd6dd6d	d
6dd6d
d6dd6dd6dd6dd6dd6dd6dd6dd6dd 6d!d"6dd#6d$d%6d&d'6d(d)6d*d+6d,d-6d.d/6d0d16d2d36d4d56d6d76d8d96d:d;6d<d=6d>d?6d@dA6dBdC6dDdE6dFdG6dHdI6dJdK6dLdM6dNdO6}g}|j|d/|g|j|d1t|g|j|d?t|gx5|jD]'}|j||t||gqWt||S(PslExecute and retrieve data from standalone BLASTPGP as handles.
    
    Execute and retrieve data from blastpgp.  blastcmd is the command
    used to launch the 'blastpgp' executable.  database is the path to the
    database to search against.  infile is the path to the file containing
    the sequence to search with.

    The return values are two handles, for standard output and standard error.

    You may pass more parameters to **keywds to change the behavior of
    the search.  Otherwise, optional values will be chosen by blastpgp.
    The Blast output is by default in XML format. Use the align_view keyword
    for output in a different format.

        Scoring
    matrix              Matrix to use.
    gap_open            Gap open penalty.
    gap_extend          Gap extension penalty.
    window_size         Multiple hits window size.
    npasses             Number of passes.
    passes              Hits/passes.  Integer 0-2.

        Algorithm
    gapped              Whether to do a gapped alignment.  T/F
    expectation         Expectation value cutoff.
    wordsize            Word size.
    keep_hits           Number of beset hits from a region to keep.
    xdrop               Dropoff value (bits) for gapped alignments.
    hit_extend          Threshold for extending hits.
    region_length       Length of region used to judge hits.
    db_length           Effective database length.
    search_length       Effective length of search space.
    nbits_gapping       Number of bits to trigger gapping.
    pseudocounts        Pseudocounts constants for multiple passes.
    xdrop_final         X dropoff for final gapped alignment.
    xdrop_extension     Dropoff for blast extensions.
    model_threshold     E-value threshold to include in multipass model.
    required_start      Start of required region in query.
    required_end        End of required region in query.

        Processing
    XXX should document default values
    program             The blast program to use. (PHI-BLAST)
    filter              Filter query sequence  for low complexity (with SEG)?  T/F
    believe_query       Believe the query defline?  T/F
    nprocessors         Number of processors to use.

        Formatting
    html                Produce HTML output?  T/F
    descriptions        Number of one-line descriptions.
    alignments          Number of alignments.
    align_view          Alignment view.  Integer 0-11,
                        passed as a string or integer.
    show_gi             Show GI's in deflines?  T/F
    seqalign_file       seqalign file to output.
    align_outfile       Output file for alignment.
    checkpoint_outfile  Output file for PSI-BLAST checkpointing.
    restart_infile      Input file for PSI-BLAST restart.
    hit_infile          Hit file for PHI-BLAST.
    matrix_outfile      Output file for PSI-BLAST matrix in ASCII.
    align_outfile       Output file for alignment.  Filename to write to, if
                        ommitted standard output is used (which you can access
                        from the returned handles).

    align_infile        Input alignment file for PSI-BLAST restart.
    
    s-MR~s-GR$s-ER%s-ARs-jtnpassess-Ptpassess-gRns-eR*s-WR+s-KR-s-XR.s-fR/s-LR0s-ZR1s-YR2s-Nt
nbits_gappings-ctpseudocountstxdrop_finals-ytxdrop_extensions-htmodel_thresholds-Strequired_starts-Htrequired_ends-pR3s-dRhs-iR4s-FR5s-JR6s-aR8s-TR:s-vRs-bRs-mR;s-IR<s-OR=s-ot
align_outfiles-Ctcheckpoint_outfiles-Rtrestart_infiles-kt
hit_infiles-Qtmatrix_outfiles-Btalign_infile(R?RR@RpRARB(RCRhR4R;RDRERFRG((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pytblastpgpsbE

%cKs[t|idd6dd6dd6dd6d	d
6dd6d
d6dd6dd6dd6dd6dd6dd6dd6dd6dd 6d!d"6d#d$6d%d&6d'd(6d)d*6d+d,6d-d.6d/d06d1d26}g}|j|d|g|j|dt|g|j|d,t|gx5|jD]'}|j||t||gq#Wt||S(3s_Execute and retrieve data from standalone RPS-BLAST as handles.
    
    Execute and retrieve data from standalone RPS-BLAST.  blastcmd is the
    command used to launch the 'rpsblast' executable.  database is the path
    to the database to search against.  infile is the path to the file
    containing the sequence to search with.

    The return values are two handles, for standard output and standard error.

    You may pass more parameters to **keywds to change the behavior of
    the search.  Otherwise, optional values will be chosen by rpsblast.

    Please note that this function will give XML output by default, by
    setting align_view to seven (i.e. command line option -m 7).
    You should use the NCBIXML.parse() function to read the resulting output.
    This is because NCBIStandalone.BlastParser() does not understand the
    plain text output format from rpsblast.

    WARNING - The following text and associated parameter handling has not
    received extensive testing.  Please report any errors we might have made...

        Algorithm/Scoring
    gapped              Whether to do a gapped alignment.  T/F
    multihit            0 for multiple hit (default), 1 for single hit
    expectation         Expectation value cutoff.
    range_restriction   Range restriction on query sequence (Format: start,stop) blastp only
                        0 in 'start' refers to the beginning of the sequence
                        0 in 'stop' refers to the end of the sequence
                        Default = 0,0
    xdrop               Dropoff value (bits) for gapped alignments.
    xdrop_final         X dropoff for final gapped alignment (in bits).
    xdrop_extension     Dropoff for blast extensions (in bits).
    search_length       Effective length of search space.
    nbits_gapping       Number of bits to trigger gapping.
    protein             Query sequence is protein.  T/F
    db_length           Effective database length.

        Processing
    filter              Filter query sequence for low complexity?  T/F
    case_filter         Use lower case filtering of FASTA sequence T/F, default F
    believe_query       Believe the query defline.  T/F
    nprocessors         Number of processors to use.
    logfile             Name of log file to use, default rpsblast.log

        Formatting
    html                Produce HTML output?  T/F
    descriptions        Number of one-line descriptions.
    alignments          Number of alignments.
    align_view          Alignment view.  Integer 0-11,
                        passed as a string or integer.
    show_gi             Show GI's in deflines?  T/F
    seqalign_file       seqalign file to output.
    align_outfile       Output file for alignment.  Filename to write to, if
                        ommitted standard output is used (which you can access
                        from the returned handles).
    s-Ptmultihits-gRns-eR*s-Ltrange_restrictions-XR.s-ZRMs-yRNs-YR2s-NRKs-ptproteins-zR1s-dRhs-iR4s-FR5s-Utcase_filters-JR6s-aR8s-ltlogfiles-TR:s-vRs-bRs-mR;s-IR<s-OR=s-oRR(R?RR@RpRARB(RCRhR4R;RDRERFRG((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pytrpsblastsD:

%cCs1tj||}|s't|n|jS(N(R2R3R-R(tregexR/t	error_msgR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pyRmscCs|j}|dk	rLt||krLtd|t||fnxH|jD]:}||||krYtd||||fqYqYWg}x|D]}|j||qWt|S(Ns)I expected %d columns (got %d) in line
%ss'I expected '%s' in column %d in line
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cCs>d|kr|S|jdr2|jdr2|Sd|SdS(s'Escape filenames with spaces (PRIVATE).Rt"s"%s"N(R'R(tfilename((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pyR@s
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sStart BLAST and returns handles for stdout and stderr (PRIVATE).

    Tries to deal with spaces in the BLAST executable path.
    s%BLAST executable does not exist at %sRiNtstdintstdouttstderrtshelltwin32(tostpathtexistsR-RR@t
subprocesstsystPopentPIPEtplatformRmtcloseRnRotImportErrortpopen3(	t	blast_cmdRFt
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blast_processtwrite_handlet
result_handleterror_handle((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIStandalone.pyRBs 			


cCslxe|jD]W\}}t|}x<dddddgD]%}||kr;td|q;q;Wq
WdS(s8Look for any attempt to insert a command into a parameter.

    e.g. blastall(..., matrix='IDENTITY -F 0; rm -rf /etc/passwd')

    Looks for ";" or "&&" in the strings (Unix and Windows syntax
    for appending a command line), or ">", "<" or "|" (redirection)
    and if any are found raises an exception.
    t;s&&R<t#sZ
-O~+327le