o Rŀg@s6dZddlmZddlmZddlmZGdddeZGdddeZGd d d eZGd d d eZGd ddeZ GdddeZ GdddeZ GdddeZ GdddeZ GdddeZGdddeZGdddeZGdddeZGdd d eZGd!d"d"eZd#d$Zed%kred&Sd&S)'aDefinitions for interacting with BLAST related applications (OBSOLETE). Wrappers for the new NCBI BLAST+ tools (written in C++): - NcbiblastpCommandline - Protein-Protein BLAST - NcbiblastnCommandline - Nucleotide-Nucleotide BLAST - NcbiblastxCommandline - Translated Query-Protein Subject BLAST - NcbitblastnCommandline - Protein Query-Translated Subject BLAST - NcbitblastxCommandline - Translated Query-Protein Subject BLAST - NcbipsiblastCommandline - Position-Specific Initiated BLAST - NcbirpsblastCommandline - Reverse Position Specific BLAST - NcbirpstblastnCommandline - Translated Reverse Position Specific BLAST - NcbideltablastCommandline - Protein-Protein domain enhanced lookup time accelerated blast - NcbiblastformatterCommandline - Convert ASN.1 to other BLAST output formats - NcbimakeblastdbCommandline - Application to create BLAST databases For further details, see: Camacho et al. BLAST+: architecture and applications BMC Bioinformatics 2009, 10:421 https://doi.org/10.1186/1471-2105-10-421 We have decided to remove this module in future, and instead recommend building your command and invoking it via the subprocess module directly. )_Option)_Switch)AbstractCommandlinec@"eZdZdZdddZddZdS)_NcbibaseblastCommandlinezBase Commandline object for (new) NCBI BLAST+ wrappers (PRIVATE). This is provided for subclassing, it deals with shared options common to all the BLAST tools (blastn, rpsblast, rpsblast, etc AND blast_formatter). Nc Ks|dusJtddgdtddgdtddgd td d gd d ddtddgdd ddtddgdtddgdddtddgdddtddgdddtd d!gd"td#d$gd%g }z||j|_Wn tyj||_Ynwtj||fi|dS)&N-hhz5Print USAGE and DESCRIPTION; ignore other arguments.-helphelpKPrint USAGE, DESCRIPTION and ARGUMENTS description; ignore other arguments.-versionversion.Print version number; ignore other arguments.-outoutOutput file for alignment.TFfilenameequatez-outfmtoutfmtzAlignment view. Typically an integer 0-14 but for some formats can be named columns like '6 qseqid sseqid'. Use 5 for XML output (differs from classic BLAST which used 7 for XML).z -show_gisshow_giszShow NCBI GIs in deflines?z-num_descriptionsnum_descriptionszNumber of database sequences to show one-line descriptions for. Integer argument (at least zero). Default is 500. See also num_alignments.rz-num_alignmentsnum_alignmentszNumber of database sequences to show num_alignments for. Integer argument (at least zero). Default is 200. See also num_alignments.z -line_length line_lengthzLine length for formatting alignments (integer, at least 1, default 60). Not applicable for outfmt > 4. Added in BLAST+ 2.2.30.z-htmlhtmlz0Produce HTML output? See also the outfmt option.z-parse_deflinesparse_deflinesz2Should the query and subject defline(s) be parsed?)rr parametersAttributeErrorr__init__selfcmdkwargsextra_parametersr%J/var/www/html/myenv/lib/python3.10/site-packages/Bio/Blast/Applications.pyr0sl  ?  z"_NcbibaseblastCommandline.__init__cCsF|D]}||r ||D]}||rtd|d|dq qdS)zdValidate parameters for incompatibilities (PRIVATE). Used by the _validate method. Options  and  are incompatible.N)_get_parameter ValueErrorr! incompatiblesabr%r%r&_validate_incompatibilitieszs   z5_NcbibaseblastCommandline._validate_incompatibilitiesN)__name__ __module__ __qualname____doc__rr0r%r%r%r&r(s  Jrc@r)_NcbiblastCommandlinezBase Commandline object for (new) NCBI BLAST+ wrappers (PRIVATE). This is provided for subclassing, it deals with shared options common to all the BLAST tools (blastn, rpsblast, rpsblast, etc). NcKs|dusJtddgddddtddgd dd td d gd dd tddgddd tddgddd tddgddd tddgdtddgddddtddgddddtd d!gd"dddtd#d$gd%dddtd&d'gd(dd td)d*gd+dd td,d-gd.dd td/d0gd1dd td2d3gd4dd td5d6gd7dd td8d9gd:dd td;dd?gd@dd tdAdBgdCdd tdDdEgdFdd tdGdHgdIdd tdJdKgdLdd tdMdNgdOdddtdPdQgdRdddtdSdTgdUdd tdVdWgdXg}z||j|_Wn ty||_Ynwtj||fi|dS)YNz-queryqueryzThe sequence to search with.TFrz -query_loc query_locz4Location on the query sequence (Format: start-stop).rz-dbdbzThe database to BLAST against.z-evalueevaluezExpectation value cutoff.z -word_size word_sizez8Word size for wordfinder algorithm. Integer. Minimum 2.z -soft_masking soft_maskingzBApply filtering locations as soft masks (Boolean, Default = true).z-lcase_masking lcase_maskingz:Use lower case filtering in query and subject sequence(s)?z-gilistgilistzRestrict search of database to list of GI's. Incompatible with: negative_gilist, seqidlist, negative_seqidlist, remote, subject, subject_locz-negative_gilistnegative_gilistzRestrict search of database to everything except the listed GIs. Incompatible with: gilist, seqidlist, remote, subject, subject_locz -seqidlist seqidlistzyRestrict search of database to list of SeqID's. Incompatible with: gilist, negative_gilist, remote, subject, subject_locz-negative_seqidlistnegative_seqidlistzRestrict search of database to everything except listed SeqID's. Incompatible with: gilist, seqidlist, remote, subject, subject_locz -entrez_query entrez_queryz>Restrict search with the given Entrez query (requires remote).z-qcov_hsp_perc qcov_hsp_perczJPercent query coverage per hsp (float, 0 to 100). Added in BLAST+ 2.2.30.-max_target_seqsmax_target_seqszDMaximum number of aligned sequences to keep (integer, at least one).z-dbsizedbsizez+Effective length of the database (integer).z -searchspsearchspz/Effective length of the search space (integer).z-max_hsps_per_subjectmax_hsps_per_subjectzNOverride max number of HSPs per subject saved for ungapped searches (integer).z -max_hspsmax_hspszMSet max number of HSPs saved per subject sequence Ddefault 0 means no limit.z-sum_statisticssum_statisticszUse sum statistics.z -sum_stats sum_statsz6Use sum statistics (boolean). Added in BLAST+ 2.2.30.z -xdrop_ungap xdrop_ungapz:X-dropoff value (in bits) for ungapped extensions (float).z -xdrop_gap xdrop_gapzDX-dropoff value (in bits) for preliminary gapped extensions (float).z-xdrop_gap_finalxdrop_gap_finalz=X-dropoff value (in bits) for final gapped alignment (float).z -window_size window_sizezFMultiple hits window size, use 0 to specify 1-hit algorithm (integer).z-import_search_strategyimport_search_strategyzBSearch strategy to use. Incompatible with: export_search_strategyz-export_search_strategyexport_search_strategyzXFile name to record the search strategy used. Incompatible with: import_search_strategyz -num_threads num_threadszoNumber of threads to use in the BLAST search. Integer, at least one. Default is one. Incompatible with: remotez-remoteremotezcExecute search remotely? Incompatible with: gilist, negative_gilist, subject_loc, num_threads, ...)rrrrrrr r%r%r&rs   $  z_NcbiblastCommandline.__init__cCsFgddgdggdd}|||jr|jstdt|dS)N)r>r?rRrQr?)r>r?rS)rSrPr>r@z+Option entrez_query requires remote option.)r0rBrSr+r _validater!r-r%r%r&rT;s  z_NcbiblastCommandline._validater1r2r3r4r5rrTr%r%r%r&r6s   /r6c@r)_Ncbiblast2SeqCommandlineaBase Commandline object for (new) NCBI BLAST+ wrappers (PRIVATE). This is provided for subclassing, it deals with shared options common to all the BLAST tools supporting two-sequence BLAST (blastn, psiblast, etc) but not rpsblast or rpstblastn. Nc Ks|dusJtddgdddtddgdddtd d gd d dd tddgdddtddgdddtddgdddtddgdddg}z||j|_Wn tyU||_Ynwtj||fi|dS)Nz-gapopengapopenzCost to open a gap (integer).Frz -gapextend gapextendzCost to extend a gap (integer).z-subjectsubjectzSubject sequence(s) to search. Incompatible with: db, gilist, seqidlist, negative_gilist, negative_seqidlist, db_soft_mask, db_hard_mask See also subject_loc.Trz -subject_loc subject_loczLocation on the subject sequence (Format: start-stop). Incompatible with: db, gilist, seqidlist, negative_gilist, negative_seqidlist, db_soft_mask, db_hard_mask, remote. See also subject.-culling_limit culling_limitzHit culling limit (integer). If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit. Incompatible with: best_hit_overhang, best_hit_score_edge.-best_hit_overhangbest_hit_overhangzBest Hit algorithm overhang value (float, recommended value: 0.1) Float between 0.0 and 0.5 inclusive. Incompatible with: culling_limit.-best_hit_score_edgebest_hit_score_edgezBest Hit algorithm score edge value (float). Float between 0.0 and 0.5 inclusive. Recommended value: 0.1 Incompatible with: culling_limit.)rrrr6rr r%r%r&rPsT    4  z"_Ncbiblast2SeqCommandline.__init__cCs0gdddggdd}||t|dS)N)r9r>r?r@rSr_ra)r9r>r?r@)r[r]rZr0r6rTrUr%r%r&rTs  z#_Ncbiblast2SeqCommandline._validater1rVr%r%r%r&rWHs  ?rWc@r)_NcbiblastMain2SeqCommandlineaBase Commandline object for (new) NCBI BLAST+ wrappers (PRIVATE). This is provided for subclassing, it deals with shared options common to the main BLAST tools blastp, blastn, blastx, tblastx, tblastn but not psiblast, rpsblast or rpstblastn. NcKsr|dusJtddgdddtddgdddg}z||j|_Wn ty,||_Ynwtj||fi|dS) Nz -db_soft_mask db_soft_maskzFiltering algorithm for soft masking (integer). Filtering algorithm ID to apply to BLAST database as soft masking. Incompatible with: db_hard_mask, subject, subject_locFrz -db_hard_mask db_hard_maskzFiltering algorithm for hard masking (integer). Filtering algorithm ID to apply to BLAST database as hard masking. Incompatible with: db_soft_mask, subject, subject_loc)rrrrWrr r%r%r&rs$   z&_NcbiblastMain2SeqCommandline.__init__cCs*gdgdd}||t|dS)N)rerZr[)rdrZr[)rdrer0rWrTrUr%r%r&rTs  z'_NcbiblastMain2SeqCommandline._validater1rVr%r%r%r&rcs  rcc@eZdZdZdddZdS)NcbiblastpCommandlineayCreate a commandline for the NCBI BLAST+ program blastp (for proteins). With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI replaced the old blastall tool with separate tools for each of the searches. This wrapper therefore replaces BlastallCommandline with option -p blastp. >>> from Bio.Blast.Applications import NcbiblastpCommandline >>> cline = NcbiblastpCommandline(query="rosemary.pro", db="nr", ... evalue=0.001, remote=True, ungapped=True) >>> cline NcbiblastpCommandline(cmd='blastp', query='rosemary.pro', db='nr', evalue=0.001, remote=True, ungapped=True) >>> print(cline) blastp -query rosemary.pro -db nr -evalue 0.001 -remote -ungapped You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial. blastpc Kstddgdddddtdd gd td d gd ddtddgdddddtddgdddtddgdtddgdg|_tj||fi|dS)Initialize the class.-tasktaskzHTask to execute (string, blastp (default), blastp-fast or blastp-short).cS|dvS)N)riz blastp-fastz blastp-shortr%valuer%r%r&z0NcbiblastpCommandline.__init__..Fchecker_functionr-matrixmatrix'Scoring matrix name (default BLOSUM62). -threshold thresholdFMinimum score for words to be added to the BLAST lookup table (float).r-comp_based_statscomp_based_stats"Use composition-based statistics (string, default 2, i.e. True). 0, F or f: no composition-based statistics 2, T or t, D or d : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties Note that tblastn also supports values of 1 and 3.cSrmN0Ft2TtDdr%rnr%r%r&rp-segsegzyFilter query sequence with SEG (string). Format: "yes", "window locut hicut", or "no" to disable Default is "12 2.2 2.5" -ungappedungapped Perform ungapped alignment only? -use_sw_tback use_sw_tback2Compute locally optimal Smith-Waterman alignments?Nrrrrcrr!r"r#r%r%r&rs<   *zNcbiblastpCommandline.__init__N)rir2r3r4r5rr%r%r%r&rhsrhc@"eZdZdZdddZddZdS) NcbiblastnCommandlineaWrapper for the NCBI BLAST+ program blastn (for nucleotides). With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI replaced the old blastall tool with separate tools for each of the searches. This wrapper therefore replaces BlastallCommandline with option -p blastn. For example, to run a search against the "nt" nucleotide database using the FASTA nucleotide file "m_code.fasta" as the query, with an expectation value cut off of 0.001, saving the output to a file in XML format: >>> from Bio.Blast.Applications import NcbiblastnCommandline >>> cline = NcbiblastnCommandline(query="m_cold.fasta", db="nt", strand="plus", ... evalue=0.001, out="m_cold.xml", outfmt=5) >>> cline NcbiblastnCommandline(cmd='blastn', out='m_cold.xml', outfmt=5, query='m_cold.fasta', db='nt', evalue=0.001, strand='plus') >>> print(cline) blastn -out m_cold.xml -outfmt 5 -query m_cold.fasta -db nt -evalue 0.001 -strand plus You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial. blastncKs>tddgdddddtdd gd d dddtd d gdddtddgdddtddgdddtddgdddtddgdddtddgdddtdd gd!ddtd"d#gd$ddtd%d&gd'ddtd(d)gd*d+dddtd,d-gd.d/dddtd0d1gd2td3d4gd5ddtd6d7gd8td9d:gd;ddg|_tj||fi|d.FrrrkrlzTask to execute (string, default 'megablast') Allowed values 'blastn', 'blastn-short', 'dc-megablast', 'megablast' (the default), or 'vecscreen'.cSrm)N)rz blastn-shortz dc-megablast megablast vecscreenr%rnr%r%r&rp0rqz-penaltypenaltyz:Penalty for a nucleotide mismatch (integer, at most zero).rz-rewardrewardz7Reward for a nucleotide match (integer, at least zero).z -use_index use_indexz7Use MegaBLAST database index (Boolean, Default = False)z -index_name index_namezMegaBLAST database index name.z-dustdustzzFilter query sequence with DUST (string). Format: 'yes', 'level window linker', or 'no' to disable. Default = '20 64 1'.z -filtering_db filtering_dbz>> from Bio.Blast.Applications import NcbiblastxCommandline >>> cline = NcbiblastxCommandline(query="m_cold.fasta", db="nr", evalue=0.001) >>> cline NcbiblastxCommandline(cmd='blastx', query='m_cold.fasta', db='nr', evalue=0.001) >>> print(cline) blastx -query m_cold.fasta -db nr -evalue 0.001 You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial. blastxc Kstddgdddddtdd gd d dddtd d gdddtddgdddtddgdddtddgdddtddgdddtddgdddtdd gd!ddtd"d#gd$td%d&gd'g |_tj||fi|d(S))rjrkrlz:Task to execute (string, blastx (default) or blastx-fast).cSrm)N)rz blastx-fastr%rnr%r%r&rprz0NcbiblastxCommandline.__init__..FrrrrrcSrmrr%rnr%r%r&rpr-query_gencode query_gencode>> from Bio.Blast.Applications import NcbitblastnCommandline >>> cline = NcbitblastnCommandline(help=True) >>> cline NcbitblastnCommandline(cmd='tblastn', help=True) >>> print(cline) tblastn -help You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial. tblastncKstddgdddddtdd gd dd td d gddd tddgddd tddgddd tddgddd tddgdddddtddgddd tdd gd!td"d#gd$td%d&gd'd(dd)g |_tj||fi|d*S)+rjrkrlz.Frr -db_gencode db_gencoderrrrrrrrrtrurvrwrxryrzr{aUse composition-based statistics (string, default 2, i.e. True). 0, F or f: no composition-based statistics 1: Composition-based statistics as in NAR 29:2994-3005, 2001 2, T or t, D or d : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties 3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally Note that only tblastn supports values of 1 and 3.cSrm)N 0Ft12TtDd3r%rnr%r%r&rp>rrr{Filter query sequence with SEG (string). Format: "yes", "window locut hicut", or "no" to disable. Default is "12 2.2 2.5"rrrrrr-in_pssmin_pssmz>> from Bio.Blast.Applications import NcbitblastxCommandline >>> cline = NcbitblastxCommandline(help=True) >>> cline NcbitblastxCommandline(cmd='tblastx', help=True) >>> print(cline) tblastx -help You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial. tblastxc Kstddgdddddtdd gd dd td d gd dd tddgddd tddgddd tddgddd tddgddd g|_tj||fi|dS)rjrrrcSrmrr%rnr%r%r&rpurz1NcbitblastxCommandline.__init__..FrrrrrrrrrrrrtrurvrwrxryrrrN)rrrcrrr%r%r&rmsL0zNcbitblastxCommandline.__init__N)rrr%r%r%r&r[rrc@r) NcbipsiblastCommandlineaWrapper for the NCBI BLAST+ program psiblast. With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI replaced the old blastpgp tool with a similar tool psiblast. This wrapper therefore replaces BlastpgpCommandline, the wrapper for blastpgp. >>> from Bio.Blast.Applications import NcbipsiblastCommandline >>> cline = NcbipsiblastCommandline(help=True) >>> cline NcbipsiblastCommandline(cmd='psiblast', help=True) >>> print(cline) psiblast -help You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial. psiblastcKs>tddgdddtddgdddtd d gd d d ddtddgdddtddgdddtddgdtddgdddtddgddddtd d!gd"dddtd#d$gd%td&d'gd(td)d*gd+dddtd,d-gd.ddtd/d0gd1dddtd2d3gd4ddtd5d6gd7ddtd8d9gd:td;dS)?rjrtrurvFrrwrxryrzr{r|cSrmr}r%rnr%r%r&rprz2NcbipsiblastCommandline.__init__..rrrrzFilter query sequence with SEG (string). Format: "yes", "window locut hicut", or "no" to disable. Default is "12 2.2 2.5" -gap_trigger gap_triggerz6Number of bits to trigger gapping (float, default 22).rrr-num_iterationsnum_iterationszcNumber of iterations to perform (integer, at least one). Default is one. Incompatible with: remote -out_pssmout_pssm#File name to store checkpoint file.Tr-out_ascii_pssmout_ascii_pssm)File name to store ASCII version of PSSM.-save_pssm_after_last_roundsave_pssm_after_last_round)Save PSSM after the last database search.-save_each_pssmsave_each_pssmz]Save PSSM after each iteration File name is given in -save_pssm or -save_ascii_pssm options.z-in_msain_msazaFile name of multiple sequence alignment to restart PSI-BLAST. Incompatible with: in_pssm, queryz-msa_master_idxmsa_master_idxzIndex of sequence to use as master in MSA. Index (1-based) of sequence to use as the master in the multiple sequence alignment. If not specified, the first sequence is used.rrzIPSI-BLAST checkpoint file. Incompatible with: in_msa, query, phi_pattern -pseudocount pseudocountzJPseudo-count value used when constructing PSSM. Integer. Default is zero.-inclusion_ethreshinclusion_ethreshzKE-value inclusion threshold for pairwise alignments (float, default 0.002).z-ignore_msa_masterignore_msa_masterzIgnore the master sequence when creating PSSM. Requires: in_msa Incompatible with: msa_master_idx, in_pssm, query, query_loc, phi_patternz -phi_pattern phi_patternzCFile name containing pattern to search. Incompatible with: in_pssmNrrrrWrrr%r%r&rs vz NcbipsiblastCommandline.__init__cCs4dgddggdgdd}||t|dS)NrSrr7)rr7r)rrr7r8r)rrrrrfrUr%r%r&rT.s z!NcbipsiblastCommandline._validateN)rrVr%r%r%r&rs  zrc@r) NcbirpsblastCommandlineaWrapper for the NCBI BLAST+ program rpsblast. With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI replaced the old rpsblast tool with a similar tool of the same name. This wrapper replaces RpsBlastCommandline, the wrapper for the old rpsblast. >>> from Bio.Blast.Applications import NcbirpsblastCommandline >>> cline = NcbirpsblastCommandline(help=True) >>> cline NcbirpsblastCommandline(cmd='rpsblast', help=True) >>> print(cline) rpsblast -help You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial. rpsblastc Kstddgdddtddgdddtd d gd ddtd d gdddtddgdddddtddgdg|_tj||fi|dS)rjrrrFrr\r]zHit culling limit (integer). If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit. Incompatible with: best_hit_overhang, best_hit_score_edge.r^r_zBest Hit algorithm overhang value (recommended value: 0.1). Float between 0.0 and 0.5 inclusive. Incompatible with: culling_limit.r`razBest Hit algorithm score edge value (recommended value: 0.1). Float between 0.0 and 0.5 inclusive. Incompatible with: culling_limit.rzr{Use composition-based statistics. D or d: default (equivalent to 0) 0 or F or f: Simplified Composition-based statistics as in Bioinformatics 15:1000-1011, 1999 1 or T or t: Composition-based statistics as in NAR 29:2994-3005, 2001 Default = 0.cSrmNDd0Ff1Ttr%rnr%r%r&rprz2NcbirpsblastCommandline.__init__..rrrrrNrrrr6rrr%r%r&rQs@ 3z NcbirpsblastCommandline.__init__cCs$dddgi}||t|dS)Nr]r_rarbrUr%r%r&rTs  z!NcbirpsblastCommandline._validateN)rrVr%r%r%r&r?s  ;rc@rg)NcbirpstblastnCommandlineaWrapper for the NCBI BLAST+ program rpstblastn. With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI replaced the old rpsblast tool with a similar tool of the same name, and a separate tool rpstblastn for Translated Reverse Position Specific BLAST. >>> from Bio.Blast.Applications import NcbirpstblastnCommandline >>> cline = NcbirpstblastnCommandline(help=True) >>> cline NcbirpstblastnCommandline(cmd='rpstblastn', help=True) >>> print(cline) rpstblastn -help You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial. rpstblastnc Kstddgdddddtdd gd dd td d gddd tddgdddddtddgdtddgdg|_tj||fi|dS)rjrrrcSrmrr%rnr%r%r&rprz4NcbirpstblastnCommandline.__init__..Frrrrrrrrrrzr{rcSrmrr%rnr%r%r&rprrrrrrrNrrr%r%r&rs: ,z"NcbirpstblastnCommandline.__init__N)rrr%r%r%r&rrrc@r) NcbiblastformatterCommandlinea:Wrapper for the NCBI BLAST+ program blast_formatter. With the release of BLAST 2.2.24+ (i.e. the BLAST suite rewritten in C++ instead of C), the NCBI added the ASN.1 output format option to all the search tools, and extended the blast_formatter to support this as input. The blast_formatter command allows you to convert the ASN.1 output into the other output formats (XML, tabular, plain text, HTML). >>> from Bio.Blast.Applications import NcbiblastformatterCommandline >>> cline = NcbiblastformatterCommandline(archive="example.asn", outfmt=5, out="example.xml") >>> cline NcbiblastformatterCommandline(cmd='blast_formatter', out='example.xml', outfmt=5, archive='example.asn') >>> print(cline) blast_formatter -out example.xml -outfmt 5 -archive example.asn You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial. Note that this wrapper is for the version of blast_formatter from BLAST 2.2.24+ (or later) which is when the NCBI first announced the inclusion this tool. There was actually an early version in BLAST 2.2.23+ (and possibly in older releases) but this did not have the -archive option (instead -rid is a mandatory argument), and is not supported by this wrapper. blast_formattercKsVtddgdddtddgdd dd td d gd ddddg|_tj||fi|dS)rjz-ridridz8BLAST Request ID (RID), not compatible with archive arg.Frz-archivearchivez5Archive file of results, not compatible with rid arg.TrrDrEz,Maximum number of aligned sequences to keep.cSs|dkS)Nr%rnr%r%r&rprz8NcbiblastformatterCommandline.__init__..rrN)rrrrrr%r%r&rs&z&NcbiblastformatterCommandline.__init__cCs"ddgi}||t|dS)Nrr)r0rrTrUr%r%r&rTs  z'NcbiblastformatterCommandline._validateN)rrVr%r%r%r&rs  rc@rg)NcbideltablastCommandlineaCreate a commandline for the NCBI BLAST+ program deltablast (for proteins). This is a wrapper for the deltablast command line command included in the NCBI BLAST+ software (not present in the original BLAST). >>> from Bio.Blast.Applications import NcbideltablastCommandline >>> cline = NcbideltablastCommandline(query="rosemary.pro", db="nr", ... evalue=0.001, remote=True) >>> cline NcbideltablastCommandline(cmd='deltablast', query='rosemary.pro', db='nr', evalue=0.001, remote=True) >>> print(cline) deltablast -query rosemary.pro -db nr -evalue 0.001 -remote You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial. deltablastcKstddgdtddgdddtd d gd d d ddtddgdddtddgdddtddgdtddgdddtddgddddtd d!gd"dddtd#d$gd%td&d'gd(td)d*gd+ddtd,d-gd.ddtd/d0gd1ddtd2d3gd4ddtd5d6gd7g|_tj||fi|d8S)9rjrtrurvrwrxryFrrzr{a#Use composition-based statistics (string, default 2, i.e. True). 0, F or f: no composition-based statistics. 2, T or t, D or d : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties Note that tblastn also supports values of 1 and 3.cSrmr}r%rnr%r%r&rp7rz4NcbideltablastCommandline.__init__..rrrrrrrz0Number of bits to trigger gapping. Default = 22.rrrrrzXNumber of iterations to perform. (integer >=1, Default is 1). Incompatible with: remoterrrTrrrrrrrrrz^Save PSSM after each iteration. File name is given in -save_pssm or -save_ascii_pssm options.rrzDPseudo-count value used when constructing PSSM (integer, default 0).z-domain_inclusion_ethreshdomain_inclusion_ethreshz\E-value inclusion threshold for alignments with conserved domains. (float, Default is 0.05)rrzFPairwise alignment e-value inclusion threshold (float, default 0.002).z-rpsdbrpsdbz;BLAST domain database name (dtring, Default = 'cdd_delta').z-show_domain_hitsshow_domain_hitsz5Show domain hits? Incompatible with: remote, subjectNrrr%r%r&r&s  ]z"NcbideltablastCommandline.__init__N)rrr%r%r%r&rrrc@s*eZdZdZd ddZddZddZd S) NcbimakeblastdbCommandlinea2Wrapper for the NCBI BLAST+ program makeblastdb. This is a wrapper for the NCBI BLAST+ makeblastdb application to create BLAST databases. By default, this creates a blast database with the same name as the input file. The default output location is the same directory as the input. >>> from Bio.Blast.Applications import NcbimakeblastdbCommandline >>> cline = NcbimakeblastdbCommandline(dbtype="prot", ... input_file="NC_005816.faa") >>> cline NcbimakeblastdbCommandline(cmd='makeblastdb', dbtype='prot', input_file='NC_005816.faa') >>> print(cline) makeblastdb -dbtype prot -in NC_005816.faa You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial. makeblastdbcKsvtddgdtddgdtddgd td d gd d ddtddgdddddtddgddd dddtddgdd ddtddgd dd|jd!td"d#gd$dddtd%d&gd'td(d)gd*td+d,gd-d ddtd.d/gd0dddtd1d2gd3dddtd4d5gd6td7d8gd9dddtd:d;gdgd?d ddtd@dAgdBdddCdd!tdDdEgdFd ddg|_tj||fi|dGS)Hrjrrz4Print USAGE and DESCRIPTION; ignore other arguments.r r r r r rrrrTFrz-blastdb_versionblastdb_versionzeVersion of BLAST database to be created. Tip: use BLAST database version 4 on 32 bit CPU. Default = 5cS|dkp|dkS)Nr%xr%r%r&rpz5NcbimakeblastdbCommandline.__init__..)rrsz-dbtypedbtypez.Molecule type of target db ('nucl' or 'prot').cSr)Nnuclprotr%rr%r%r&rpr)r is_requiredrsz-in input_filezInput file/database name.z -input_type input_typezTType of the data specified in input_file. Default = 'fasta'. Added in BLAST 2.2.26.)rrrsz-titletitlezTitle for BLAST database.z -parse_seqids parse_seqidsziOption to parse seqid for FASTA input if set. For all other input types, seqids are parsed automaticallyz -hash_index hash_indexz%Create index of sequence hash values.z -mask_data mask_datazComma-separated list of input files containing masking data as produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker).z-mask_idmask_idzKComma-separated list of strings to uniquely identify the masking algorithm.z -mask_desc mask_desczTComma-separated list of free form strings to describe the masking algorithm details.z-gi_maskgi_maskzCreate GI indexed masking data.z -gi_mask_name gi_mask_namez2Comma-separated list of masking data output files.z -max_file_sz max_file_szz N)rr_input_type_checkerrrrrr%r%r&rs yz#NcbimakeblastdbCommandline.__init__cCs|dvS)N)asn1_binasn1_txtblastdbfastar%)r!commandr%r%r&rsz.NcbimakeblastdbCommandline._input_type_checkercCsdgdgdgd}|D]}||r)||D]}||r(td|d|dqq |jr4|js4td|jr>|js>td |jrH|jsHtd |jrU|jrQ|jsUtd |jr_|js_td t |dS) Nrrr)rrr r'r(r)z,Option mask_id requires mask_data to be set.z,Option mask_desc requires mask_id to be set.z/Option gi_mask requires parse_seqids to be set.z=Option gi_mask_name requires mask_data and gi_mask to be set.z1Option taxid_map requires parse_seqids to be set.) r*r+rrrrrrrrrTr,r%r%r&rTs0       z$NcbimakeblastdbCommandline._validateN)r)r2r3r4r5rrrTr%r%r%r&rs  } rcCsddl}|jdddS)z;Run the Bio.Blast.Applications module's doctests (PRIVATE).rNr)verbose)doctesttestmod)rr%r%r&_test;sr__main__N)r5Bio.Applicationrrrrr6rWrcrhrrrrrrrrrrrr2r%r%r%r&s6   ^CQ-Bd`GSG;t4