Package org.veupathdb.lib.blast.common.fields
See: Description
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Class Summary Class Description AutoCPUCores -num_threads <Integer, >=0>Number of threads to use in RPS BLAST search:0 (auto = num of databases)
1 (disable)
1BestHitOverhang -best_hit_overhang <Real, (>0 and <0.5)>Best Hit algorithm overhang value (recommended value: 0.BestHitScoreEdge -best_hit_score_edge <Real, (>0 and <0.5)>Best Hit algorithm score edge value (recommended value: 0.CullingLimit -culling_limit <Integer, >=0>If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hitDBFile -db <String>BLAST database nameDBGenCode -db_gencode <Integer>Permissible values between:1..6
9..16
21..31
33
1DBHardMask -db_hard_mask <String>Filtering algorithm ID to apply to the BLAST database as hard maskingDBSize -dbsize <Int8>Effective length of the databaseDBSoftMask -db_soft_mask <String>Filtering algorithm ID to apply to the BLAST database as soft maskingEntrezQuery -entrez_query <String>Restrict search with the given Entrez queryExpectValue -evalue <Real>Expectation value (E) threshold for saving hitsDefault =10GIList -gilist <String>Restrict search of database to list of GIsGapExtend -gapextend <Integer>Cost to extend a gapGapOpen -gapopen <Integer>Cost to open a gapGapTrigger -gap_trigger <Real>Number of bits to trigger gappingDefault =22HTML -htmlProduce HTML output HelpLong -helpPrint USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters. HelpShort -hPrint USAGE and DESCRIPTION; ignore all other parameters. IPGList -ipglist <String>Restrict search of database to list of IPGsInPSSMFile -in_pssm <File_In>PSI-BLAST checkpoint fileInclusionEValueThreshold -inclusion_ethresh <Real>E-value inclusion threshold for pairwise alignmentsDefault =0.002LineLength -line_length <Integer, >=1>Line length for formatting alignmentsNot applicable for outfmt 4Default =60LowercaseMasking -lcase_maskingUse lower case filtering in query and subject sequence(s) MaxHSPs -max_hsps <Integer, >=1>Set maximum number of HSPs per subject sequence to save for each query.MaxIntronLength -max_intron_length <Integer, >=0>Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignmentsDefault =0MaxTargetSeqs -max_target_seqs <Integer, >=1>Maximum number of aligned sequences to keep (value of 5 or more is recommended)Default =500MultiThreadingMode -mt_mode <Integer, (>=0 and =<1)>Multi-thread mode to use in RPS BLAST search:0 (auto) split by database vols
1 split by queries
0NegativeGIList -negative_gilist <String>Restrict search of database to everything except the specified GIsNegativeIPGList -negative_ipglist <String>Restrict search of database to everything except the specified IPGsNegativeSeqIDList -negative_seqidlist <String>Restrict search of database to everything except the specified SeqIDsNegativeTaxIDList -negative_taxidlist <String>Restrict search of database to everything except the specified taxonomy IDsNegativeTaxIDs -negative_taxids <String>Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',')NumAlignments -num_alignments <Integer, >=0>Number of database sequences to show alignments forDefault =250NumCPUCores NumDescriptions -num_descriptions <Integer, >=0>Number of database sequences to show one-line descriptions forNot applicable for outfmt 4Default =500NumIterations -num_iterations <Integer, >=0>Number of iterations to perform (0 means run until convergence)Default =1OutASCIIPSSMFile -out_ascii_pssm <File_Out>File name to store ASCII version of PSSMOutFile -out <File_Out>Output file nameDefault =-OutFormat -outfmt <String>Alignment view options:
Options 6, 7, 10 and 17 can be additionally configured to produce a custom format specified by space delimited format specifiers, or in the case of options 6, 7, and 10, by a token specified by the delim keyword.0 = Pairwise 1 = Query-anchored showing identities 2 = Query-anchored no identities 3 = Flat query-anchored showing identities 4 = Flat query-anchored no identities 5 = BLAST XML 6 = Tabular 7 = Tabular with comment lines 8 = Seqalign (Text ASN.1) 9 = Seqalign (Binary ASN.1) 10 = Comma-separated values 11 = BLAST archive (ASN.1) 12 = Seqalign (JSON) 13 = Multiple-file BLAST JSON 14 = Multiple-file BLAST XML2 15 = Single-file BLAST JSON 16 = Single-file BLAST XML2 17 = Sequence Alignment/Map (SAM) 18 = Organism ReportFormatDelimiter FormatFields OutPSSMFile -out_pssm <File_Out>File name to store checkpoint fileParseDefLines -parse_deflinesShould the query and subject defline(s) be parsed? PseudoCount -pseudocount <Integer>Pseudo-count value used when constructing PSSMDefault =0QueryCoverageHSPPercent -qcov_hsp_perc <Real, 0..100>Percent query coverage per hspQueryFile -query <File_In>Input file nameDefault =-QueryGenCode -query_gencode <Integer>Permissible values between:1..6
9..16
21..31
33
QueryLocation -query_loc <String>Location on the query sequence in 1-based offsets (Format: start-stop)Remote -remoteExecute search remotely? SaveEachPSSM -save_each_pssmSave PSSM after each iteration (file name is given in -save_pssm or -save_ascii_pssm options) SavePSSMAfterLastRound -save_pssm_after_last_roundSave PSSM after the last database search SearchSpace -searchsp <Int8, >=0>Effective length of the search spaceImportSearchStrategy -import_search_strategy <File_In>Search strategy to useExportSearchStrategy SeqIDList -seqidlist <String>Restrict search of database to list of SeqIDsShowGIs -show_gisShow NCBI GIs in deflines? SortHSPs -sorthsps <Integer, (>=0 and =<4)>Sorting option for HSPs:0= Sort by hsp evalue1= Sort by hsp score2= Sort by hsp query start3= Sort by hsp percent identity4= Sort by hsp subject start
SortHits -sorthits <Integer, (>=0 and =<4)>Sorting option for hits.Strand -strand <String>Permissible values:both
minus
plus
bothSubjectBestHit -subject_besthitTurn on best hit per subject sequence SubjectFile -subject <File_In>Subject sequence(s) to searchSubjectLocation -subject_loc <String>Location on the subject sequence in 1-based offsets (Format: start-stop)SumStats -sum_stats <Boolean>Use sum statisticsTaxIDList -taxidlist <String>Restrict search of database to include only the specified taxonomy IDsTaxIDs -taxids <String>Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',')Threshold -threshold <Real, >=0>Minimum word score such that the word is added to the BLAST lookup tableUngappedAlignmentsOnly -ungappedPerform ungapped alignment only? UseSmithWatermanTraceback -use_sw_tbackCompute locally optimal Smith-Waterman alignments? Version -versionPrint version number; ignore other arguments WindowSize -window_size <Integer, >=0>Multiple hits window size, use 0 to specify 1-hit algorithmExtensionDropoffUngapped -xdrop_ungap <Real>X-dropoff value (in bits) for ungapped extensionsExtensionDropoffPrelimGapped -xdrop_gap <Real>X-dropoff value (in bits) for preliminary gapped extensionsExtensionDropoffFinalGapped -xdrop_gap_final <Real>X-dropoff value (in bits) for final gapped alignment -
Enum Summary Enum Description AutoCPUCoresValue MultiThreadingModeValue FormatType FormatField HSPSorting HitSorting StrandType -
Interface Summary Interface Description Seg Low complexity region masker based on the SEG algorithm.