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localblast
Module AssemblyName: file:///G:/GCModeller/manual/bin/localblast.exe Root namespace: NCBI.localblast.CLI
All of the command that available in this program has been list below:
| Function API | Info |
|---|---|
| /add.locus_tag | Add locus_tag qualifier into the feature slot. |
| /add.names | |
| /Bash.Venn | |
| /bbh.Export | |
| /BBH.Merge | |
| /BestHits.Filtering | |
| /blastn.Query | |
| /blastn.Query.All | |
| /Blastp.BBH.Query | |
| /Chromosomes.Export | |
| /COG.Statics | |
| /Contacts | |
| /Copy.PTT | |
| /Copys | |
| /Export.Blastn | |
| /Export.blastnMaps | |
| /Export.blastnMaps.Batch | |
| /Export.blastnMaps.littles | |
| /Export.BlastX | |
| /EXPORT.COGs.from.DOOR | |
| /Export.gb | Export the *.fna, *.faa, *.ptt file from the gbk file. |
| /Export.gpff | |
| /Export.gpffs | |
| /Export.Locus | |
| /export.prot | |
| /Fasta.Filters | |
| /Identities.Matrix | |
| /locus.Selects | |
| /MAT.evalue | |
| /Merge.faa | |
| /Paralog | |
| /SBH.BBH.Batch | |
| /SBH.Export.Large | |
| /SBH.Trim | |
| /sbh2bbh | |
| /Select.Meta | |
| /SSBH2BH_LDM | |
| /SSDB.Export | |
| /Taxonomy.efetch | |
| /Taxonomy.efetch.Merge | |
| /venn.BBH | 2. Build venn table And bbh data from the blastp result out Or sbh data cache. |
| /venn.BlastAll | Completely paired combos blastp bbh operations for the venn diagram Or network builder. |
| /venn.cache | 1. [SBH_Batch] Creates the sbh cache data for the downstream bbh analysis. |
And this batch function is suitable with any scale of the blastp sbh data output.|
|/venn.sbh.thread|| |/Venn.Single|| |--bbh.export|Batch export bbh result data from a directory.| |blast|In order to draw as venn diagram for a specific set of genome and study the diferrence and consists between these genomes, you should do the blast operation from the protein amino aciad sequence first. The blastp operation can be performenced by the blast+ program which you can download from the NCBI website, this command is a interop service for the NCBI blast program, you should install the blast+ program at first.| |--blast.self|| |-copy|| |--Export.Fasta|| |--Export.Overviews|| |--Export.SBH|| |-export_besthit|| |grep|The gene id in the blast output log file are not well format for reading and program processing, so before you generate the venn diagram you should call this command to parse the gene id from the log file. You can also done this id parsing job using other tools.| |logs_analysis|Parsing the xml format blast log into a csv data file that use for venn diagram drawing.| |merge|This program can not use the blast parsing result for the venn diagram drawing operation, and this command is using for generate the drawing data for the venn diagram drawing command, this command merge the blast log parsing result and then using the parsing result for drawing a venn diagram.| |-merge_besthit|| |--Xml2Excel|| |--Xml2Excel.Batch||
Prototype: NCBI.localblast.CLI::Int32 AddLocusTag(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Add locus_tag qualifier into the feature slot.
Usage: G:\GCModeller\manual\bin\localblast.exe /add.locus_tag /gb <gb.gbk> /prefix <prefix> [/add.gene /out <out.gb>]
Example: localblast /add.locus_tag
Parameters information:
[/add.gene]
Description: Add gene features?
Example: /add.gene ""
Prototype: NCBI.localblast.CLI::Int32 AddNames(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /add.names /anno <anno.csv> /gb <genbank.gbk> [/out <out.gbk> /tag <overrides_name>]
Example: localblast /add.names
Prototype: NCBI.localblast.CLI::Int32 BashShell(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /Bash.Venn /blast <blastDIR> /inDIR <fasta.DIR> /inRef <inRefAs.DIR> [/out <outDIR> /evalue <evalue:10>]
Example: localblast /Bash.Venn
Prototype: NCBI.localblast.CLI::Int32 BBHExportFile(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /bbh.Export /query <query.blastp_out> /subject <subject.blast_out> [/out <bbh.csv> /evalue 1e-3 /coverage 0.85 /identities 0.3]
Example: localblast /bbh.Export
Prototype: NCBI.localblast.CLI::Int32 MergeBBH(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /BBH.Merge /in <inDIR> [/out <out.csv>]
Example: localblast /BBH.Merge
Prototype: NCBI.localblast.CLI::Int32 BestHitFiltering(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /BestHits.Filtering /in <besthit.xml> /sp <table.txt> [/out <out.Xml>]
Example: localblast /BestHits.Filtering
Prototype: NCBI.localblast.CLI::Int32 BlastnQuery(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /blastn.Query /query <query.fna> /db <db.DIR> [/thread /evalue 1e-5 /word_size <-1> /out <out.DIR>]
Example: localblast /blastn.Query
Prototype: NCBI.localblast.CLI::Int32 BlastnQueryAll(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /blastn.Query.All /query <query.fasta.DIR> /db <db.DIR> [/skip-format /evalue 10 /word_size <-1> /out <out.DIR> /parallel /penalty <penalty> /reward <reward>]
Example: localblast /blastn.Query.All
Prototype: NCBI.localblast.CLI::Int32 BlastpBBHQuery(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /Blastp.BBH.Query /query <query.fasta> /hit <hit.source> [/out <outDIR> /overrides /num_threads <-1>]
Example: localblast /Blastp.BBH.Query
Prototype: NCBI.localblast.CLI::Int32 ChromosomesBlastnResult(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /Chromosomes.Export /reads <reads.fasta/DIR> /maps <blastnMappings.Csv/DIR> [/out <outDIR>]
Example: localblast /Chromosomes.Export
Prototype: NCBI.localblast.CLI::Int32 COGStatics(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /COG.Statics /in <myva_cogs.csv> [/locus <locus.txt/csv> /locuMap <Gene> /out <out.csv>]
Example: localblast /COG.Statics
Prototype: NCBI.localblast.CLI::Int32 Contacts(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /Contacts /in <in.fasta> [/out <out.DIR>]
Example: localblast /Contacts
Prototype: NCBI.localblast.CLI::Int32 CopyPTT(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /Copy.PTT /in <inDIR> [/out <outDIR>]
Example: localblast /Copy.PTT
Prototype: NCBI.localblast.CLI::Int32 Copys(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /Copys /imports <DIR> [/out <outDIR>]
Example: localblast /Copys
Prototype: NCBI.localblast.CLI::Int32 ExportBlastn(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /Export.Blastn /in <in.txt> [/out <out.csv>]
Example: localblast /Export.Blastn
Prototype: NCBI.localblast.CLI::Int32 ExportBlastnMaps(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /Export.blastnMaps /in <blastn.txt> [/out <out.csv>]
Example: localblast /Export.blastnMaps
Prototype: NCBI.localblast.CLI::Int32 ExportBlastnMapsBatch(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /Export.blastnMaps.Batch /in <blastn_out.DIR> [/out <out.DIR> /num_threads <-1>]
Example: localblast /Export.blastnMaps.Batch
Prototype: NCBI.localblast.CLI::Int32 ExportBlastnMapsSmall(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /Export.blastnMaps.littles /in <blastn.txt.DIR> [/out <out.csv.DIR>]
Example: localblast /Export.blastnMaps.littles
Prototype: NCBI.localblast.CLI::Int32 ExportBlastX(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /Export.BlastX /in <blastx.txt> [/out <out.csv>]
Example: localblast /Export.BlastX
Prototype: NCBI.localblast.CLI::Int32 ExportDOORCogs(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /EXPORT.COGs.from.DOOR /in <DOOR.opr> [/out <out.csv>]
Example: localblast /EXPORT.COGs.from.DOOR
Prototype: NCBI.localblast.CLI::Int32 ExportPTTDb(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Export the *.fna, *.faa, *.ptt file from the gbk file.
Usage: G:\GCModeller\manual\bin\localblast.exe /Export.gb /gb <genbank.gb/DIR> [/out <outDIR> /simple /batch]
Example: localblast /Export.gb
Parameters information:
[/simple]
Description: Fasta sequence short title, which is just only contains locus_tag
Example: /simple ""
Decalre: System.Boolean Example:
truePrototype: NCBI.localblast.CLI::Int32 EXPORTgpff(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /Export.gpff /in <genome.gpff> /gff <genome.gff> [/out <out.PTT>]
Example: localblast /Export.gpff
Prototype: NCBI.localblast.CLI::Int32 EXPORTgpffs(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /Export.gpffs [/in <inDIR>]
Example: localblast /Export.gpffs
Prototype: NCBI.localblast.CLI::Int32 ExportLocus(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /Export.Locus /in <sbh/bbh_DIR> [/hit /out <out.txt>]
Example: localblast /Export.Locus
Prototype: NCBI.localblast.CLI::Int32 ExportProt(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /export.prot /gb <genome.gbk> [/out <out.fasta>]
Example: localblast /export.prot
Prototype: NCBI.localblast.CLI::Int32 Filter(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /Fasta.Filters /in <nt.fasta> /key <regex> [/out <out.fasta> /p]
Example: localblast /Fasta.Filters
Parameters information:
[/p]
Description: Using the parallel edition?? If GCModeller running in a 32bit environment, do not use this option.
Example: /p ""
Decalre: System.Boolean Example:
truePrototype: NCBI.localblast.CLI::Int32 IdentitiesMAT(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /Identities.Matrix /hit <sbh/bbh.csv> [/out <out.csv> /cut 0.65]
Example: localblast /Identities.Matrix
Prototype: NCBI.localblast.CLI::Int32 LocusSelects(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /locus.Selects /locus <locus.txt> /bh <bbhindex.csv> [/out <out.csv>]
Example: localblast /locus.Selects
Prototype: NCBI.localblast.CLI::Int32 EvalueMatrix(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /MAT.evalue /in <sbh.csv> [/out <mat.csv> /flip]
Example: localblast /MAT.evalue
Prototype: NCBI.localblast.CLI::Int32 MergeFaa(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /Merge.faa /in <DIR> /out <out.fasta>
Example: localblast /Merge.faa
Prototype: NCBI.localblast.CLI::Int32 ExportParalog(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /Paralog /blastp <blastp.txt> [/coverage 0.5 /identities 0.3 /out <out.csv>]
Example: localblast /Paralog
Prototype: NCBI.localblast.CLI::Int32 Print(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /Print /in <inDIR> [/ext <ext> /out <out.Csv>]
Example: localblast /Print
Prototype: NCBI.localblast.CLI::Int32 SBH_BBH_Batch(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /SBH.BBH.Batch /in <sbh.DIR> [/identities <-1> /coverage <-1> /all /out <bbh.DIR> /num_threads <-1>]
Example: localblast /SBH.BBH.Batch
Prototype: NCBI.localblast.CLI::Int32 ExportBBHLarge(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /SBH.Export.Large /in <blast_out.txt> [/trim-kegg /out <bbh.csv> /identities 0.15 /coverage 0.5]
Example: localblast /SBH.Export.Large
Parameters information:
[/trim-KEGG]
Description: If the fasta sequence source is comes from the KEGG database, and you want to removes the kegg species brief code for the locus_tag, then enable this option.
Example: /trim-KEGG ""
Prototype: NCBI.localblast.CLI::Int32 SBHTrim(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /SBH.Trim /in <sbh.csv> /evalue <evalue> [/identities 0.15 /coverage 0.5 /out <out.csv>]
Example: localblast /SBH.Trim
Prototype: NCBI.localblast.CLI::Int32 BBHExport2(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /sbh2bbh /qvs <qvs.sbh.csv> /svq <svq.sbh.csv> [/identities <-1> /coverage <-1> /all /out <bbh.csv>]
Example: localblast /sbh2bbh
Parameters information:
[/identities]
Description: Makes a further filtering on the bbh by using this option, default value is -1, so that this means no filter.
Example: /identities ""
[/coverage]
Description: Makes a further filtering on the bbh by using this option, default value is -1, so that this means no filter.
Example: /coverage ""
Prototype: NCBI.localblast.CLI::Int32 SelectsMeta(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /Select.Meta /in <meta.Xml> /bbh <bbh.csv> [/out <out.csv>]
Example: localblast /Select.Meta
Prototype: NCBI.localblast.CLI::Int32 KEGGSSOrtholog2Bh(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /SSBH2BH_LDM /in <ssbh.csv> [/xml /coverage 0.8 /identities 0.3 /out <out.xml>]
Example: localblast /SSBH2BH_LDM
Prototype: NCBI.localblast.CLI::Int32 KEGGSSDBExport(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /SSDB.Export /in <inDIR> [/coverage 0.8 /identities 0.3 /out <out.Xml>]
Example: localblast /SSDB.Export
Prototype: NCBI.localblast.CLI::Int32 FetchTaxnData(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /Taxonomy.efetch /in <nt.fasta> [/out <out.DIR>]
Example: localblast /Taxonomy.efetch
Prototype: NCBI.localblast.CLI::Int32 MergeFetchTaxonData(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /Taxonomy.efetch.Merge /in <in.DIR> [/out <out.Csv>]
Example: localblast /Taxonomy.efetch.Merge
Prototype: NCBI.localblast.CLI::Int32 VennBBH(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: 2. Build venn table And bbh data from the blastp result out Or sbh data cache.
Usage: G:\GCModeller\manual\bin\localblast.exe /venn.BBH /imports <blastp_out.DIR> [/skip-load /query <queryName> /all /coverage <0.6> /identities <0.3> /out <outDIR>]
Example: localblast /venn.BBH
Parameters information:
[/skip-load]
Description: If the data source in the imports directory Is already the sbh data source, then using this parameter to skip the blastp file parsing.
Example: /skip-load ""
Prototype: NCBI.localblast.CLI::Int32 vennBlastAll(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Completely paired combos blastp bbh operations for the venn diagram Or network builder.
Usage: G:\GCModeller\manual\bin\localblast.exe /venn.BlastAll /query <queryDIR> /out <outDIR> [/num_threads <-1> /evalue 10 /overrides /all /coverage <0.8> /identities <0.3>]
Example: localblast /venn.BlastAll
Parameters information:
/query
Description: Recommended format of the fasta title Is that the fasta title only contains gene locus_tag.
Example: /query ""
[/num_threads]
Description: The number of the parallel blast task in this command, default value Is -1 which means the number of the blast threads Is determined by system automatically.
Example: /num_threads ""
[/all]
Description: If this parameter Is represent, then all of the paired best hit will be export, otherwise only the top best will be export.
Example: /all ""
Prototype: NCBI.localblast.CLI::Int32 VennCache(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: 1. [SBH_Batch] Creates the sbh cache data for the downstream bbh analysis.
And this batch function is suitable with any scale of the blastp sbh data output.
Usage: G:\GCModeller\manual\bin\localblast.exe /venn.cache /imports <blastp.DIR> [/out <sbh.out.DIR> /coverage <0.6> /identities <0.3> /num_threads <-1> /overrides]
Example: localblast /venn.cache
Parameters information:
[/num_threads]
Description: The number of the sub process thread. -1 value is stands for auto config by the system.
Example: /num_threads ""
Prototype: NCBI.localblast.CLI::Int32 SBHThread(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /venn.sbh.thread /in <blastp.txt> [/out <out.sbh.csv> /coverage <0.6> /identities <0.3> /overrides]
Example: localblast /venn.sbh.thread
Prototype: NCBI.localblast.CLI::Int32 VennSingle(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe /Venn.Single /in <besthits.Xml> [/out <out.csv>]
Example: localblast /Venn.Single
Prototype: NCBI.localblast.CLI::Int32 ExportBBH(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Batch export bbh result data from a directory.
Usage: G:\GCModeller\manual\bin\localblast.exe --bbh.export /in <blast_out.DIR> [/all /out <out.DIR> /single-query <queryName> /coverage <0.5> /identities 0.15]
Example: localblast --bbh.export
Parameters information:
[/all]
Description: If this all Boolean value is specific, then the program will export all hits for the bbh not the top 1 best.
Example: /all ""
Prototype: NCBI.localblast.CLI::Int32 BLASTA(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: In order to draw as venn diagram for a specific set of genome and study the diferrence and consists between these genomes, you should do the blast operation from the protein amino aciad sequence first. The blastp operation can be performenced by the blast+ program which you can download from the NCBI website, this command is a interop service for the NCBI blast program, you should install the blast+ program at first.
Usage: G:\GCModeller\manual\bin\localblast.exe blast -i <file_directory> -blast_bin <BLAST_program_directory> -program <program_type_name> [-ld <log_dir> -xld <xml_log_dir>]
Example: localblast blast blast -i /home/xieguigang/GCModeller/examples/blast_test/ -ld ~/Desktop/logs -xld ~/Desktop/xmls -blast_bin ~/BLAST/bin
Parameters information:
-i
Description: The input data directory which is contains the FASTA format protein amino acid sequence data file.
Example: -i "~/Desktop/8004"
-blast_bin
Description: The localtion for the blast+ program, you should specific this switch value or this program will throw an exception.
Example: -blast_bin "~/BLAST/bin"
-program
Description: The program type name for the NCBI local blast executable assembly.
Example: -program "blast+"
[-xld]
Description: Optional, the parsed and well organized blast log file output directory, if this switch value is not specific by the user then the user desktop directoy will be used as default.
Example: -xld "~/Desktop/xml_logs"
[-ld]
Description: Optional, the blastp log file output directory for the NCBI blast+ program. If this switch value is not specific by the user then the user desktop directory will be specific for the logs file output as default.
Example: -ld "~/Desktop/logs/"
Prototype: NCBI.localblast.CLI::Int32 SelfBlast(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe --blast.self /query <query.fasta> [/blast <blast_HOME> /out <out.csv>]
Example: localblast --blast.self
Prototype: NCBI.localblast.CLI::Int32 Copy(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe -copy -i <index_file> -os <output_saved> [-osidx <id_column_index> -os_skip_first <T/F>]
Example: localblast -copy
Prototype: NCBI.localblast.CLI::Int32 ExportFasta(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe --Export.Fasta /hits <query-hits.csv> /query <query.fasta> /subject <subject.fasta>
Example: localblast --Export.Fasta
Prototype: NCBI.localblast.CLI::Int32 ExportOverviews(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe --Export.Overviews /blast <blastout.txt> [/out <overview.csv>]
Example: localblast --Export.Overviews
Prototype: NCBI.localblast.CLI::Int32 ExportSBH(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe --Export.SBH /in <in.DIR> /prefix <queryName> /out <out.csv> [/txt]
Example: localblast --Export.SBH
Prototype: NCBI.localblast.CLI::Int32 ExportBestHit(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe -export_besthit -i <input_csv_file> -o <output_saved_csv>
Example: localblast -export_besthit
Prototype: NCBI.localblast.CLI::Int32 Grep(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: The gene id in the blast output log file are not well format for reading and program processing, so before you generate the venn diagram you should call this command to parse the gene id from the log file. You can also done this id parsing job using other tools.
Usage: G:\GCModeller\manual\bin\localblast.exe grep -i <xml_log_file> -q <script_statements> -h <script_statements>
Example: localblast grep grep -i C:\Users\WORKGROUP\Desktop\blast_xml_logs\1__8004_ecoli_prot.log.xml -q "tokens | 4" -h "'tokens | 2';'tokens ' ' 0'"
Parameters information:
-q
Description: The parsing script for parsing the gene_id from the blast log file, this switch value is consist of sevral operation tokens, and each token is separate by the ';' character and the token unit in each script token should seperate by the ' character.
There are two basic operation in this parsing script:
tokens - Split the query or hit name string into sevral piece of string by the specific delimiter character and get the specifc location unit in the return string array.
Usage: tokens <delimiter> <position>
Example: tokens | 3 match - match a gene id using a specific pattern regular expression.
usage: match <regular_expression>
Example: match .+[-]\d{5}
Example: -q "'tokens | 5';'match .+[-].+'"
-h
Description: The parsing script for parsing the gene_id from the blast log file, this switch value is consist of sevral operation tokens, and each token is separate by the ';' character and the token unit in each script token should seperate by the ' character.
There are two basic operation in this parsing script:
tokens - Split the query or hit name string into sevral piece of string by the specific delimiter character and get the specifc location unit in the return string array.
Usage: tokens <delimiter> <position>
Example: tokens | 3 match - match a gene id using a specific pattern regular expression.
usage: match <regular_expression>
Example: match .+[-]\d{5}
Example: -h "'tokens | 5';'match .+[-].+'"
Prototype: NCBI.localblast.CLI::Int32 bLogAnalysis(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Parsing the xml format blast log into a csv data file that use for venn diagram drawing.
Usage: G:\GCModeller\manual\bin\localblast.exe logs_analysis -d <xml_logs_directory> -export <export_csv_file>
Example: localblast logs_analysis logs_analysis -d ~/xml_logs -export ~/Desktop/result.csv
Parameters information:
-d
Description: The data directory which contains the xml format blast log file, those xml format log file were generated from the 'venn -> blast' command.
Example: -d "~/xml_logs"
-export
Description: The save file path for the venn diagram drawing data csv file.
Example: -export "~/Documents/8004_venn.csv"
Prototype: NCBI.localblast.CLI::Int32 Merge(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: This program can not use the blast parsing result for the venn diagram drawing operation, and this command is using for generate the drawing data for the venn diagram drawing command, this command merge the blast log parsing result and then using the parsing result for drawing a venn diagram.
Usage: G:\GCModeller\manual\bin\localblast.exe merge -d <directory> -o <output_file>
Example: localblast merge merge -d ~/blast_besthit/ -o ~/Desktop/compared.csv
Parameters information:
-d
Description: The directory that contains some blast log parsing csv data file.
Example: -d "~/Desktop/blast/result/"
-o
Description: The save file name for the output result, the program willl save the merge result in the csv format
Example: -o "~/Desktop/8004_venn.csv"
Prototype: NCBI.localblast.CLI::Int32 MergeBestHits(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe -merge_besthit -i <input_file_list> -o <output_file> -os <original_idlist_sequence_file> [-osidx <id_column_index> -os_skip_first <T/F>]
Example: localblast -merge_besthit
Parameters information:
-i
Description: Each file path in the filelist should be separated by a "|" character.
Example: -i ""
Prototype: NCBI.localblast.CLI::Int32 XmlToExcel(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe --Xml2Excel /in <in.xml> [/out <out.csv>]
Example: localblast --Xml2Excel
Prototype: NCBI.localblast.CLI::Int32 XmlToExcelBatch(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\localblast.exe --Xml2Excel.Batch /in <inDIR> [/out <outDIR> /Merge]
Example: localblast --Xml2Excel.Batch
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