1. 1. GCModeller [version 1.0.0.0]
    1. 1.1. Commands
      1. 1.1.0.0.1. Help for command ‘/add.locus_tag’:
    2. 1.1.0.1. Accepted Types
      1. 1.1.0.1.1. /add.gene
      2. 1.1.0.1.2. Help for command ‘/add.names’:
      3. 1.1.0.1.3. Help for command ‘/Bash.Venn’:
      4. 1.1.0.1.4. Help for command ‘/bbh.Export’:
      5. 1.1.0.1.5. Help for command ‘/BBH.Merge’:
      6. 1.1.0.1.6. Help for command ‘/BestHits.Filtering’:
      7. 1.1.0.1.7. Help for command ‘/blastn.Query’:
      8. 1.1.0.1.8. Help for command ‘/blastn.Query.All’:
      9. 1.1.0.1.9. Help for command ‘/Blastp.BBH.Query’:
      10. 1.1.0.1.10. Help for command ‘/Chromosomes.Export’:
      11. 1.1.0.1.11. Help for command ‘/COG.Statics’:
      12. 1.1.0.1.12. Help for command ‘/Contacts’:
      13. 1.1.0.1.13. Help for command ‘/Copy.PTT’:
      14. 1.1.0.1.14. Help for command ‘/Copys’:
      15. 1.1.0.1.15. Help for command ‘/Export.Blastn’:
      16. 1.1.0.1.16. Help for command ‘/Export.blastnMaps’:
      17. 1.1.0.1.17. Help for command ‘/Export.blastnMaps.Batch’:
      18. 1.1.0.1.18. Help for command ‘/Export.blastnMaps.littles’:
      19. 1.1.0.1.19. Help for command ‘/Export.BlastX’:
      20. 1.1.0.1.20. Help for command ‘/EXPORT.COGs.from.DOOR’:
      21. 1.1.0.1.21. Help for command ‘/Export.gb’:
    3. 1.1.0.2. Accepted Types
      1. 1.1.0.2.1. /simple
      2. 1.1.0.2.2. Help for command ‘/Export.gpff’:
      3. 1.1.0.2.3. Help for command ‘/Export.gpffs’:
      4. 1.1.0.2.4. Help for command ‘/Export.Locus’:
      5. 1.1.0.2.5. Help for command ‘/export.prot’:
      6. 1.1.0.2.6. Help for command ‘/Fasta.Filters’:
    4. 1.1.0.3. Accepted Types
      1. 1.1.0.3.1. /p
      2. 1.1.0.3.2. Help for command ‘/Identities.Matrix’:
      3. 1.1.0.3.3. Help for command ‘/locus.Selects’:
      4. 1.1.0.3.4. Help for command ‘/MAT.evalue’:
      5. 1.1.0.3.5. Help for command ‘/Merge.faa’:
      6. 1.1.0.3.6. Help for command ‘/Paralog’:
      7. 1.1.0.3.7. Help for command ‘/Print’:
      8. 1.1.0.3.8. Help for command ‘/SBH.BBH.Batch’:
      9. 1.1.0.3.9. Help for command ‘/SBH.Export.Large’:
    5. 1.1.0.4. Accepted Types
      1. 1.1.0.4.1. /trim-KEGG
      2. 1.1.0.4.2. Help for command ‘/SBH.Trim’:
      3. 1.1.0.4.3. Help for command ‘/sbh2bbh’:
    6. 1.1.0.5. Accepted Types
      1. 1.1.0.5.1. /identities
      2. 1.1.0.5.2. /coverage
      3. 1.1.0.5.3. Help for command ‘/Select.Meta’:
      4. 1.1.0.5.4. Help for command ‘/SSBH2BH_LDM’:
      5. 1.1.0.5.5. Help for command ‘/SSDB.Export’:
      6. 1.1.0.5.6. Help for command ‘/Taxonomy.efetch’:
      7. 1.1.0.5.7. Help for command ‘/Taxonomy.efetch.Merge’:
      8. 1.1.0.5.8. Help for command ‘/venn.BBH’:
    7. 1.1.0.6. Accepted Types
      1. 1.1.0.6.1. /skip-load
      2. 1.1.0.6.2. Help for command ‘/venn.BlastAll’:
    8. 1.1.0.7. Accepted Types
      1. 1.1.0.7.1. /query
      2. 1.1.0.7.2. /num_threads
      3. 1.1.0.7.3. /all
      4. 1.1.0.7.4. Help for command ‘/venn.cache’:
    9. 1.1.0.8. Accepted Types
      1. 1.1.0.8.1. /num_threads
      2. 1.1.0.8.2. Help for command ‘/venn.sbh.thread’:
      3. 1.1.0.8.3. Help for command ‘/Venn.Single’:
      4. 1.1.0.8.4. Help for command ‘–bbh.export’:
    10. 1.1.0.9. Accepted Types
      1. 1.1.0.9.1. /all
      2. 1.1.0.9.2. Help for command ‘blast’:
    11. 1.1.0.10. Accepted Types
      1. 1.1.0.10.1. -i
      2. 1.1.0.10.2. -blast_bin
      3. 1.1.0.10.3. -program
      4. 1.1.0.10.4. -xld
      5. 1.1.0.10.5. -ld
      6. 1.1.0.10.6. Help for command ‘–blast.self’:
      7. 1.1.0.10.7. Help for command ‘-copy’:
      8. 1.1.0.10.8. Help for command ‘–Export.Fasta’:
      9. 1.1.0.10.9. Help for command ‘–Export.Overviews’:
      10. 1.1.0.10.10. Help for command ‘–Export.SBH’:
      11. 1.1.0.10.11. Help for command ‘-export_besthit’:
      12. 1.1.0.10.12. Help for command ‘grep’:
    12. 1.1.0.11. Accepted Types
      1. 1.1.0.11.1. -q
      2. 1.1.0.11.2. -h
      3. 1.1.0.11.3. Help for command ‘logs_analysis’:
    13. 1.1.0.12. Accepted Types
      1. 1.1.0.12.1. -d
      2. 1.1.0.12.2. -export
      3. 1.1.0.12.3. Help for command ‘merge’:
    14. 1.1.0.13. Accepted Types
      1. 1.1.0.13.1. -d
      2. 1.1.0.13.2. -o
      3. 1.1.0.13.3. Help for command ‘-merge_besthit’:
    15. 1.1.0.14. Accepted Types
      1. 1.1.0.14.1. -i
      2. 1.1.0.14.2. Help for command ‘–Xml2Excel’:
      3. 1.1.0.14.3. Help for command ‘–Xml2Excel.Batch’:

GCModeller [version 1.0.0.0]

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
/Print
/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||

Commands


Help for command ‘/add.locus_tag’:

Prototype: NCBI.localblast.CLI::Int32 AddLocusTag(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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   [/add.gene]
Description: Add gene features?

Example: /add.gene ""

Accepted Types

/add.gene
Help for command ‘/add.names’:

Prototype: NCBI.localblast.CLI::Int32 AddNames(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Bash.Venn’:

Prototype: NCBI.localblast.CLI::Int32 BashShell(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/bbh.Export’:

Prototype: NCBI.localblast.CLI::Int32 BBHExportFile(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/BBH.Merge’:

Prototype: NCBI.localblast.CLI::Int32 MergeBBH(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /BBH.Merge /in <inDIR> [/out <out.csv>]
Example: localblast /BBH.Merge
Help for command ‘/BestHits.Filtering’:

Prototype: NCBI.localblast.CLI::Int32 BestHitFiltering(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /BestHits.Filtering /in <besthit.xml> /sp <table.txt> [/out <out.Xml>]
Example: localblast /BestHits.Filtering
Help for command ‘/blastn.Query’:

Prototype: NCBI.localblast.CLI::Int32 BlastnQuery(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/blastn.Query.All’:

Prototype: NCBI.localblast.CLI::Int32 BlastnQueryAll(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Blastp.BBH.Query’:

Prototype: NCBI.localblast.CLI::Int32 BlastpBBHQuery(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Chromosomes.Export’:

Prototype: NCBI.localblast.CLI::Int32 ChromosomesBlastnResult(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /Chromosomes.Export /reads <reads.fasta/DIR> /maps <blastnMappings.Csv/DIR> [/out <outDIR>]
Example: localblast /Chromosomes.Export
Help for command ‘/COG.Statics’:

Prototype: NCBI.localblast.CLI::Int32 COGStatics(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Contacts’:

Prototype: NCBI.localblast.CLI::Int32 Contacts(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /Contacts /in <in.fasta> [/out <out.DIR>]
Example: localblast /Contacts
Help for command ‘/Copy.PTT’:

Prototype: NCBI.localblast.CLI::Int32 CopyPTT(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /Copy.PTT /in <inDIR> [/out <outDIR>]
Example: localblast /Copy.PTT
Help for command ‘/Copys’:

Prototype: NCBI.localblast.CLI::Int32 Copys(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /Copys /imports <DIR> [/out <outDIR>]
Example: localblast /Copys
Help for command ‘/Export.Blastn’:

Prototype: NCBI.localblast.CLI::Int32 ExportBlastn(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /Export.Blastn /in <in.txt> [/out <out.csv>]
Example: localblast /Export.Blastn
Help for command ‘/Export.blastnMaps’:

Prototype: NCBI.localblast.CLI::Int32 ExportBlastnMaps(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /Export.blastnMaps /in <blastn.txt> [/out <out.csv>]
Example: localblast /Export.blastnMaps
Help for command ‘/Export.blastnMaps.Batch’:

Prototype: NCBI.localblast.CLI::Int32 ExportBlastnMapsBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Export.blastnMaps.littles’:

Prototype: NCBI.localblast.CLI::Int32 ExportBlastnMapsSmall(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /Export.blastnMaps.littles /in <blastn.txt.DIR> [/out <out.csv.DIR>]
Example: localblast /Export.blastnMaps.littles
Help for command ‘/Export.BlastX’:

Prototype: NCBI.localblast.CLI::Int32 ExportBlastX(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /Export.BlastX /in <blastx.txt> [/out <out.csv>]
Example: localblast /Export.BlastX
Help for command ‘/EXPORT.COGs.from.DOOR’:

Prototype: NCBI.localblast.CLI::Int32 ExportDOORCogs(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /EXPORT.COGs.from.DOOR /in <DOOR.opr> [/out <out.csv>]
Example: localblast /EXPORT.COGs.from.DOOR
Help for command ‘/Export.gb’:

Prototype: NCBI.localblast.CLI::Int32 ExportPTTDb(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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   [/simple]
Description: Fasta sequence short title, which is just only contains locus_tag

Example: /simple ""

Accepted Types

/simple

Decalre: System.Boolean
Example:

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true

Help for command ‘/Export.gpff’:

Prototype: NCBI.localblast.CLI::Int32 EXPORTgpff(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /Export.gpff /in <genome.gpff> /gff <genome.gff> [/out <out.PTT>]
Example: localblast /Export.gpff
Help for command ‘/Export.gpffs’:

Prototype: NCBI.localblast.CLI::Int32 EXPORTgpffs(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /Export.gpffs [/in <inDIR>]
Example: localblast /Export.gpffs
Help for command ‘/Export.Locus’:

Prototype: NCBI.localblast.CLI::Int32 ExportLocus(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /Export.Locus /in <sbh/bbh_DIR> [/hit /out <out.txt>]
Example: localblast /Export.Locus
Help for command ‘/export.prot’:

Prototype: NCBI.localblast.CLI::Int32 ExportProt(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /export.prot /gb <genome.gbk> [/out <out.fasta>]
Example: localblast /export.prot
Help for command ‘/Fasta.Filters’:

Prototype: NCBI.localblast.CLI::Int32 Filter(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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   [/p]
Description: Using the parallel edition?? If GCModeller running in a 32bit environment, do not use this option.

Example: /p ""

Accepted Types

/p

Decalre: System.Boolean
Example:

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true

Help for command ‘/Identities.Matrix’:

Prototype: NCBI.localblast.CLI::Int32 IdentitiesMAT(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /Identities.Matrix /hit <sbh/bbh.csv> [/out <out.csv> /cut 0.65]
Example: localblast /Identities.Matrix
Help for command ‘/locus.Selects’:

Prototype: NCBI.localblast.CLI::Int32 LocusSelects(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /locus.Selects /locus <locus.txt> /bh <bbhindex.csv> [/out <out.csv>]
Example: localblast /locus.Selects
Help for command ‘/MAT.evalue’:

Prototype: NCBI.localblast.CLI::Int32 EvalueMatrix(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /MAT.evalue /in <sbh.csv> [/out <mat.csv> /flip]
Example: localblast /MAT.evalue
Help for command ‘/Merge.faa’:

Prototype: NCBI.localblast.CLI::Int32 MergeFaa(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /Merge.faa /in <DIR> /out <out.fasta>
Example: localblast /Merge.faa
Help for command ‘/Paralog’:

Prototype: NCBI.localblast.CLI::Int32 ExportParalog(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /Paralog /blastp <blastp.txt> [/coverage 0.5 /identities 0.3 /out <out.csv>]
Example: localblast /Paralog
Help for command ‘/Print’:

Prototype: NCBI.localblast.CLI::Int32 Print(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /Print /in <inDIR> [/ext <ext> /out <out.Csv>]
Example: localblast /Print
Help for command ‘/SBH.BBH.Batch’:

Prototype: NCBI.localblast.CLI::Int32 SBH_BBH_Batch(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/SBH.Export.Large’:

Prototype: NCBI.localblast.CLI::Int32 ExportBBHLarge(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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   [/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 ""

Accepted Types

/trim-KEGG
Help for command ‘/SBH.Trim’:

Prototype: NCBI.localblast.CLI::Int32 SBHTrim(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/sbh2bbh’:

Prototype: NCBI.localblast.CLI::Int32 BBHExport2(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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    [/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 ""

Accepted Types

/identities
/coverage
Help for command ‘/Select.Meta’:

Prototype: NCBI.localblast.CLI::Int32 SelectsMeta(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /Select.Meta /in <meta.Xml> /bbh <bbh.csv> [/out <out.csv>]
Example: localblast /Select.Meta
Help for command ‘/SSBH2BH_LDM’:

Prototype: NCBI.localblast.CLI::Int32 KEGGSSOrtholog2Bh(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/SSDB.Export’:

Prototype: NCBI.localblast.CLI::Int32 KEGGSSDBExport(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Taxonomy.efetch’:

Prototype: NCBI.localblast.CLI::Int32 FetchTaxnData(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /Taxonomy.efetch /in <nt.fasta> [/out <out.DIR>]
Example: localblast /Taxonomy.efetch
Help for command ‘/Taxonomy.efetch.Merge’:

Prototype: NCBI.localblast.CLI::Int32 MergeFetchTaxonData(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /Taxonomy.efetch.Merge /in <in.DIR> [/out <out.Csv>]
Example: localblast /Taxonomy.efetch.Merge
Help for command ‘/venn.BBH’:

Prototype: NCBI.localblast.CLI::Int32 VennBBH(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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   [/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 ""

Accepted Types

/skip-load
Help for command ‘/venn.BlastAll’:

Prototype: NCBI.localblast.CLI::Int32 vennBlastAll(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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 /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 ""

Accepted Types

/query
/num_threads
/all
Help for command ‘/venn.cache’:

Prototype: NCBI.localblast.CLI::Int32 VennCache(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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   [/num_threads]
Description: The number of the sub process thread. -1 value is stands for auto config by the system.

Example: /num_threads ""

Accepted Types

/num_threads
Help for command ‘/venn.sbh.thread’:

Prototype: NCBI.localblast.CLI::Int32 SBHThread(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Venn.Single’:

Prototype: NCBI.localblast.CLI::Int32 VennSingle(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe /Venn.Single /in <besthits.Xml> [/out <out.csv>]
Example: localblast /Venn.Single
Help for command ‘–bbh.export’:

Prototype: NCBI.localblast.CLI::Int32 ExportBBH(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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   [/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 ""

Accepted Types

/all
Help for command ‘blast’:

Prototype: NCBI.localblast.CLI::Int32 BLASTA(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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    -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/"

Accepted Types

-i
-blast_bin
-program
-xld
-ld
Help for command ‘–blast.self’:

Prototype: NCBI.localblast.CLI::Int32 SelfBlast(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe --blast.self /query <query.fasta> [/blast <blast_HOME> /out <out.csv>]
Example: localblast --blast.self
Help for command ‘-copy’:

Prototype: NCBI.localblast.CLI::Int32 Copy(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘–Export.Fasta’:

Prototype: NCBI.localblast.CLI::Int32 ExportFasta(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe --Export.Fasta /hits <query-hits.csv> /query <query.fasta> /subject <subject.fasta>
Example: localblast --Export.Fasta
Help for command ‘–Export.Overviews’:

Prototype: NCBI.localblast.CLI::Int32 ExportOverviews(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe --Export.Overviews /blast <blastout.txt> [/out <overview.csv>]
Example: localblast --Export.Overviews
Help for command ‘–Export.SBH’:

Prototype: NCBI.localblast.CLI::Int32 ExportSBH(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe --Export.SBH /in <in.DIR> /prefix <queryName> /out <out.csv> [/txt]
Example: localblast --Export.SBH
Help for command ‘-export_besthit’:

Prototype: NCBI.localblast.CLI::Int32 ExportBestHit(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe -export_besthit -i <input_csv_file> -o <output_saved_csv>
Example: localblast -export_besthit
Help for command ‘grep’:

Prototype: NCBI.localblast.CLI::Int32 Grep(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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    -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 .+[-].+'"

Accepted Types

-q
-h
Help for command ‘logs_analysis’:

Prototype: NCBI.localblast.CLI::Int32 bLogAnalysis(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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    -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"

Accepted Types

-d
-export
Help for command ‘merge’:

Prototype: NCBI.localblast.CLI::Int32 Merge(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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    -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"

Accepted Types

-d
-o
Help for command ‘-merge_besthit’:

Prototype: NCBI.localblast.CLI::Int32 MergeBestHits(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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-i
Description: Each file path in the filelist should be separated by a "|" character.

Example: -i ""

Accepted Types

-i
Help for command ‘–Xml2Excel’:

Prototype: NCBI.localblast.CLI::Int32 XmlToExcel(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe --Xml2Excel /in <in.xml> [/out <out.csv>]
Example: localblast --Xml2Excel
Help for command ‘–Xml2Excel.Batch’:

Prototype: NCBI.localblast.CLI::Int32 XmlToExcelBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\localblast.exe --Xml2Excel.Batch /in <inDIR> [/out <outDIR> /Merge]
Example: localblast --Xml2Excel.Batch