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

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

Example:      /add.gene ""

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

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

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

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe /BBH.Merge /in <inDIR> [/out <out.csv>]
Example:      localblast /BBH.Merge

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe /BestHits.Filtering /in <besthit.xml> /sp <table.txt> [/out <out.Xml>]
Example:      localblast /BestHits.Filtering

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

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

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

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe /Chromosomes.Export /reads <reads.fasta/DIR> /maps <blastnMappings.Csv/DIR> [/out <outDIR>]
Example:      localblast /Chromosomes.Export

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

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe /Contacts /in <in.fasta> [/out <out.DIR>]
Example:      localblast /Contacts

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe /Copy.PTT /in <inDIR> [/out <outDIR>]
Example:      localblast /Copy.PTT

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe /Copys /imports <DIR> [/out <outDIR>]
Example:      localblast /Copys

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe /Export.Blastn /in <in.txt> [/out <out.csv>]
Example:      localblast /Export.Blastn

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

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

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

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe /Export.BlastX /in <blastx.txt> [/out <out.csv>]
Example:      localblast /Export.BlastX

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe /EXPORT.COGs.from.DOOR /in <DOOR.opr> [/out <out.csv>]
Example:      localblast /EXPORT.COGs.from.DOOR

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

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

Example:      /simple ""

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

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe /Export.gpffs [/in <inDIR>]
Example:      localblast /Export.gpffs

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe /Export.Locus /in <sbh/bbh_DIR> [/hit /out <out.txt>]
Example:      localblast /Export.Locus

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe /export.prot /gb <genome.gbk> [/out <out.fasta>]
Example:      localblast /export.prot

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe /Fasta.Filters /in <nt.fasta> /key <regex> [/out <out.fasta> /p]
Example:      localblast /Fasta.Filters

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

Example:      /p ""

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe /Identities.Matrix /hit <sbh/bbh.csv> [/out <out.csv> /cut 0.65]
Example:      localblast /Identities.Matrix

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe /locus.Selects /locus <locus.txt> /bh <bbhindex.csv> [/out <out.csv>]
Example:      localblast /locus.Selects

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe /MAT.evalue /in <sbh.csv> [/out <mat.csv> /flip]
Example:      localblast /MAT.evalue

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe /Merge.faa /in <DIR> /out <out.fasta>
Example:      localblast /Merge.faa

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

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe /Print /in <inDIR> [/ext <ext> /out <out.Csv>]
Example:      localblast /Print

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

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

   [/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 ""

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

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

    [/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 ""

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

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

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

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

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe /Taxonomy.efetch.Merge /in <in.DIR> [/out <out.Csv>]
Example:      localblast /Taxonomy.efetch.Merge

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

   [/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 ""

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

 /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 ""

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

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

Example:      /num_threads ""

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

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe /Venn.Single /in <besthits.Xml> [/out <out.csv>]
Example:      localblast /Venn.Single

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

   [/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 ""

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

    -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/"

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

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

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe --Export.Fasta /hits <query-hits.csv> /query <query.fasta> /subject <subject.fasta>
Example:      localblast --Export.Fasta

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe --Export.Overviews /blast <blastout.txt> [/out <overview.csv>]
Example:      localblast --Export.Overviews

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

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe -export_besthit -i <input_csv_file> -o <output_saved_csv>
Example:      localblast -export_besthit

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'"

    -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 .+[-].+'"

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

    -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"

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

    -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"

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

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

Example:      -i ""

Information:  
Usage:        G:\GCModeller\manual\bin\localblast.exe --Xml2Excel /in <in.xml> [/out <out.csv>]
Example:      localblast --Xml2Excel

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