Usage Examples

Before We Start

This section provides several usage examples for Blast2GO Command Line. Please read the Setup chapter carefully and configure the GO Mapping database in your properties file before you continue.

Important things to consider:

  • If you are using MS Windows, all commands must be changed accordingly. Please replace ./blast2go_cli.run with blast2go_cli.exe
  • A properties file is always necessary, create it with:
    ./blast2go_cli.run -createproperties cli.prop
  • GO Annotation, Enzyme Code Mapping, Statistics, GO Slim and various import and export functions make use of the obo file (-useobo). Blast2GO CLI comes with a default obo file, however, we recommend downloading the latest version.

    The obo file version should match the GO Mapping database version. http://resources.biobam.com/b2g_res/obo_files/index.html

    The latest version can always be found here: http://resources.biobam.com/b2g_res/obo_files/go_latest.obo.gz
    Just provide this file additionally when executing a command:
    ./blast2go_cli.run -useobo go_latest.obo.gz -properties cli.prop -annotation ...

  • Make sure having a working MongoDB server, with the GO Mapping database dump imported (see setup chapter).

Examples

  1. Load a DNA fasta file, add the corresponding BLAST results and perform GO Mapping and Annotation. Furthermore, we want to save the .box file and the PDF report into the current directory.

    ./blast2go_cli.run -properties cli.prop -loadfasta \
    example_data/plant_nucleotide.fasta -loadblast31 example_data/plant_blast_31.zip \
    -mapping -annotation -savebox example_1.box -savereport example_1.pdf

  2. This example requires a local Swissprot Database installation. Therefore, simply download and extract the file from: ftp.ncbi.nlm.nih.gov/blast/db/swissprot.tar.gz. Load nucleotide sequences, run local BLAST against the Swissprot database, GO Mapping and Annotation. We also create various statistics. Finally, the whole project will be saved in .box format with the chosen name prefix together with the log file. The LocalBlastAlgoParameters have to be configured:

    // ** LocalBlastAlgoParameters **
    LocalBlastAlgoParameters.blastProgram=blastx-fast
    LocalBlastAlgoParameters.blastDbFile=/path/to/swissprot.pal
    LocalBlastAlgoParameters.blastXML2ResultEnable=true
    LocalBlastAlgoParameters.blastXML2Result=blast_xmls

    Command line command:
    ./blast2go_cli.run -properties cli.prop -loadfasta example_data/plant_nucleotide.fasta \
    -workspace example_data -nameprefix localblastSwissprot \
    -localblast -mapping -annotation -statistics \
    bspecdis,mdbresmap,aannotscore -savebox -savelog blast2go.log

  3. Load example_1.box from the first example and run Cloud-InterProScan (online). We will save the project, as well as the InterProScan results (default configuration):

    ./blast2go_cli.run -properties cli.prop -loadbox example_1.box \
    -cloudips <cloud-key> -savebox example_data/example_ips.box

  4. Convert sequences to proteins and save them into a fasta file.

    ./blast2go_cli.run -properties cli.prop -useobo go_latest.obo.gz -loadfasta \
    example_data/plant_nucleotide.fasta -savelorf plant_protein.fasta

  5. Load a Blast2GO project file, apply plants GO Slim and save the results as .box, which will be saved with the default name prefix “b2g_project” into the current directory.

    ./blast2go_cli.run -properties cli.prop -useobo go_latest.obo.gz -loadbox \
    example_data/plant_annotated.box -goslim example_data/goslim_plant.obo -savebox

  6. To run this example, we need the results from the previous example. Run CloudBlast, GO Mapping, Annotation on the protein sequences and save the results as .box and customized annotation format. Please configure the following properties sections:

    // ** CloudBlastAlgoParameters **
    CloudBlastAlgoParameters.blastProgram=blastp-fast
    CloudBlastAlgoParameters.blastDB=nr_alias_viridiplantae
    CloudBlastAlgoParameters.blastXML2ResultEnable=true
    CloudBlastAlgoParameters.blastXML2Result=blast_xmls

    // ** ExportAnnotParameters **
    ExportAnnotParameters.format=custom
    ExportAnnotParameters.desc=true
    ExportAnnotParameters.go=category_and_id_and_term
    ExportAnnotParameters.goseparator=tabulator
    ExportAnnotParameters.column=tabulator
    ExportAnnotParameters.row=sequence

    Command line command:
    ./blast2go_cli.run -properties cli.prop -loadfasta \
    example_data/plant_protein.fasta -cloudblast <cloud-key> \
    -mapping -annotation -savebox plant_protein.box \
    -saveannot plant_annotation.annot

  7. Load a protein fasta file, add the corresponding BLAST results and execute GO Mapping and Annotation. All files (.box, .pdf, .annot and .txt) will be saved with the name prefix "example_7" in the "working dir" in the current directory. Additionally, the data distribution pie chart and enzyme statistics will also be saved in the “work dir” folder.

    Command line command:
    ./blast2go_cli.run -properties cli.prop \
    -loadfasta example_data/plant_protein.fasta \
    -loadblast31 example_data/plant_blast_31.zip \
    -mapping -annotation -workspace work_dir \
    -nameprefix example_7 -savebox -saveannot \
    -savereport -saveseqtable -statistics gdatadispie,aecdis



  8. Load a fasta file, a BLAST result file, and InterProScan 5.0 files, perform GO mapping, annotation. Then create all the statistical charts. As a result, we want to obtain the .box and the PDF report, which will be saved with the default name prefix “b2g_project” into the current directory.

    Command line command:
    ./blast2go_cli.run -properties cli.prop -loadfasta example_data/plant_nucleotide.fasta \
    -loadblast31 example_data/plant_blast_31.zip -loadips50 \
    example_data/plant_ips_50.xml -mapping -annotation \
    -statistics all -savebox -savereport

  9. Load an example data-set and export user-defined columns for each sequence. Please configure the following properties section:

    // ** GenericExportParameters **
    GenericExportParameters.columnSeparator=tabulator
    GenericExportParameters.itemSeparator=semicolon
    GenericExportParameters.itemsToExport=seq_name,blast_hit_count, \
    mapping_genename,mapping_xref,mapping_goid,annot_goid,enzyme_code

    Command line command:
    ./blast2go_cli.run -properties cli.prop -loadbox example_data/plant_annotated.box \
    -exportgeneric blast_top_hit.txt