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Command line

Isopret offers most functionality via its graphical user interface (GUI) version, but does have a command-line tool that can be used to perform Gene Ontology (GO) overrepresentation analysis from the shell.

The build process described in setup creates both a GUI app (in the isopret-gui/target subdirectory) and a command-line app (in the isopret-cli/target subdirectory). It is fine to leave both apps in these directories if you like. For the following explanation, we will assume that the command-line app isopret-cli is in the current working directory.

The download command

isopretGO requires some additional files to run.

  1. go.json. The main Gene Ontology file
  2. goa_human.gaf. The Gene Ontology annotation file
  3. hg38_ensembl.ser The Jannovar transcript information file
  4. hgnc_complete_set.txt A file from HGNC with information about human genes
  5. interpro_domains.txt A file from the isopret GitHub derived from interpro biomaRt data
  6. interpro_domain_desc.txt A file from the isopret GitHub derived from interpro biomaRt data
  7. isoform_function_list_mf.txt A file that is generated by the isoform function (GO molecular function) inference algorithm described in the manuscript.
  8. isoform_function_list_bp.txt A file that is generated by the isoform function (GO biological process) inference algorithm described in the manuscript.

isopretGO offers a convenience function to download all the files to a local directory (by default a subdirectory data is created in the current working directory). You can change this default with the -d or --data options (If you change this, then you will need to pass the location of your directory to all other isopret commands using the -d flag). Download the files automatically as follows.

java -jar isopret-cli.jar download

isopret will not download the files if they are already present unless the --overwrite argument is passed. For instance, the following command would download the four files to a directory called datafiles and would overwrite any previously downloaded files.

java -jar isopret-cli.jar download -d datafiles --overwrite

If desired, you can download these files on your own, but you need to place them all in the same directory to run isopret. The GUI uses the same functionality to download these files to a directory that is chosen or created by the user; this directory can be used by both the command-line and the GUI version of isopret.

The GO command

This command performs Gene Ontology overrepresentation analysis. The download command must be run before running this command. The --hbadeals option is required and indicates the path to an HBA-DEALS output file.

java -jar isopret-cli.jar GO --hbadeals <path>

The options are

Option Explanation
-b,--hbadeals Path to HBA-DEALS output file (required)
-c,--calculation Ontologizer calculation (Term-for-Term, PC-Union, PC-Intersection; default: TfT)
--mtc Multiple-Testing-Correction for GO analysis (default Bonferroni)
-v", --verbose Print stats in shell
--outfile Name of output file to write stats (default gene-ontology-overrep-{input}.tsv

The interpro command

This command performs interpro domain overrepresentation analysis. The download command must be run before running this command. The --hbadeals option is required and indicates the path to an HBA-DEALS output file.

java -jar isopret-cli.jar interpro --hbadeals <path>

The options are

Option Explanation
-b,--hbadeals Path to HBA-DEALS output file (required)
-d,--download data download directory (data by default)
--outfile Name of output file to write stats (default gene-ontology-overrep-{input}.tsv