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API Commands

The gweave client has a command group for interacting with the Geneweaver API. This allows you to do many of the tasks you would usually do on the website from the command line.

This can be useful for automating tasks, or for running analysis tools locally.

Requirements

You will need to have installed the gweave tool. See Command Line Interface for installation instructions.

You will need to have logged in to the gweave tool. See Logging In for instructions on how to log in.

The api Command Group

Still in alpha!

The api command group is still in alpha! In the following examples we will prepend the alpha command group to all of our examples.

The api command group collects all api interaction commands into a single group. There are several subgroups, each with their own set of commands.

Command Groups

If you are not familiar with command groups, see the documentation on gweave Command Groups.

Genesets

The genesets command group is for interacting with genesets.

You can see up-to-date documentation on the command group by using the following help command: 

gweaver alpha api genesets --help

Downloading a Geneset

Downloading a geneset can be as simple as specifying the geneset ID (without the GS prefix).

gweave -p alpha api genesets get $GS_ID

For example, to download geneset GS1234, you can use the following command:

gweave -p alpha api genesets get 1234

If you want to download the geneset in a specific gene ID type, you can specify the --gene-id-type flag.

gweave -p alpha api genesets get 1234 --gene-id-type=Wormbase

To save the geneset to a file, you can use the > operator.

gweave -p alpha api genesets get 1234 --gene-id-type=Wormbase > geneset_123.json

Pretty Printing

The -p flag will format the results in a way that is easier to read.

You can save the results to a file by using the > operator. 

gweave -p alpha api genesets get 1234 --gene-id-type=Wormbase > geneset_123.json

GeneIdentifier Types

Warning

The GeneIdentifier types are reproduced here for convenience, but the most up-to-date list can be found in the geneweaver-core package by using the geneweaver.core.enum.GeneIdentifier class.

  • "Entrez"
  • "Ensemble Gene"
  • "Ensemble Protein"
  • "Ensemble Transcript"
  • "Unigene"
  • "Gene Symbol"
  • "Unannotated"
  • "MGI"
  • "HGNC"
  • "RGD"
  • "ZFIN"
  • "FlyBase"
  • "Wormbase"
  • "SGD"
  • "miRBase"
  • "CGNC"