Description

Fetch the GO concepts for a list of genes

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

gene_list:file

A tsv/csv file that contains a list of gene ids in one of the columns. By default, the column name should be “gene_id”, but this can be changed by using “—columname gene_id” in ext.args.

*.{csv,tsv}

Output

name:type
description
pattern

gmt

meta:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

*.gmt:file

Each row contains the GO id, a description, and a list of gene ids.

*.gmt

tsv

meta:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

*.tsv:file

(optional) A tsv file with the following columns: query, mygene_id, go_id, go_term, go_evidence, go_category, symbol, name, taxid

*.tsv

versions

versions.yml:file

File containing software versions

versions.yml

Tools

mygene
Apache-2.0

A python wrapper to query/retrieve gene annotation data from Mygene.info.