Microbial 'omics


Brought to you by

groups-txt [artifact]

Table of Contents

TXT

A TXT-type anvi’o artifact. This artifact is typically provided by the user for anvi’o to import into its databases, process, and/or use.

Back to the main page of anvi’o programs and artifacts.

Provided by

There are no anvi’o tools that generate this artifact, which means it is most likely provided to the anvi’o ecosystem by the user.

Required or used by

anvi-compute-functional-enrichment anvi-display-functions

Description

This is a 2-column TAB-delimited text file to associate a given set of items with a set of groups. Depending on the context, items here may be individual samples or genomes. The first column can have a header name item, sample, genome or anything else that is appropriate, and list the items that are relevant to your input data. The second column should have the header group, and associate each item in your data with a group.

Each item should be associated with a single group, and it is always a good idea to define groups using single words without any fancy characters. For instance, HIGH_TEMPERATURE or LOW_FITNESS are good group names. In contrast, my group #1 or IS-THIS-OK?, are not quite good names for groups and may cause issues downstream depending on who uses this file.

Here is an example groups-txt file:

item group
item_01 GROUP_A
item_02 GROUP_B
item_03 GROUP_A
(…) (…)

If you are passing this file to the program anvi-compute-functional-enrichment with the “INPUT OPTION #2: ESTIMATED METABOLISM”, the names in the sample column must match those in the “modules” mode output file that you provide to the anvi-compute-functional-enrichment program via the --modules-txt parameter. If you know that the sample names match but you are still getting errors, you might need to specify which column in the “modules” mode output contains those sample names using the --sample-header parameter of anvi-compute-functional-enrichment.

Edit this file to update this information.