– Collapse table data to a specified level in a hierarchy.


This script collapses hierarchical data to a specified level. For instance, often it is useful to examine KEGG results from a higher level within the pathway hierarchy. Many genes are sometimes involved in multiple pathways, and in these circumstances (also know as a one-to-many relationship), the gene is counted for each pathway. This has a side effect of increasing the total count of genes in the table.

Usage: [options]

Input Arguments:



-i, --input_fp
The predicted metagenome table
-o, --output_fp
The resulting table
-c, --metadata_category
The metadata category that describes the hierarchy
-l, --level
The level in the hierarchy to collapse to. A value of 0 is not allowed, a value of 1 is the highest level, and any higher value nears the leaves of the hierarchy. For instance, if the hierarchy contains 4 levels, specifying 3 would collapse at one level above being fully specified.


Ignore the comma separated list of names. For instance, specifying –ignore_unknown=unknown,unclassified will ignore those labels while collapsing. The default is to not ignore anything. [default: None]
-f, --format_tab_delimited
Output the predicted metagenome table in tab-delimited format [default: False]


Output table is contains gene counts at a higher level within a hierarchy.

Collapse predicted metagenome using KEGG Pathway metadata. -i predicted_metagenomes.biom -c KEGG_Pathways -l 3 -o predicted_metagenomes.L3.biom

Change output to tab-delimited format (instead of BIOM). -f -i predicted_metagenomes.biom -c KEGG_Pathways -l 3 -o predicted_metagenomes.L3.txt

Collapse predicted metagenome using taxonomy metadata (not one-to-many). -i observation_table.biom -c taxonomy -l 1 -o observation_table.L1.biom