PhyloToAST API script biom_calc to transform OTU reads from a biom OTU table

Question

[olli.laroche]

Hi dear Biostars community,

I am trying to find a quick and easy way to square root transform my the read counts of my biom OTU table using the PhyloToAST program. After installing the program and all dependencies, I run the following command in my terminal: phylotoast.biom_calc.transform_raw_abundance(otu_table.biom, fn=math.log10, sampleIDs=True, sample_abd=True) and get the following error -bash: syntax error near unexpected token `otu_table.biom,'

Surely I'm doing something wrong and probably very obvious but unfortunately I can't find the solution as there is little information on how to use the script (http://phylotoast.readthedocs.io/en/latest/scripts/biom_calc.html).

Help on this issue would be greatly appreciated. Thanks!

Answer 1

[Shareef Dabdoub]

Hi Ollie,

The command you mention is part of the PhyloToAST API, so it's not a command that can be run at the bash prompt. It's meant to be used within a python program.

However, the most recent update to PhyloToAST includes a new command-line script: transform_biom.py that provides a way to do exactly what you were asking your question about. PyPI hasn't been updated with a new version of PhyloToAST yet, but you can install the latest version directly from GitHub. The README file on GitHub contains instructions on how to do that: https://github.com/smdabdoub/phylotoast. The main site (http://phylotoast.org) also has a link to the GitHub page.

Shareef Dabdoub

Answer 2

[olli.laroche]

Thank you Shareef, it works great!

[sridhar56]

This is a little out of context to the question, I was curious to know why do you want to transform the read counts of the OTU table.

[Shareef Dabdoub]

Generally transformations are used as a means of normalizing the data to account for differences in (for example) sequencing effort or to normalize the data for use with certain statistical tests.

For more detail, check out Multivariate analyses in microbial ecology (section on Data Transforms).