PSMPA

PSMPA is a Python pipeline to predict secondary metabolism potential using amplicans for a single strain or microbial communities. We provide a web version for the convenience of users, you can click here.

Requirements

Specific libraries are required for PSMPA. We provide a requirements file to install everything at once. Here, We recommende Conda for environment deployment.

conda env create -f environment.yml

If you have successfully created this environment, don't forget to activate it.

conda activate psmpa

Installation & Help

Install the PSMPA package to the environment.

pip install psmpa

So far, if you installed successfully, you can run this command for more help information.

psmpa1 -h

or

psmpa2 -h

Sample

psmpa1

Usage:

• for single or multiple bacteria analysis

psmpa1 -s 16S.fna -o psmpa1_test_out

• for microbiological samples analysis

psmpa1 -s sequences.fasta -i feature-table.biom -o psmpa1_sample_test_out

psmpa2

Usage:

• for single or multiple bacteria analysis

psmpa2 -s 16S.fna -o psmpa2_test_out

• for microbiological samples analysis

psmpa2 -s sequences.fasta -i feature-table.biom -o psmpa2_sample_test_out

Explanation

If empty rows appear in the BGCs predicted result, the likely reason is that the BLAST analysis did not match any sequences. So, if sample analysis is performed, sequences with no results are ignored.