CDS Periodicity Plot Utility#

Overview#

This script is an additional tool for ORFribo, located in the Extra_Scripts directory on Github. It visualizes peridicity in ribosome profiling data. It generates bar plots showing in-frame and out-of-frame ribosome occupancy across coding sequences (CDS).

Installation Requirements#

Before running the script, ensure that the following Python packages are installed.

Note: This script cannot be executed inside a container because the package versions are not compatible with the script.

pip install matplotlib pandas numpy

Usage#

1. Individual Mode (Single File)#

To generate a periodicity plot from a single .tab file:

python metagenome_plotting.py --individual --tab path/to/file.tab --cds_name CDS001

Parameters:

--individual : Enables individual mode.

--tab : Path to the Exome_XX_periodicity_all.tab .tab file.

--cds_name : Name of the CDS to analyze.

2. Processing multiple CDS from a File#

If you have multiple .tab and multiple CDS names in a text file, use:

python metagenome_plotting.py --pooled --directory path/to/directory --cds_file cds_list.txt

Parameters:

--cds_file : Path to a text file containaing one CDS name per line.

--pooled : Enables pooled mode to process multiple files.

--directory: Path to the directory containing multiple Exome_XX_periodicity_all.tab .tab files.

Output#

The script generates bar plots where:

Orange bars: In-frame reads (P0).
Blue bars: Out-of-frame reads (P1 & P2).

The plot is saved as a .png file with the CDS name.

Example :#

1. Individual Mode (Single File):#

python3 metagenome_plotting.py --individual --tab Exome_28_periodicity_all.tab --cds_name YNL046W 

-------

Individual mode selected...
Looking for: CDS:YNL046W_CDS
Processing file: Exome_28_periodicity_all.tab
Plot saved to YNL046W.png

My Image

2. Multiple files :#

python3 metagenome_plotting.py --pooled --directory Tabs/ --cds_file cds.txt --nb_cds 20



-------
Pooled mode selected...
Looking for: CDS:YLL048C_CDS
Processing file: Tabs/Exome_30_periodicity_all.tab
Processing file: Tabs/Exome_29_periodicity_all.tab
Processing file: Tabs/Exome_28_periodicity_all.tab
Plot saved to YLL048C_pooled.png
Looking for: CDS:YNL046W_CDS
Processing file: Tabs/Exome_30_periodicity_all.tab
Processing file: Tabs/Exome_29_periodicity_all.tab
Processing file: Tabs/Exome_28_periodicity_all.tab
Plot saved to YNL046W_pooled.png

--nb_cds 20: argument limits the number of CDS processed by the script.

cds.txt: file containaing one CDS name per line:

YLL048C
YNL046W

YLL048C_pooled.png

My Image

YNL046W_pooled.png

My Image