This folder brings the different steps to generate the files used in the analysis made and shown in the AMPSphere resource paper. Among the folders there are those needed to generate the data in the AMPSphere as well as those needed to rearrange data needed for those steps, such as working the metadata and merging information.
All data needed throughout the analysis are linked as soft links in the respective folders. The structure for each analysis is basically in three folders:
- data - contains the links to the data used in the analysis
- utils - contains the scripts for the different analysis
- analysis - where the results will be saved
It is also available a README.md file with general and specific information of the analysis goals, steps, input and output files as well as brief info for the scripts and functions.
In a general way, the script saved in the analysis folder as main.py is the only command needed to execute the entire action by typing:
$ python main.py
or
$ ./main.sh
The files used in all analysis are saved in the data_folder,
which the contents are listed in the link below:
To verify each analysis in this folder, you can quickly follow the links below to move to their functionalities and specificities.
- 01_resource_generation
- 02_clustering_significance
- 03_metadata_analysis
- 04_rnacode_amp_families
- 05_quality
- 06_homologs_and_overlap
- 07_taxonomy_core_analysis
- 08_amps_in_progenomes_ANI_core
- 09_AMPs_from_Mpneumoniae
- 10_rarity
- 11_host_non_host_amps
- 12_genome_context
- 13_transmissibility
- 14_BGI_peptides
- 15_select_candidates_for_synthesis
A complete relationship of input and output files per analysis is available here