specI_utilities

genomes_to_taxonomy.py

Script that given a file like genome_ID\tNCBI_species_ID print the full taxonomy. Example input:

155920.SAMN02441076	1562720
1559982.SAMD00020875	1559982

Another input is necessary: the NCBI tax dump (like: https://zenodo.org/record/3357977#.YFoeUuYo-fU). The input should be changed in the script and the result is printed to the stdout:

155920.SAMN02441076	2 Bacteria	1117 Cyanobacteria	NA Cyanobacteria class incertae sedis	1118 Chroococcales	1890452 Cyanobacteriaceae	102234 Cyanobacterium	1562720 Cyanobacterium sp. IPPAS B-1200
1559982.SAMD00020875	2 Bacteria	201174 Actinobacteria	1760 Actinobacteria	85011 Streptomycetales	2062 Streptomycetaceae	1883 Streptomyces	1559982 Streptomyces sp. NBRC 109436

Note that we fill in the missing levels (example: NA Cyanobacteria class incertae sedis) There are two possible issues:

1. NOT_SPECIES_ID if the tax id is not at species level
2. NO_NCBI_ID if the speciesID is not in the NCBI dump

evaluate_clustering.py

Script that given a folder with different clusterings creates an evaluation table with precision, recall and f1_score. As input arguments it requires the path to the clustering files and the name of the evaluation table. Moreover, the script requires the installation of pandas and numpy.

python evaluate_clustering.py path/to/clustering/files output_filename