Tutorial

The common-mechanism repo contains some example FASTA queries pulled from the iGEM registry, including some that should be flagged in screening.

Example data

See common-mechanism/example-data/README.md for more information on the queries.

• common-mechanism/example-data/test_igem_queries.fasta: a multifasta with all the test sequences
• common-mechanism/example-data/test_igem_queries/BBa_*: individual FASTA files for each record in test_igem_queries.fasta

Example --fast mode screen

Running the following command

commec screen -d ~/repos/cm_databases/ -o ./fast-test igem_test_queries/BBa_K380009_A_20830_Coding_Protein_A_Z-domain.fasta --fast

will produce the following fast-test.screen output (with different timestamps):

>> STEP 1: Checking for biorisk genes...
                 --> Biorisks: Regulated gene in bases 2 to 58: FLAG
                     Gene: Immunoglobulin G-binding protein A 
 STEP 1 completed at 2024-05-07 13:36:26
 >> FAST MODE: Skipping steps 2-3
 SKIPPING STEP 3: Nucleotide search
>> STEP 4: Checking any pathogen regions for benign components...
        ...no regulated regions to clear
>> COMPLETED AT 2024-05-07 13:36:27

If you then run commec flag . you will see the following output:

Flags:  1 / 1
Errors:  0

and two flag files should be created, with the following content:

> cat flags.csv
filename,biorisk,virulence_factor,regulated_virus,regulated_bacteria,regulated_eukaryote,mixed_regulated_and_non_reg,benign
fast-test.screen,F,P,-,-,-,-,-
> cat flags_recommended.csv
fast-test.screen,F