Repo to run alphafold2 over multiple fasta files in a slurm hpc environment.

To use the script type:

python3 distribute_alphafold2.py --fasta_file_dir ../fasta_files/ --alphafold_out_dir ../save_alpha_fold_files_here --sif_file ../sif_file/alphafold.sif  --run_script run.sh

For additional help, use:

python3 distribute_alphafold2.py --help

to return the parser help output:

usage: distribute_alphafold2.py [-h] [-f fasta_file_dir] [-o alphafold_out_dir] [-s sif_file] [-r run_script] [--force_overwrite]

Distribute AlphaFold2

options:
  -h, --help            show this help message and exit
  -f fasta_file_dir, --fasta_file_dir fasta_file_dir
                        Directory containing the fasta files EX: ./fasta_files/
  -o alphafold_out_dir, --alphafold_out_dir alphafold_out_dir
                        Path to the output directory for AlphaFold2 results EX: ./alphafold_out_dir/
  -s sif_file, --sif_file sif_file
                        Path to the AlphaFold2 singularity image file EX: ./sif_file/alphafold.sif
  -r run_script, --run_script run_script
                        Path to the run script EX: ./run.sh
  --force_overwrite     Force overwrite of existing results if they exist to rerun AlphaFold2 for all fasta files.

To use the strucutre homology search script type first download FATCAT and TMalign (USalign) using:

chmod +x download_fatcat_tm_align.sh
bash download_fatcat_tm_align.sh

And then run:

python3 fatcat_tmalign_proteome_search.py --query_file_dir ../query_pbs --proteome_dirs ../proteomes --fatcat_install_dir ./fatcat_tmalign/FATCAT-dist --tm_align_install_dir ./fatcat_tmalign/USalign

For additional help, use:

python3 fatcat_tmalign_proteome_search.py -h

to return the parser help output:

usage: fatcat_tmalign_proteome_search.py [-h] [-q query_file_dir] [-p proteome_dirs] [-f fatcat_install_dir] [-t tm_align_install_dir] [--force_overwrite]

FATCAT and TM-Align Strucutral Homology Screens

options:
  -h, --help            show this help message and exit
  -q query_file_dir, --query_file_dir query_file_dir
                        Directory containing the query PDB files EX: ./query_dir/
  -p proteome_dirs, --proteome_dirs proteome_dirs
                        Directory of proteome directories EX: ./proteomes/ (where ./proteomes contains multiple dirs called i.e human, mouse, drome)
  -f fatcat_install_dir, --fatcat_install_dir fatcat_install_dir
                        Path to the fatcat github directory EX: ./FATCAT-dist/
  -t tm_align_install_dir, --tm_align_install_dir tm_align_install_dir
                        Path to the USAlign github directory EX: ./USalign
  --force_overwrite     Force overwrite of existing results if they exist to rerun AlphaFold2 for all fasta files.