relax.snk

import os
import glob

#To run on cluster:
#snakemake --cluster "bsub -u /dev/null -q new-short -R rusage[mem=1024] -C 1 -G fleishman-wx-grp-lsf -o logs/{rule}.{wildcards}.out -e logs/{rule}.{wildcards}.err" --cores 1000 --snakefile relax.snk --configfile relax_config.yaml

DIRS,PDBS,=glob_wildcards('in/{DIRS}/{PDBS}.pdb')

targets=[]
for i in range(len(DIRS)):
    targets.append(f'relax/{DIRS[i]}/{PDBS[i]}.pdb')
print(targets)

localrules: select_best
rule all:
  input:
    targets

rule rosetta_relax:
  input:
    pdb='in/{D}/{A}.pdb'
  output:
    pdb=temporary('temp/{D}/{num}_{A}_0001.pdb')
  params:
    dir='temp/{D}'
  run:
    command = f'{config["rosetta_exec"]} -parser:protocol  {config["autocab_dir"]}/xmls/refine_Ag.xml -s {input.pdb}  @{config["autocab_dir"]}/flags/flags_refinement -out:prefix {params.dir}/{wildcards.num}_ -out:file:scorefile {params.dir}/{wildcards.A}.sc '
    print(command)
    os.system(command)

rule select_best:
  input:
    pdb=expand('temp/{{D}}/{num}_{{A}}_0001.pdb', num=range(config["trajectories"]))
  output:
    pdb='relax/{D}/{A}.pdb'
  params:
    score='temp/{D}/{A}.sc'
  run:
    command = f'cp `python {config["flab_dir"]}/bin/rosetta/parse_scores.py --scorefile {params.score} --operations "sort total_score Asc cols description" | ' + "awk 'NR==2{print $0 \".pdb\"}'`"+" {out_pdb}".format(out_pdb=output.pdb)
    print(command)
    os.system(command)