import sys from icecream import ic ic.configureOutput(outputFunction=lambda *a: print(*a, file=sys.stderr)) ic.configureOutput(prefix='> ') import pandas as pd df = pd.read_csv('triple-db.csv') import argparse def get_parser(): parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) #parser.add_argument('-', "--", help="", default="") parser.add_argument("-v", "--verbose", action="store_true", help="be verbose") #parser.add_argument("seq", help="U57:A27.A53 / wt UAA", default="UAA") # nargs='+') #parser.add_argument("--d2", help="U6-A59:U2-U23 / wt AU", default="UA") # nargs='+') #parser.add_argument("--growth", help="experimental results", default=0) # nargs='+') return parser def score_trx_double(seq, tindex): rmsd, triple, rmsd2, triple2 = get_trx(seq, tindex) # t1_3, 't1_3') cs = get_clashscore(triple) inst = get_instances(triple) cs2 = get_clashscore(triple2) inst2 = get_instances(triple2) print('>> triplex 1 triple 3: \n %s with rmsd score of %.2f of clashscore %i and instances %i' % (triple, rmsd, cs, inst)) print(' \n %s with rmsd score of %.2f of clashscore %i and instances %i' % (triple2, rmsd2, cs2, inst2)) return (triple, rmsd, cs, inst) def score_trx(seq, triple_id): """ seq: 'UUA' triple_id: 't1_3' """ return get_trx(seq, triple_id) rmsd, triple, l = get_trx(seq, triple_id) ic(triple) cs = get_clashscore(triple) inst = get_instances(triple) print(triple_id + ': %s with rmsd score of %.2f of clashscore %i and instances %i' % (triple, rmsd, cs, inst)) return (triple, rmsd, cs, inst) def duplex_energy(s): """ cGAUCgaaaGAUCg (((((....))))) rna_secondary_structure_prediction.py --method mcfold --file wt.fa """ s = 'cG' + s[1] + 'GCgaaaGC' + s[0] + 'Cg' ss = '(((((....)))))' from rna_tools.Seq import RNASequence seq = RNASequence(s) en, ss, comment = seq.predict_ss('mcfold', constraints=ss) print(' ', s, en, ss) return en """ if s == 'AU': return -15.81 if s == 'AA': return -13.42 if s == 'UA': return -15.81 if s == 'CA': return -13.0 if s == 'GA': return -13.73 return -1 # write them down """ def duplex2_energy(s): s = 'c' + s[1] + 'GCgaaaGC' + s[0] + 'c' ss = '((((....))))' from rna_tools.Seq import RNASequence seq = RNASequence(s) en, ss, comment = seq.predict_ss('mcfold', constraints=ss) # print(' ', s, en, ss) return en def get_trx_double(seq, triple): # ic('>>', seq, triple) if triple == 't1_3': f = 'db/t1-3_cWW_tHW_UAA_exemplar_rpr_rmsd.csv' elif triple == 't2_3': f = 'db/t2-3-UAU_rmsd.csv' elif triple == 't2_4': f = 'db/t2-4-ACA_rmsd.csv' elif triple == 't3_3': f = 'db/t3-3_AUA_rmsd.csv' rmsd1, line1 = -1, -1 rmsd2, line2 = -1, -1 for l in open(f): if seq.lower() in l.lower(): triple, rmsd = l.split(',') # Triple_cWW_tHS_AUG_exemplar_rpr.pdb,3.804 if rmsd1 == -1: rmsd1 = round(float(rmsd), 2) line1 = triple else: rmsd2 = round(float(rmsd), 2) line2 = triple break #if r > 2: # 1.75: # print(' ' + l.strip()) return rmsd1, line1, rmsd2, line2 def get_trx(seq, triple_id): """ db/t1-3_cWW_tHW_UAA_exemplar_rpr_Triple_cWW_*_rpr.pdb_sugar_rmsd.csv' t1-3_cWW_tHW_UAA_exemplar_rpr_Triple_*ex*_rpr.pdb_sugar_rmsd.csv """ rmsds = [] lines = [] scores = [] headers = [] c = 0 for s in ['t1-3_cWW_tHW_UAA_exemplar_rpr', 't2-3-UAU', 't2-4-ACA', 't3-3_AUA']: for mode in ['backbone+sugar']: # , 'c1', 'c1+Nx']: ['sugar', for f in [#'Triple_cWW_*_rpr.pdb', 'Triple_*_rpr.pdb', #'Triple_*ex*_rpr.pdb', #'Triple_cWW_*ex*_rpr.pdb', ]: #'Triple_*_rpr.pdb']: fdb = "db/%s_%s_%s_rmsd.csv" % (s, f.replace('*','X') ,mode) rmsd = -1 if triple_id.replace('_', '-') in fdb: for l in open(fdb): if seq.lower() in l.lower() and rmsd == -1: # if -1 then there is no rmsd # for this triple triple, rmsd = l.split(',') # Triple_cWW_tHS_AUG_exemplar_rpr.pdb,3.804 cs = get_clashscore(triple) if cs != 0: rmsd = -1 # reset the flag continue # cs not zero, so go ahead else: ins = get_instances(triple) rmsd = round(float(rmsd), 2) headers.extend(['%s_%s_%s' % (s, f.replace('*','X') ,mode) + '_rmsd', '%s_%s_%s' % (s, f.replace('*','X') ,mode) + '_cs', '%s_%s_%s' % (s, f.replace('*','X') ,mode) + '_ins']) scores.extend([rmsd, cs, ins]) if rmsd == -1: # still at the end of the loop headers.extend(['%s_%s_%s' % (s, f.replace('*','X') ,mode) + '_rmsd', '%s_%s_%s' % (s, f.replace('*','X') ,mode) + '_cs', '%s_%s_%s' % (s, f.replace('*','X') ,mode) + '_ins']) scores.extend([-1, -1, -1]) return scores, headers def get_trx_(seq, triple): # ic('>>', seq, triple) if triple == 't1_3': f = 'db/t1-3_cWW_tHW_UAA_exemplar_rpr_rmsd.csv' elif triple == 't2_3': f = 'db/t2-3-UAU_rmsd.csv' elif triple == 't2_4': f = 'db/t2-4-ACA_rmsd.csv' elif triple == 't3_3': f = 'db/t3-3_AUA_rmsd.csv' rmsd1, line1 = -1, -1 rmsd2, line2 = -1, -1 for l in open(f): if seq.lower() in l.lower(): triple, rmsd = l.split(',') # Triple_cWW_tHS_AUG_exemplar_rpr.pdb,3.804 rmsd = round(float(rmsd), 2) cs = get_clashscore(triple) ic(triple, rmsd, cs) if cs != 0: continue # cs not zero, so go ahead else: break # stop this cycle and leave ;-) return rmsd, triple, l def get_clashscore(t): """ Triple_cWW_tHW_UAA_exemplar_rpr.pdb """ t = t.replace('Triple_', '').replace('_rpr.pdb', '').replace('_exemplar', '') t = t.replace('tsS','tSS') x = df[df['triple'] == t] return int(x['clashes']) def get_instances(t): """ Triple_cWW_tHW_UAA_exemplar_rpr.pdb """ t = t.replace('Triple_', '').replace('_rpr.pdb', '').replace('_exemplar', '') t = t.replace('tsS','tSS') x = df[df['triple'] == t] return int(x['instances'])