5 prediction tools are used instead of 7

[jud-b]

Hi,

I noticed that in the CancerVar.py script in the check_Prep function MetaSVM and MetaLR scores are not used (commented out in the code), and the scoring system based on the included predictive software is different from the scoring system that is presented in the supplementary materials of your published paper (https://www.science.org/doi/10.1126/sciadv.abj1624, Table-S2 CancerVar clinical evidence features and score system). Could you please explain me why?

Thanks.

def check_PreP(line,Funcanno_flgs,Allels_flgs,lof_genes_dict):
    '''Predictive software: SIFT, PolyPhen2, MutTaster, CADD, MetaSVM  GERP++, 
   2 Mostly damaging; information to be used for reference only >6
   1 Mostly damaging; information to be used for reference only >3
   0 Variable; information to be used for reference only
   -1 Mostly benign; information to be used for reference only
    '''
    # MetaSVM SIFT Polyphen2_HDIV MetaLR FATHMM  MutationAssessor
	# remove MetaSVM and MetaLR
    sift_cutoff=0.05 #SIFT_score,SIFT_pred, The smaller the score the more likely the SNP has damaging effect
    metasvm_cutoff=0 # greater scores indicating more likely deleterious effects
    cutoff_conserv=2 # for GERP++_RS

    dam=0;
    var=0;
    ben=0;
    PreP=0;

    cls=line.split('\t')
#    try:
#        if float(cls[Funcanno_flgs['MetaSVM_score']]) <  metasvm_cutoff:
#            ben=ben+1
#        else:
#            dam=dam+1
#    except ValueError:  
#        var=var+1
#    else:
#        pass

    try:
        if float(cls[Funcanno_flgs['SIFT_score']]) >= sift_cutoff:
            ben=ben+1
        else:
            dam=dam+1
    except ValueError:  # the sift absent means many:  synonymous indel  stop, but synonymous also is no impact
        var=var+1
    else:
        pass


    if cls[Funcanno_flgs['Polyphen2_HDIV_pred']] == "P" or cls[Funcanno_flgs['Polyphen2_HDIV_pred']] == "D":
        dam=dam+1
    if cls[Funcanno_flgs['Polyphen2_HDIV_pred']] == "B" :
        ben=ben+1
    if cls[Funcanno_flgs['Polyphen2_HDIV_pred']] == "." :
        var=var+1

#    if cls[Funcanno_flgs['MetaLR_pred']] == "D":
#        dam=dam+1
#    if cls[Funcanno_flgs['MetaLR_pred']] == "T" :
#        ben=ben+1
#    if cls[Funcanno_flgs['MetaLR_pred']] == "." :
#        var=var+1


    if cls[Funcanno_flgs['FATHMM_pred']] == "D":
        dam=dam+1
    if cls[Funcanno_flgs['FATHMM_pred']] == "T" :
        ben=ben+1
    if cls[Funcanno_flgs['FATHMM_pred']] == "." :
        var=var+1

    if cls[Funcanno_flgs['MutationAssessor_pred']] == "H" or cls[Funcanno_flgs['MutationAssessor_pred']] == "M":
        dam=dam+1
    if cls[Funcanno_flgs['MutationAssessor_pred']] == "L" or cls[Funcanno_flgs['MutationAssessor_pred']] == "N":
        ben=ben+1
    if cls[Funcanno_flgs['MutationAssessor_pred']] == "." :
        var=var+1
    
    if cls[Funcanno_flgs['GERP++_RS']] == ".": 
        var=var+1
    else:
        if float(cls[Funcanno_flgs['GERP++_RS']])>= cutoff_conserv:
            dam=dam+1
        else:
            ben=ben+1
        


    if dam >2: PreP=1;
    if dam >4: PreP=2;
    if ben >2: PreP=-1;
    if var >2: Prep=0;
    if dam==ben: PreP=0;

    #print "PreP=",PreP,dam,ben,var
    return(PreP)