error using model ensemble

[evelingonzalezfeliu]

Hi !

Excellent tool!! Congratulations.

I have a question, when using the ensemble model in feature_preprocess.py I get the following error. When changing the -m parameter to evs I don't get any errors.

python3.6 /home/administrador/Documentos/Programas/CancerVar/OPAI/scripts/feature_preprocess.py -a 10021246-1_DNA.hg19_multianno.txt.grl_p -c 10021246-1_DNA.hg19_multianno.txt.cancervar -m ensemble -n 5 -d /home/administrador/Documentos/Programas/CancerVar/OPAI/saves/nonmissing_db.npy -o 10021246-1_DNA.hg19_multianno.txt.cancervar.ensemble.csv

Traceback (most recent call last):
  File "/home/administrador/Documentos/Programas/CancerVar/OPAI/scripts/feature_preprocess.py", line 204, in <module>
    main()
  File "/home/administrador/Documentos/Programas/CancerVar/OPAI/scripts/feature_preprocess.py", line 54, in main
    evs_feature, fun_feature = data_loader(args, fun_name, evs_name, gaussian_params)
  File "/home/administrador/Documentos/Programas/CancerVar/OPAI/scripts/feature_preprocess.py", line 116, in data_loader
    if not all( cancervar_dat['index'] == annovar_dat['index'] ):
  File "/home/administrador/miniconda3/envs/opai/lib/python3.6/site-packages/pandas/core/ops/common.py", line 65, in new_method
    return method(self, other)
  File "/home/administrador/miniconda3/envs/opai/lib/python3.6/site-packages/pandas/core/ops/__init__.py", line 365, in wrapper
    raise ValueError("Can only compare identically-labeled Series objects")
ValueError: Can only compare identically-labeled Series objects

• 10021246-1_DNA.hg19_multianno.txt.cancervar

  cat 10021246-1_DNA.hg19_multianno.txt.cancervar
  #Chr    Start   End Ref Alt Ref.Gene    Func.refGene    ExonicFunc.refGene  Gene.ensGene    avsnp147    AAChange.ensGene    AAChange.refGene    clinvar: Clinvar     CancerVar: CancerVar and Evidence  Freq_ExAC_ALL   Freq_esp6500siv2_all    Freq_1000g2015aug_all   Freq_gnomAD_genome_ALL  CADD_raw    CADD_phred  SIFT_score  GERP++_RS   phastCons20way_mammalian    dbscSNV_ADA_SCORE   dbscSNV_RF_SCORE    Interpro_domain AAChange.knownGene  MetaSVM_score   Freq_gnomAD_genome_POPsOMIM Phenotype_MIM   OrphaNumber Orpha   Pathway Therap_list Diag_list   Prog_list   Polyphen2_HDIV_score    FATHMM_score    MetaLR_score    MutationAssessor_scorecosmic91  icgc28
  19  3118934 3118934 G   -   716.28  exonic  frameshift deletion GNA11   .   GNA11:ENST00000078429.9_1:exon5:c.618delG:p.V206fs  GNA11:NM_002067:exon5:c.618delG:p.V206fs    clinvar: UNK     CancerVar: 3#Tier_III_Uncertain EVS=[1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1]   .   .   .   .   .   .   .   .   .   ..  .   GNA11:uc002lxd.3:exon5:c.618delG:p.V206fs   .   AFR:.,AMR:.,EAS:.,FIN:.,NFE:.,OTH:.,ASJ:.   .   .   .   .   .   ,5850,5859,5852,5857,5849,5854,5856,5858,5853,5851,5855

• cat 10021246-1_DNA.hg19_multianno.txt.grl_p

  
  cat 10021246-1_DNA.hg19_multianno.txt.grl_p
  Chr Start   End Ref Alt Func.refGene    Gene.refGene    GeneDetail.refGene  ExonicFunc.refGene  AAChange.refGene    Func.ensGene    Gene.ensGene    GeneDetail.ensGene  ExonicFunc.ensGene  AAChange.ensGene    Func.knownGene  Gene.knownGene  GeneDetail.knownGene    ExonicFunc.knownGene    AAChange.knownGene  esp6500siv2_all1000g2015aug_all ExAC_ALL    ExAC_AFR    ExAC_AMR    ExAC_EAS    ExAC_FIN    ExAC_NFE    ExAC_OTH    ExAC_SAS    avsnp147    SIFT_score  SIFT_pred   Polyphen2_HDIV_score    Polyphen2_HDIV_pred Polyphen2_HVAR_score    Polyphen2_HVAR_pred LRT_score   LRT_pred    MutationTaster_score    MutationTaster_pred MutationAssessor_score  MutationAssessor_pred   FATHMM_score    FATHMM_pred PROVEAN_score   PROVEAN_pred    VEST3_score CADD_raw    CADD_phred  DANN_score  fathmm-MKL_coding_score fathmm-MKL_coding_pred  MetaSVM_score   MetaSVM_pred    MetaLR_score    MetaLR_pred integrated_fitCons_score    integrated_confidence_value GERP++_RS   phyloP7way_vertebrate   phyloP20way_mammalian   phastCons7way_vertebrate    phastCons20way_mammalian    SiPhy_29way_logOdds dbscSNV_ADA_SCORE   dbscSNV_RF_SCORE    Interpro_domain CLNALLELEID CLNDN   CLNDISDB    CLNREVSTAT  CLNSIG  cosmic91    ICGC_Id ICGC_Occurrence gnomAD_genome_ALL   gnomAD_genome_AFR   gnomAD_genome_AMR   gnomAD_genome_ASJ   gnomAD_genome_EAS   gnomAD_genome_FIN   gnomAD_genome_NFE   gnomAD_genome_OTH   Otherinfo   Gene
  19  3118934 3118934 G   -   exonic  GNA11   .   frameshift deletion GNA11:NM_002067:exon5:c.618delG:p.V206fs    exonic  GNA11   .   frameshift deletion GNA11:ENST00000078429.9_1:exon5:c.618delG:p.V206fs  exonic  GNA11   .   frameshift deletion GNA11:uc002lxd.3:exon5:c.618delG:p.V206fs   .   .   .   .   ..  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   ..  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   ..  .   .   .   .   .   .   .   .   .   .   het 716.28  1322    GNA11