merge.py 文件源码

def __init__(self, vcffile=None):

        self.vcffile = vcffile

        self.filename = os.path.splitext(os.path.basename(str(vcffile)))[0]

        # create folder merge if it doesn't exists
        if not os.path.exists('merge'):
            os.makedirs('merge')
        # enter inside folder
        os.chdir('merge')

        self.annotation_files = OrderedDict()

        pysam.tabix_index('../snpeff/snpeff.output.vcf', preset='vcf')

        self.annotation_files['snpeff'] = {
            'info': 'EFF',
            'file': pysam.Tabixfile('../snpeff/snpeff.output.vcf.gz', 'r', encoding="utf-8")
        }

        pysam.tabix_index('../vep/vep.output.sorted.vcf', preset='vcf')

        self.annotation_files['vep'] = {
            'info': 'CSQ',
            'file': pysam.Tabixfile('../vep/vep.output.sorted.vcf.gz', 'r', encoding="utf-8")
        }

        pysam.tabix_index('../snpsift/snpsift.final.vcf', preset='vcf')

        self.annotation_files['vartype'] = {
            'info': 'VARTYPE,SNP,MNP,INS,DEL,MIXED,HOM,HET',
            'file': pysam.Tabixfile('../snpsift/snpsift.final.vcf.gz', 'r', encoding="utf-8")
        }

        pysam.tabix_index('../decipher/hi_predictions.vcf', preset='vcf')

        self.annotation_files['decipher'] = {
            'info': 'HI_PREDICTIONS',
            'file': pysam.Tabixfile('../decipher/hi_predictions.vcf.gz', 'r', encoding="utf-8")
        }

        pysam.tabix_index('../pynnotator/pynnotator.vcf', preset='vcf')

        # genomes1k dbsnp clinvar esp6500 ensembl_phen ensembl_clin
        self.pynnotator_tags = ['genomes1k', 'dbsnp', 'clinvar', 'esp6500', 'ensembl_phen', 'ensembl_clin']

        self.annotation_files['pynnotator'] = {
            'info': 'ALL',
            'file': pysam.Tabixfile('../pynnotator/pynnotator.vcf.gz', 'r', encoding="utf-8")
        }

        pysam.tabix_index('../func_pred/func_pred_sorted.vcf', preset='vcf')

        self.annotation_files['dbnfsp'] = {
            'info': 'dbNSFP_SIFT_score,dbNSFP_SIFT_converted_rankscore,dbNSFP_SIFT_pred,dbNSFP_Uniprot_acc_Polyphen2,dbNSFP_Uniprot_id_Polyphen2,dbNSFP_Uniprot_aapos_Polyphen2,dbNSFP_Polyphen2_HDIV_score,dbNSFP_Polyphen2_HDIV_rankscore,dbNSFP_Polyphen2_HDIV_pred,dbNSFP_Polyphen2_HVAR_score,dbNSFP_Polyphen2_HVAR_rankscore,dbNSFP_Polyphen2_HVAR_pred,dbNSFP_LRT_score,dbNSFP_LRT_converted_rankscore,dbNSFP_LRT_pred,dbNSFP_LRT_Omega,dbNSFP_MutationTaster_score,dbNSFP_MutationTaster_converted_rankscore,dbNSFP_MutationTaster_pred,dbNSFP_MutationTaster_model,dbNSFP_MutationTaster_AAE,dbNSFP_MutationAssessor_UniprotID,dbNSFP_MutationAssessor_variant,dbNSFP_MutationAssessor_score,dbNSFP_MutationAssessor_rankscore,dbNSFP_MutationAssessor_pred,dbNSFP_FATHMM_score,dbNSFP_FATHMM_converted_rankscore,dbNSFP_FATHMM_pred,dbNSFP_PROVEAN_score,dbNSFP_PROVEAN_converted_rankscore,dbNSFP_PROVEAN_pred,dbNSFP_Transcript_id_VEST3,dbNSFP_Transcript_var_VEST3,dbNSFP_VEST3_score,dbNSFP_VEST3_rankscore,dbNSFP_MetaSVM_score,dbNSFP_MetaSVM_rankscore,dbNSFP_MetaSVM_pred,dbNSFP_MetaLR_score,dbNSFP_MetaLR_rankscore,dbNSFP_MetaLR_pred,dbNSFP_Reliability_index,dbNSFP_M-CAP_score,dbNSFP_M-CAP_rankscore,dbNSFP_M-CAP_pred,dbNSFP_REVEL_score,dbNSFP_REVEL_rankscore,dbNSFP_MutPred_score,dbNSFP_MutPred_rankscore,dbNSFP_MutPred_protID,dbNSFP_MutPred_AAchange,dbNSFP_MutPred_Top5features,dbNSFP_CADD_raw,dbNSFP_CADD_raw_rankscore,dbNSFP_CADD_phred,dbNSFP_DANN_score,dbNSFP_DANN_rankscore,dbNSFP_fathmm-MKL_coding_score,dbNSFP_fathmm-MKL_coding_rankscore,dbNSFP_fathmm-MKL_coding_pred,dbNSFP_fathmm-MKL_coding_group,dbNSFP_Eigen_coding_or_noncoding,dbNSFP_Eigen-raw,dbNSFP_Eigen-phred,dbNSFP_Eigen-PC-raw,dbNSFP_Eigen-PC-phred,dbNSFP_Eigen-PC-raw_rankscore,dbNSFP_GenoCanyon_score,dbNSFP_GenoCanyon_score_rankscore,dbNSFP_integrated_fitCons_score,dbNSFP_integrated_fitCons_rankscore,dbNSFP_integrated_confidence_value,dbNSFP_GM12878_fitCons_score,dbNSFP_GM12878_fitCons_rankscore,dbNSFP_GM12878_confidence_value,dbNSFP_H1-hESC_fitCons_score,dbNSFP_H1-hESC_fitCons_rankscore,dbNSFP_H1-hESC_confidence_value,dbNSFP_HUVEC_fitCons_score,dbNSFP_HUVEC_fitCons_rankscore,dbNSFP_clinvar_rs,dbNSFP_clinvar_clnsig,dbNSFP_clinvar_trait,dbNSFP_clinvar_golden_stars',
            'file': pysam.Tabixfile('../func_pred/func_pred_sorted.vcf.gz', 'r', encoding="utf-8")
        }

        self.dbsnp = pysam.Tabixfile(settings.dbsnp, 'r', encoding="utf-8")