Did I find the right examples for you? yes no

All Samples(0)  |  Call(0)  |  Derive(0)  |  Import(0)
str(object='') -> string

Return a nice string representation of the object.
If the argument is a string, the return value is the same object.

src/c/o/CombiVEP-0.1.2/combivep/preproc/dataset.py   CombiVEP(Download)
        vcf_reader.read(file_name)
        for rec in vcf_reader.fetch_hash_snps():
            snp_data = {combivep_settings.KEY_CHROM : rec[combivep_settings.KEY_SNP_INFO_SECTION][combivep_settings.KEY_VCF_CHROM],
                        combivep_settings.KEY_POS   : rec[combivep_settings.KEY_SNP_INFO_SECTION][combivep_settings.KEY_VCF_POS],
                        combivep_settings.KEY_REF   : rec[combivep_settings.KEY_SNP_INFO_SECTION][combivep_settings.KEY_VCF_REF],
        cbv_reader.read(file_name)
        for rec in cbv_reader.fetch_hash_snps():
            snp_data = {combivep_settings.KEY_CHROM : rec[combivep_settings.KEY_SNP_INFO_SECTION][combivep_settings.KEY_CBV_CHROM],
                        combivep_settings.KEY_POS   : rec[combivep_settings.KEY_SNP_INFO_SECTION][combivep_settings.KEY_CBV_POS],
                        combivep_settings.KEY_REF   : rec[combivep_settings.KEY_SNP_INFO_SECTION][combivep_settings.KEY_CBV_REF],
    def validate_data(self):
        #to prevent misintepret due to different version between each data point by 
        #removing items from self.dataset if they are not exist in certain UCSC database
        self.dataset[:] = [item for item in self.dataset if self.referer.validate_snp(item[combivep_settings.KEY_SNP_INFO_SECTION][combivep_settings.KEY_CHROM],
                                                                                      item[combivep_settings.KEY_SNP_INFO_SECTION][combivep_settings.KEY_POS],
    def calculate_scores(self):
        #get scores from LJB database
        for item in self.dataset:
            item[combivep_settings.KEY_SCORES_SECTION] = self.referer.get_scores(item[combivep_settings.KEY_SNP_INFO_SECTION][combivep_settings.KEY_CHROM],
                                                                                 item[combivep_settings.KEY_SNP_INFO_SECTION][combivep_settings.KEY_POS],

src/c/o/CombiVEP-0.1.2/combivep/app.py   CombiVEP(Download)
    print >> sys.stdout, "#%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" % ("CHROM", "POS", "REF", "ALT", "ACTUAL_DELETERIOUS_EFFECT", "PREDICTED_DELETERIOUS_PROBABILITY", "PHYLOP_SCORE", "SIFT_SCORE", "PP2_SCORE", "LRT_SCORT", "MT_SCORE", "GERP_SCORE")
    for i in xrange(len(dm.dataset)):
        print >> sys.stdout, "%s\t%s\t%s\t%s\t%s\t%6.4f\t%s\t%s\t%s\t%s\t%s\t%s" % (dm.dataset[i][combivep_settings.KEY_SNP_INFO_SECTION][combivep_settings.KEY_CHROM],
                                                        dm.dataset[i][combivep_settings.KEY_SNP_INFO_SECTION][combivep_settings.KEY_POS],
                                                        dm.dataset[i][combivep_settings.KEY_SNP_INFO_SECTION][combivep_settings.KEY_REF],